BICYCLIC HETEROCYCLIC COMPOUNDS FOR PROPHYLAXIS AND TREATMENT OF VIRAL INFECTIONS

Abstract

Bicyclic heterocyclic compounds and derivatives thereof that have antiviral properties are disclosed. Pharmaceutical compositions and pharmaceutical formulations in unit dosage form suitable for the delivery of the compounds to a subject in need thereof are disclosed. The pharmaceutical compositions or formulations may include one or more active agents in addition to the compounds, such as one or more antiviral agents and/or one or more anti-inflammatory agents. Methods for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in a subject are also disclosed. The methods include (i) administering to a subject an effective amount of the compound(s) to prevent, treat, or ameliorate one or more symptoms associated with a viral infection in the subject. The compound(s) can be administered by oral administration, parenteral administration, inhalation, mucosal administration, or a combination thereof.

Claims

1. A compound having the structure of ##STR00175## (a) wherein A are independently an unsubstituted heterocyclic group or a substituted heterocyclic group; (b) wherein X is a carbon or a nitrogen; (c) wherein L, M, L, and M are independently a carbon or a nitrogen; (d) wherein P.sub.1, P.sub.1, and G.sub.1 are independently CR.sub.20 or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (e) wherein R.sub.2 and R.sub.2 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; (f) wherein R.sub.3 and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (g) A is ##STR00176## (gi) wherein X is a carbon or a nitrogen, (gii) wherein E.sub.2, E.sub.2, G.sub.2, G.sub.2, Q.sub.2, Q.sub.2, and W.sub.2 are independently an oxygen, a sulfur, CR.sub.20, or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, (giii) wherein Q.sub.1 and Q.sub.1 are carbon; and (h) wherein the substituents are independently a phosphoramidate, a heterocyclic group, a halogen, a sulfonic acid, an azide group, a cyanate group, an isocyanate group, a nitrate group, a nitrile group, an isonitrile group, a nitrosooxy group, a nitroso group, a nitro group, an aldehyde group, an alkoxy group, an acyl halide group, a carboxylic acid group, a carboxylate group, an alkyl group, a heteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, a heteroaryl group, polyaryl group, a heteropoly aryl group, a alkyl aryl group, an amino group, an ester group, a hydroxyl group, a thiol group, a sulfonyl group, an ester group, an aliphatic ester group, an amide group, an aliphatic amide group, an azo group, an acyl group, a carbonyl group, a carbonate ester group, an ether group, an aminooxy group, or a hydroxyamino group.

2. The compound of claim 1, wherein the compound has the structure of ##STR00177## (a) wherein X is a carbon or a nitrogen; (b) wherein L, M, L, and L.sub.1-L.sub.3 are carbon or nitrogen; (c) wherein X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (d) wherein Y is a nitrogen; (e) wherein Z is a an oxygen, a nitrogen, or a carbon; (f) wherein J is an oxygen or OR.sub.3; (g) wherein R.sub.1 and R.sub.23 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; (h) wherein R.sub.2, R.sub.22, R.sub.22, R.sub.22, and R.sub.22 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; (i) wherein R.sub.3, R.sub.3, and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (j) wherein R.sub.8 and R.sub.24 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and (k) wherein R.sub.4, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (l) wherein the substituents are as defined in the base claim(s).

3. The compound of claim 2, wherein: R.sub.1 or R.sub.2 of Formula VI, R.sub.22 or R.sub.23 of Formula VI, R.sub.23 or R.sub.1 of Formula VI, and R.sub.23, R.sub.22, or R.sub.22 of Formula VI is a substituted an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group, preferably an unsubstituted or substituted aliphatic ether, such as an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, or an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether; or R.sub.4 and R.sub.5 are independently absent, hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, or a substituted aliphatic-amino group; or when J is OR.sub.3, R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group; or L, M, L, and L.sub.1-L.sub.3 are nitrogen; X is carbon; Z is a nitrogen or a carbon; and R.sub.6 and R.sub.7 are independently absent or hydrogen; or a combination thereof.

4. The compound of claim 1, wherein the compound has the structure of ##STR00178##

5. The compound of claim 1, wherein the compound has the structure of ##STR00179## (a) wherein X is a carbon or a nitrogen; (b) wherein L, M, and L are independently a carbon or a nitrogen; (c) wherein Y is a nitrogen; (d) wherein Z is a an oxygen, a nitrogen, or a carbon; (e) wherein J is an oxygen or OR.sub.3; (f) wherein R.sub.1 and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; (g) wherein R.sub.2 and R.sub.25 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; (h) wherein R.sub.3, R.sub.3, and R.sub.3 is absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (i) wherein R.sub.8 and R.sub.27 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (j) wherein R.sub.4, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (k) wherein the substituents are as defined in the base claim(s).

6. The compound of claim 5, wherein: R.sub.1 or R.sub.2 of Formula XI and R.sub.25 or R.sub.26 of Formula XI is a substituted an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group, preferably an unsubstituted or substituted aliphatic ether, such as an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, or an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether; or R.sub.4 and R.sub.5 are independently absent, hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, or a substituted aliphatic-amino group; or when J is OR.sub.3, R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group; or a combination thereof.

7. The compound of claim 1, wherein the compound has the structure of ##STR00180##

8. The compound of claim 1, wherein the compound has the structure of: ##STR00181## (a) wherein X is a carbon or a nitrogen; (b) wherein L, M, and L are independently a carbon or a nitrogen; (c) wherein Y is a nitrogen; (d) wherein J is an oxygen or OR.sub.3; (e) wherein R.sub.1 and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; (f) wherein R.sub.2 and R.sub.25 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; (g) wherein R.sub.3, R.sub.3, and R.sub.3 is absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (h) wherein R.sub.8 and R.sub.27 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (i) wherein R.sub.4 and R.sub.5 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (j) wherein the substituents are as defined in the base claim(s).

9. The compound of claim 8, wherein: R.sub.1 or R.sub.2 of Formula XVI and R.sub.25 or R.sub.26 of Formula XVI is a substituted an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group, preferably an unsubstituted or substituted aliphatic ether, such as an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, or an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether; or R.sub.4 and R.sub.5 are independently absent, hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, or a substituted aliphatic-amino group; or when J is OR.sub.3, R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group; or a combination thereof.

10. The compound of claim 1, wherein the compound has the structure of ##STR00182##

11. The compound of claim 1, wherein the compound has the structure of ##STR00183## ##STR00184## ##STR00185## ##STR00186## ##STR00187## ##STR00188## ##STR00189## ##STR00190## ##STR00191## (a) wherein X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (b) wherein R.sub.1, R.sub.1, R.sub.2, R.sub.2, R.sub.22, R.sub.23, R.sub.25, and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; (c) wherein R.sub.3, R.sub.3, R.sub.3, and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (d) wherein R.sub.8 and R.sub.8 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and (e) wherein R.sub.4, R.sub.4, R.sub.5, R.sub.8, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (f) wherein the substituents are as defined in the base claim(s).

12. The compound of claim 11, wherein R.sub.1 of Formulae 1-6; R.sub.1 of Formulae 7-24; R.sub.2 of Formulae 86 and 88; R.sub.22 of Formula 85; R.sub.23 of Formulae 84, 87, and 96-102; R.sub.25 of Formulae 92 and 95; and/or R.sub.26 of Formulae 89-91, 93, and 94 are(is) an unsubstituted aliphatic ether or a substituted aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether.

13. The compound of claim 11, wherein R.sub.1 of Formulae 1-6; R.sub.1 of Formulae 7-24; R.sub.2 of Formulae 86 and 88; R.sub.22 of Formula 85; R.sub.23 of Formulae 84, 87, and 96-102; R.sub.25 of Formulae 92 and 95; and/or R.sub.26 of Formulae 89-91, 93, and 94 are(is) a substituted C.sub.1-C.sub.6 aliphatic ether having the structure of ##STR00192## (a) wherein A.sub.1 and A.sub.2 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, a cyanide group, a nitrile group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; (b) wherein A.sub.7 is a methylene group or an ethylene group; (c) wherein R.sub.9 and R.sub.10 are independently a hydrogen, a hydroxyl group, an unsubstituted alkyl group, or a substituted alkyl group, optionally wherein R.sub.9 and R.sub.10 are independently a substituted alkyl group that together form a ring; and (d) wherein B.sub.2 is hydrogen or a phosphoramidate, wherein the substituents are as defined in the base claim(s).

14. The compound of claim 13, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of ##STR00193## wherein A.sub.3, A.sub.4, A.sub.5, and A.sub.6 are independently absent, a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group

15. The compound of claim 14, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of ##STR00194## (a) wherein A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and (b) wherein A.sub.2 is a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group.

16. The compound of claim 14, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of ##STR00195## (a) wherein A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and (b) wherein A.sub.2 is a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group.

17. The compound of claim 14, wherein B.sub.2 is a phosphoramidate having the structure of ##STR00196## (a) wherein B.sub.1 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, or a substituted aryl group; (b) wherein Q is an oxygen or a sulfur; (c) wherein T is an oxygen, a sulfur, NR.sub.11, CR.sub.11R.sub.12, CR.sub.11W.sub.1, or CW.sub.1W.sub.2, wherein R.sub.11 and R.sub.12 are independently a hydrogen, an unsubstituted alkyl group, a substituted alkyl group, an unsubstituted aryl group, a substituted aryl group, and wherein W.sub.1 and W.sub.2 are independently a heteroatom; (d) wherein Y is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; and (e) wherein A is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an alkoxyl, CM.sub.1alkyl, CM.sub.1aryl, or CM.sub.1heterocyclic, wherein M.sub.1 is an oxygen or a methylene group, optionally wherein A is O-alkyl, where the alkyl can be a substituted or unsubstituted alkyl, such as an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.6 alkyl, an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.4 alkyl, or an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.3 alkyl.

18. The compound of claim 11, wherein: X is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted heterocyclic group, or a substituted heterocyclic group; or R.sub.3, R.sub.3, R.sub.3, R.sub.3, R.sub.8, and R.sub.8 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, or a substituted heterocyclic group; or R.sub.4, R.sub.4, R.sub.5, R.sub.8, R.sub.6, and R.sub.7 are independently absent, a hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; or a combination thereof.

19. A pharmaceutical composition or dosage unit comprising the compound of claim 1; and a pharmaceutically acceptable excipient, wherein the compound is in an effective amount to prevent, treat, or ameliorate one or more symptoms associated with a viral infection in a subject.

20. A method for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in a subject comprising (i) administering to the subject an effective amount of the compound of claim 1 to prevent, treat, or ameliorate one or more symptoms associated with the viral infection in the subject.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0014] FIG. 1A is a graph illustrating the hydrogen bonding between the enol form of a triazolo-pyrazine compound and a nucleoside, cytidine. FIG. 1B is a graph illustrating the hydrogen bonding between the enol form of a triazolo-pyrazine compound and an imino form of the nucleoside, cytidine.

[0015] FIG. 2A is a graph illustrating the hydrogen bonding between a triazolo-pyrazine compound and the enol form of a nucleoside, uridine. FIG. 2B is a graph illustrating the hydrogen bonding between a triazolo-pyrazine compound and the keto form of a nucleoside, uridine.

[0016] FIGS. 3A-3C are graphs illustrating bonding between the amino-keto active RTP metabolite of the compound of Formula 84 and Cytidine Monophosphate within the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) (FIG. 3A), bonding between reference compound Guanosine TP and Cytidine Monophosphate within the SARS-CoV-2 RdRp (FIG. 3B), and bonding between reference compound Bemnifosbuvir (data generated using the active metabolite, i.e., AT-9010) and Cytidine Monophosphate within the SARS-CoV-2 RdRp (FIG. 3C). The three hydrogen bonds between the nucleoside TP and cytidine MP (C, T:101), as indicated by three arrows, show Watson Crick base pairing.

[0017] FIGS. 4A-4C are graphs illustrating bonding between the amino-enol active RTP metabolite of the compound of Formula 84 and Uridine MP within the SARS-CoV-2 RdRp (FIG. 4A), bonding between reference compound Adenosine and Uridine MP within the SARS-CoV-2 RdRp (FIG. 4B), and bonding between reference compound Remdesivir (active metabolite as TP) and Uridine MP within the SARS-CoV-2 RdRp (FIG. 4C).

[0018] FIGS. 5A-5B are graphs illustrating bonding between the keto-enol active RTP metabolite of the compound of Formula 102 and Cytidine MP within the SARS-CoV-2 RdRp (FIG. 5A), and bonding between the enol-enol active RTP metabolite of the compound of Formula 102 and Uridine MP within the SARS-CoV-2 RdRp (FIG. 5B).

DETAILED DESCRIPTION OF THE INVENTION

I. Definitions

[0019] As used herein, the term aliphatic refers to hydrocarbon groups that do not contain conjugated pi-systems that obey Hickel's rule. Aliphatic groups represent saturated hydrocarbons and unsaturated hydrocarbons, including those that are linear, branched, or cyclic (either monocyclic or polycyclic). An aliphatic group can be a linear C.sub.1-C.sub.30 aliphatic, a branched C.sub.4-C.sub.30 aliphatic, a cyclic C.sub.3-C.sub.30 aliphatic, a linear C.sub.1-C.sub.30 aliphatic or a branched C.sub.4-C.sub.30 aliphatic, a linear C.sub.1-C.sub.30 aliphatic or a cyclic C.sub.3-C.sub.30 aliphatic, a branched C.sub.4-C.sub.30 aliphatic or a cyclic C.sub.3-C.sub.30 aliphatic. Optionally, aliphatic groups have up to 20 carbon atoms. An aliphatic can be a linear C.sub.1-C.sub.20 aliphatic, a branched C.sub.4-C.sub.20 aliphatic, a cyclic C.sub.3-C.sub.20 aliphatic, a linear C.sub.1-C.sub.20 aliphatic or a branched C.sub.4-C.sub.20 aliphatic, a branched C.sub.4-C.sub.20 aliphatic or a cyclic C.sub.3-C.sub.20 aliphatic, a linear C.sub.1-C.sub.20 aliphatic or a cyclic C.sub.3-C.sub.20 aliphatic. Optionally, aliphatic groups have up to 14 carbon atoms. An aliphatic can be a linear C.sub.1-C.sub.14 aliphatic, a branched C.sub.4-C.sub.14 aliphatic, a cyclic C.sub.3-C.sub.14 aliphatic, a linear C.sub.1-C.sub.14 aliphatic or a branched C.sub.4-C.sub.14 aliphatic, a branched C.sub.4-C.sub.14 aliphatic or a cyclic C.sub.3-C.sub.14 aliphatic, a linear C.sub.1-C.sub.14 aliphatic or a cyclic C.sub.3-C.sub.14 aliphatic. An aliphatic can be a linear C.sub.1-C.sub.10 aliphatic, a branched C.sub.4-C.sub.10 aliphatic, a cyclic C.sub.3-C.sub.10 aliphatic, a linear C.sub.1-C.sub.10 aliphatic or a branched C.sub.4-C.sub.10 aliphatic, a branched C.sub.4-C.sub.10 aliphatic or a cyclic C.sub.3-C.sub.10 aliphatic, a linear C.sub.1-C.sub.10 aliphatic or a cyclic C.sub.3-C.sub.10 aliphatic. Optionally, aliphatic groups have up to 6 carbon atoms. An aliphatic can be a linear C.sub.1-C.sub.6 aliphatic, a branched C.sub.4-C.sub.6 aliphatic, a cyclic C.sub.3-C.sub.6 aliphatic, a linear C.sub.1-C.sub.6 aliphatic or a branched C.sub.4-C.sub.6 aliphatic, a branched C.sub.4-C.sub.6 aliphatic or a cyclic C.sub.3-C.sub.6 aliphatic, or a linear C.sub.1-C.sub.6 aliphatic or a cyclic C.sub.3-C.sub.6 aliphatic. Optionally, aliphatic groups have up to four carbons. An aliphatic can be a linear C.sub.1-C.sub.4 aliphatic, a cyclic C.sub.3-C.sub.4 aliphatic, a linear C.sub.1-C.sub.4 aliphatic or a cyclic C.sub.3-C.sub.4 aliphatic.

[0020] As used herein, the term heterocyclic refers to a chain of carbon and heteroatoms, wherein the heteroatoms are selected from nitrogen, oxygen, and sulfur, at least a portion of which, including at least one heteroatom, form a ring.

[0021] As used herein, the term amino includes the group NH.sub.2 (primary amino), alkylamino (secondary amino), and dialkylamino (tertiary amino), where the two alkyl groups in dialkylamino may be the same or different, i.e. alkylalkylamino.

[0022] Illustratively, amino include methylamino, ethylamino, dimethylamino, and methylethylamino. In addition, it is to be understood that when amino modifies or is modified by another term, such as aminoalkyl, or acylamino, the above variations of the term amino continue to apply. Illustratively, aminoalkyl includes H.sup.2N-alkyl, methylaminoalkyl, ethylaminoalkyl, dimethylaminoalkyl, methylethylaminoalkyl, and the like. Illustratively, acylamino includes acylmethylamino, and acylethylamino.

[0023] As used herein, the term amide includes the group CONH.sub.2 (primary amide), CONHalkyl (secondary amide), and CONdialkyl (tertiary amide), where the two alkyl groups in CONdialkyl may be the same or different.

[0024] As used herein, the term prodrug generally refers to compounds that are labile in vivo under predetermined biological conditions.

[0025] As used herein, the term effective amount means a dosage sufficient to prevent, treat, or alleviate one or more symptoms of a disease state being treated or to otherwise provide a desired pharmacologic and/or physiologic effect. The precise dosage will vary according to a variety of factors such as subject-dependent variables (e.g., age, immune system health, etc.), the disease, and the treatment being administered.

[0026] As used herein, the term pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients.

[0027] As used herein, the term alkyl refers to univalent groups derived from alkanes by removal of a hydrogen atom from any carbon atom. Alkanes represent saturated hydrocarbons, including those that are linear, branched, or cyclic (either monocyclic or polycyclic). An alkyl can be a linear C.sub.1-C.sub.30 alkyl, a branched C.sub.4-C.sub.30 alkyl, a cyclic C.sub.3-C.sub.30 alkyl, a linear C.sub.1-C.sub.30 alkyl or a branched C.sub.4-C.sub.30 alkyl, a linear C.sub.1-C.sub.30 alkyl or a cyclic C.sub.3-C.sub.30 alkyl, a branched C.sub.4-C.sub.30 alkyl or a cyclic C.sub.3-C.sub.30 alkyl. Optionally, alkyl groups have up to 20 carbon atoms. An alkyl can be a linear C.sub.1-C.sub.20 alkyl, a branched C.sub.4-C.sub.20 alkyl, a cyclic C.sub.3-C.sub.20 alkyl, a linear C.sub.1-C.sub.20 alkyl or a branched C.sub.4-C.sub.20 alkyl, a branched C.sub.4-C.sub.20 alkyl or a cyclic C.sub.3-C.sub.20 alkyl, a linear C.sub.1-C.sub.20 alkyl or a cyclic C.sub.3-C.sub.20 alkyl. Optionally, alkyl groups have up to 10 carbon atoms. An alkyl can be a linear C.sub.1-C.sub.10 alkyl, a branched C.sub.4-C.sub.10 alkyl, a cyclic C.sub.3-C.sub.10 alkyl, a linear C.sub.1-C.sub.10 alkyl or a branched C.sub.4-C.sub.10 alkyl, a branched C.sub.4-C.sub.10 alkyl or a cyclic C.sub.3-C.sub.10 alkyl, a linear C.sub.1-C.sub.10 alkyl or a cyclic C.sub.3-C.sub.10 alkyl. Optionally, alkyl groups have up to 6 carbon atoms. An alkyl can be a linear C.sub.1-C.sub.6 alkyl, a branched C.sub.4-C.sub.6 alkyl, a cyclic C.sub.3-C.sub.6 alkyl, a linear C.sub.1-C.sub.6 alkyl or a branched C.sub.4-C.sub.6 alkyl, a branched C.sub.4-C.sub.6 alkyl or a cyclic C.sub.3-C.sub.6 alkyl, or a linear C.sub.1-C.sub.6 alkyl or a cyclic C.sub.3-C.sub.6 alkyl. Optionally, alkyl groups have up to four carbons. An alkyl can be a linear C.sub.1-C.sub.4 alkyl, cyclic C.sub.3-C.sub.4 alkyl, a linear C.sub.1-C.sub.4 alkyl or a cyclic C.sub.3-C.sub.4 alkyl. Preferably, the alkyl group is unsubstituted alkyl group. Preferably, the alkyl group is a linear C.sub.1-C.sub.5, C.sub.1-C.sub.4, C.sub.1-C.sub.3, C.sub.1-C.sub.2 alkyl group, such as methyl group.

[0028] As used herein, the term heteroalkyl refers to alkyl groups where one or more carbon atoms are replaced with a heteroatom, such as, O, N, or S. Heteroalkyl group can be linear, branched, or cyclic. A heteroalkyl can be a linear C.sub.1-C.sub.30 heteroalkyl, a branched C.sub.3-C.sub.30 heteroalkyl, a cyclic C.sub.2-C.sub.30 heteroalkyl, a linear C.sub.1-C.sub.30 heteroalkyl or a branched C.sub.3-C.sub.30 heteroalkyl, a linear C.sub.1-C.sub.30 heteroalkyl or a cyclic C.sub.2-C.sub.30 heteroalkyl, a branched C.sub.3-C.sub.30 heteroalkyl or a cyclic C.sub.2-C.sub.30 heteroalkyl. Optionally, heteroalkyl groups have up to 20 carbon atoms. A heteroalkyl can be a linear C.sub.1-C.sub.20 heteroalkyl, a branched C.sub.3-C.sub.20 heteroalkyl, a cyclic C.sub.2-C.sub.20 heteroalkyl, a linear C.sub.1-C.sub.20 heteroalkyl or a branched C.sub.3-C.sub.20 heteroalkyl, a branched C.sub.3-C.sub.20 heteroalkyl or a cyclic C.sub.2-C.sub.20 heteroalkyl, or a linear C.sub.1-C.sub.20 heteroalkyl or a cyclic C.sub.2-C.sub.20 heteroalkyl. Optionally, heteroalkyl groups have up to 10 carbon atoms. A heteroalkyl can be a linear C.sub.1-C.sub.10 heteroalkyl, a branched C.sub.3-C.sub.10 heteroalkyl, a cyclic C.sub.2-C.sub.10 heteroalkyl, a linear C.sub.1-C.sub.10 heteroalkyl or a branched C.sub.3-C.sub.10 heteroalkyl, a branched C.sub.3-C.sub.10 heteroalkyl or a cyclic C.sub.2-C.sub.10 heteroalkyl, or a linear C.sub.1-C.sub.10 heteroalkyl or a cyclic C.sub.2-C.sub.10 heteroalkyl. Optionally, heteroalkyl groups have up to 6 carbon atoms. A heteroalkyl can be a linear C.sub.1-C.sub.6 heteroalkyl, a branched C.sub.3-C.sub.6 heteroalkyl, a cyclic C.sub.2-C.sub.6 heteroalkyl, a linear C.sub.1-C.sub.6 heteroalkyl or a branched C.sub.3-C.sub.6 heteroalkyl, a branched C.sub.3-C.sub.6 heteroalkyl or a cyclic C.sub.2-C.sub.6 heteroalkyl, or a linear C.sub.1-C.sub.6 heteroalkyl or a cyclic C.sub.2-C.sub.6 heteroalkyl. Optionally, heteroalkyl groups have up to four carbons. A heteroalkyl can be a linear C.sub.1-C.sub.4 heteroalkyl, a branched C.sub.3-C.sub.4 heteroalkyl, a cyclic C.sub.2-C.sub.4 heteroalkyl, a linear C.sub.1-C.sub.4 heteroalkyl or a branched C.sub.3-C.sub.4 heteroalkyl, a branched C.sub.3-C.sub.4 heteroalkyl or a cyclic C.sub.2-C.sub.4 heteroalkyl, or a linear C.sub.1-C.sub.4 heteroalkyl or a cyclic C.sub.2-C.sub.4 heteroalkyl.

[0029] As used herein, the term alkenyl refers to univalent groups derived from alkenes by removal of a hydrogen atom from any carbon atom. Alkenes are unsaturated hydrocarbons that contain at least one carbon-carbon double bond. Alkenyl group can be linear, branched, or cyclic. An alkenyl can be a linear C.sub.2-C.sub.30 alkenyl, a branched C.sub.4-C.sub.30 alkenyl, a cyclic C.sub.3-C.sub.30 alkenyl, a linear C.sub.2-C.sub.30 alkenyl or a branched C.sub.4-C.sub.30 alkenyl, a linear C.sub.2-C.sub.30 alkenyl or a cyclic C.sub.3-C.sub.30 alkenyl, a branched C.sub.4-C.sub.30 alkenyl or a cyclic C.sub.3-C.sub.30 alkenyl. Optionally, alkenyl groups have up to 20 carbon atoms. An alkenyl can be a linear C.sub.2-C.sub.20 alkenyl, a branched C.sub.4-C.sub.20 alkenyl, a cyclic C.sub.3-C.sub.20 alkenyl, a linear C.sub.2-C.sub.20 alkenyl or a branched C.sub.4-C.sub.20 alkenyl, a linear C.sub.2-C.sub.20 alkenyl or a cyclic C.sub.3-C.sub.20 alkenyl, a branched C.sub.4-C.sub.20 alkenyl or a cyclic C.sub.3-C.sub.20 alkenyl. Optionally, alkenyl groups have two to 10 carbon atoms. An alkenyl can be a linear C.sub.2-C.sub.10 alkenyl, a branched C.sub.4-C.sub.10 alkenyl, a cyclic C.sub.3-C.sub.10 alkenyl, a linear C.sub.2-C.sub.10 alkenyl or a branched C.sub.4-C.sub.10 alkenyl, a linear C.sub.2-C.sub.10 alkenyl or a cyclic C.sub.3-C.sub.10 alkenyl, a branched C.sub.4-C.sub.10 alkenyl or a cyclic C.sub.3-C.sub.10 alkenyl. Optionally, alkenyl groups have two to 6 carbon atoms. An alkenyl can be a linear C.sub.2-C.sub.6 alkenyl, a branched C.sub.4-C.sub.6 alkenyl, a cyclic C.sub.3-C.sub.6 alkenyl, a linear C.sub.2-C.sub.6 alkenyl or a branched C.sub.4-C.sub.6 alkenyl, a linear C.sub.2-C.sub.6 alkenyl or a cyclic C.sub.3-C.sub.6 alkenyl, a branched C.sub.4-C.sub.6 alkenyl or a cyclic C.sub.3-C.sub.6 alkenyl. Optionally, alkenyl groups have two to four carbons. An alkenyl can be a linear C.sub.2-C.sub.4 alkenyl, a cyclic C.sub.3-C.sub.4 alkenyl, a linear C.sub.2-C.sub.4 alkenyl or a cyclic C.sub.3-C.sub.4 alkenyl.

[0030] As used herein, the term heteroalkenyl refers to alkenyl groups in which one or more doubly bonded carbon atoms are replaced by a heteroatom. Heteroalkenyl group can be linear, branched, or cyclic. A heteroalkenyl can be a linear C.sub.2-C.sub.30 heteroalkenyl, a branched C.sub.3-C.sub.30 heteroalkenyl, a cyclic C.sub.2-C.sub.30 heteroalkenyl, a linear C.sub.2-C.sub.30 heteroalkenyl or a branched C.sub.3-C.sub.30 heteroalkenyl, a linear C.sub.2-C.sub.30 heteroalkenyl or a cyclic C.sub.2-C.sub.30 heteroalkenyl, a branched C.sub.3-C.sub.30 heteroalkenyl or a cyclic C.sub.2-C.sub.30 heteroalkenyl. Optionally, heteroalkenyl groups have up to 20 carbon atoms. A heteroalkenyl can be a linear C.sub.2-C.sub.20 heteroalkenyl, a branched C.sub.3-C.sub.20 heteroalkenyl, a cyclic C.sub.2-C.sub.20 heteroalkenyl, a linear C.sub.2-C.sub.20 heteroalkenyl or a branched C.sub.3-C.sub.20 heteroalkenyl, a linear C.sub.2-C.sub.20 heteroalkenyl or a cyclic C.sub.2-C.sub.20 heteroalkenyl, a branched C.sub.3-C.sub.20 heteroalkenyl or a cyclic C.sub.2-C.sub.20 heteroalkenyl. Optionally, heteroalkenyl groups have up to 10 carbon atoms. A heteroalkenyl can be a linear C.sub.2-C.sub.10 heteroalkenyl, a branched C.sub.3-C.sub.10 heteroalkenyl, a cyclic C.sub.2-C.sub.10 heteroalkenyl, a linear C.sub.2-C.sub.10 heteroalkenyl or a branched C.sub.3-C.sub.10 heteroalkenyl, a linear C.sub.2-C.sub.10 heteroalkenyl or a cyclic C.sub.2-C.sub.10 heteroalkenyl, a branched C.sub.3-C.sub.10 heteroalkenyl or a cyclic C.sub.2-C.sub.10 heteroalkenyl. Optionally, heteroalkenyl groups have two to 6 carbon atoms. A heteroalkenyl can be a linear C.sub.2-C.sub.6 heteroalkenyl, a branched C.sub.3-C.sub.6 heteroalkenyl, a cyclic C.sub.2-C.sub.6 heteroalkenyl, a linear C.sub.2-C.sub.6 heteroalkenyl or a branched C.sub.3-C.sub.6 heteroalkenyl, a linear C.sub.2-C.sub.6 heteroalkenyl or a cyclic C.sub.2-C.sub.6 heteroalkenyl, a branched C.sub.3-C.sub.6 heteroalkenyl or a cyclic C.sub.2-C.sub.6 heteroalkenyl. Optionally, heteroalkenyl groups have two to four carbons. A heteroalkenyl can be a linear C.sub.2-C.sub.4 heteroalkenyl, a branched C.sub.3-C.sub.4 heteroalkenyl, a cyclic C.sub.2-C.sub.4 heteroalkenyl, a linear C.sub.2-C.sub.4 heteroalkenyl or a branched C.sub.3-C.sub.4 heteroalkenyl, a linear C.sub.2-C.sub.4 heteroalkenyl or a cyclic C.sub.2-C.sub.4 heteroalkenyl, a branched C.sub.3-C.sub.4 heteroalkenyl or a cyclic C.sub.2-C.sub.4 heteroalkenyl.

[0031] As used herein, the term alkynyl refers to univalent groups derived from alkenes by removal of a hydrogen atom from any carbon atom. Alkynes are unsaturated hydrocarbons that contain at least one carbon-carbon triple bond. Alkynyl group can be linear, branched, or cyclic. An alkynyl can be a linear C.sub.2-C.sub.30 alkynyl, a branched C.sub.4-C.sub.30 alkynyl, a cyclic C.sub.3-C.sub.30 alkynyl, a linear C.sub.2-C.sub.30 alkynyl or a branched C.sub.4-C.sub.30 alkynyl, a linear C.sub.2-C.sub.30 alkynyl or a cyclic C.sub.3-C.sub.30 alkynyl, a branched C.sub.4-C.sub.30 alkynyl or a cyclic C.sub.3-C.sub.30 alkynyl. Optionally, alkynyl groups have up to 20 carbon atoms. An alkynyl can be a linear C.sub.2-C.sub.20 alkynyl, a branched C.sub.4-C.sub.20 alkynyl, a cyclic C.sub.3-C.sub.20 alkynyl, a linear C.sub.2-C.sub.20 alkynyl or a branched C.sub.4-C.sub.20 alkynyl, a branched C.sub.4-C.sub.20 alkynyl or a cyclic C.sub.3-C.sub.20 alkynyl. Optionally, alkynyl groups have up to 10 carbon atoms. An alkynyl can be a linear C.sub.2-C.sub.10 alkynyl, a branched C.sub.4-C.sub.10 alkynyl, a cyclic C.sub.3-C.sub.10 alkynyl, a linear C.sub.2-C.sub.20 alkynyl or a branched C.sub.4-C.sub.10 alkynyl, a branched C.sub.4-C.sub.20 alkynyl or a cyclic C.sub.3-C.sub.10 alkynyl, a linear C.sub.2-C.sub.20 alkynyl or a cyclic C.sub.3-C.sub.20 alkynyl. Optionally, alkynyl groups have up to 6 carbon atoms. An alkynyl can be a linear C.sub.2-C.sub.6 alkynyl, a branched C.sub.4-C.sub.6 alkynyl, a cyclic C.sub.3-C.sub.6 alkynyl, a linear C.sub.2-C.sub.6 alkynyl or a branched C.sub.4-C.sub.6 alkynyl, a branched C.sub.4-C.sub.6 alkynyl or a cyclic C.sub.3-C.sub.6 alkynyl, a linear C.sub.2-C.sub.6 alkynyl or a cyclic C.sub.3-C.sub.6 alkynyl. Optionally, alkynyl groups have up to four carbons. An alkynyl can be a linear C.sub.2-C.sub.4 alkynyl, a cyclic C.sub.3-C.sub.4 alkynyl, a linear C.sub.2-C.sub.4 alkynyl or a cyclic C.sub.3-C.sub.4 alkynyl.

[0032] As used herein, the term heteroalkynyl refers to alkynyl groups in which one or more triply bonded carbon atoms are replaced by a heteroatom. Heteroalkynyl group can be linear, branched, or cyclic. A heteroalkynyl can be a linear C.sub.2-C.sub.30 heteroalkynyl, a branched C.sub.3-C.sub.30 heteroalkynyl, a cyclic C.sub.2-C.sub.30 heteroalkynyl, a linear C.sub.2-C.sub.30 heteroalkynyl or a branched C.sub.3-C.sub.30 heteroalkynyl, a linear C.sub.2-C.sub.30 heteroalkynyl or a cyclic C.sub.2-C.sub.30 heteroalkynyl, a branched C.sub.3-C.sub.30 heteroalkynyl or a cyclic C.sub.2-C.sub.30 heteroalkynyl. Optionally, heteroalkynyl groups have up to 20 carbon atoms. A heteroalkynyl can be a linear C.sub.2-C.sub.20 heteroalkynyl, a branched C.sub.3-C.sub.20 heteroalkynyl, a cyclic C.sub.2-C.sub.20 heteroalkynyl, a linear C.sub.2-C.sub.20 heteroalkynyl or a branched C.sub.3-C.sub.20 heteroalkynyl, a branched C.sub.3-C.sub.20 heteroalkynyl or a cyclic C.sub.2-C.sub.20 heteroalkynyl, a linear C.sub.2-C.sub.20 heteroalkynyl or a cyclic C.sub.2-C.sub.20 heteroalkynyl. Optionally, heteroalkynyl groups have up to 10 carbon atoms. A heteroalkynyl can be a linear C.sub.2-C.sub.10 heteroalkynyl, a branched C.sub.3-C.sub.10 heteroalkynyl, a cyclic C.sub.2-C.sub.10 heteroalkynyl, a linear C.sub.2-C.sub.10 heteroalkynyl or a branched C.sub.3-C.sub.10 heteroalkynyl, a branched C.sub.3-C.sub.10 heteroalkynyl or a cyclic C.sub.2-C.sub.10 heteroalkynyl, a linear C.sub.2-C.sub.10 heteroalkynyl or a cyclic C.sub.2-C.sub.10 heteroalkynyl. Optionally, heteroalkynyl groups have two to 6 carbon atoms. A heteroalkynyl can be a linear C.sub.2-C.sub.6 heteroalkynyl, a branched C.sub.3-C.sub.6 heteroalkynyl, a cyclic C.sub.2-C.sub.6 heteroalkynyl, a linear C.sub.2-C.sub.6 heteroalkynyl or a branched C.sub.3-C.sub.6 heteroalkynyl, a branched C.sub.3-C.sub.6 heteroalkynyl or a cyclic C.sub.2-C.sub.6 heteroalkynyl, a linear C.sub.2-C.sub.6 heteroalkynyl or a cyclic C.sub.2-C.sub.6 heteroalkynyl. Optionally, heteroalkynyl groups have up to four carbons. A heteroalkynyl can be a linear C.sub.2-C.sub.4 heteroalkynyl, a branched C.sub.3-C.sub.4 heteroalkynyl, a cyclic C.sub.2-C.sub.4 heteroalkynyl, a linear C.sub.2-C.sub.4 heteroalkynyl or a branched C.sub.3-C.sub.4 heteroalkynyl, a branched C.sub.3-C.sub.4 heteroalkynyl or a cyclic C.sub.2-C.sub.4 heteroalkynyl, a linear C.sub.2-C.sub.4 heteroalkynyl or a cyclic C.sub.2-C.sub.4 heteroalkynyl.

[0033] As used herein, the term aryl refers to univalent groups derived from arenes by removal of a hydrogen atom from a ring atom. Arenes are monocyclic and polycyclic aromatic hydrocarbons. In polycyclic aryl groups, the rings can be attached together in a pendant manner or can be fused. Aaryl group can have six to 50 carbon atoms. An aryl can be a branched C.sub.6-C.sub.50 aryl, a monocyclic C.sub.6-C.sub.50 aryl, a polycyclic C.sub.6-C.sub.50 aryl, a branched polycyclic C.sub.6-C.sub.50 aryl, a fused poly cyclic C.sub.6-C.sub.50 aryl, or a branched fused polycyclic C.sub.6-C.sub.50 aryl. Optionally, aryl groups have six to 30 carbon atoms, i.e., C.sub.6-C.sub.30 aryl. A C.sub.6-C.sub.30 aryl can be a branched C.sub.6-C.sub.30 aryl, a monocyclic C.sub.6-C.sub.30 aryl, a polycyclic C.sub.6-C.sub.30 aryl, a branched polycyclic C.sub.6-C.sub.30 aryl, a fused polycyclic C.sub.6-C.sub.30 aryl, or a branched fused polycyclic C.sub.6-C.sub.30 aryl. Optionally, aryl groups have six to 20 carbon atoms, i.e., C.sub.6-C.sub.20 aryl. A C.sub.6-C.sub.20 aryl can be a branched C.sub.6-C.sub.20 aryl, a monocyclic C.sub.6-C.sub.20 aryl, a polycyclic C.sub.6-C.sub.20 aryl, a branched polycyclic C.sub.6-C.sub.20 aryl, a fused polycyclic C.sub.6-C.sub.20 aryl, or a branched fused polycyclic C.sub.6-C.sub.20 aryl. Optionally, aryl groups have six to twelve carbon atoms, i.e., C.sub.6-C.sub.12 aryl. A C.sub.6-C.sub.12 aryl can be a branched C.sub.6-C.sub.12 aryl, a monocyclic C.sub.6-C.sub.12 aryl, a polycyclic C.sub.6-C.sub.12 aryl, a branched polycyclic C.sub.6-C.sub.12 aryl, a fused polycyclic C.sub.6-C.sub.12 aryl, or a branched fused polycyclic C.sub.6-C.sub.12 aryl. Optionally, C.sub.6-C.sub.12 aryl groups have six to eleven carbon atoms, i.e., C.sub.6-C.sub.11 aryl. A C.sub.6-C.sub.11 aryl can be a branched C.sub.6-C.sub.11 aryl, a monocyclic C.sub.6-C.sub.11 aryl, a polycyclic C.sub.6-C.sub.11 aryl, a branched polycyclic C.sub.6-C.sub.11 aryl, a fused polycyclic C.sub.6-C.sub.11 aryl, or a branched fused polycyclic C.sub.6-C.sub.11 aryl. Optionally, C.sub.6-C.sub.12 aryl groups have six to nine carbon atoms, i.e., C.sub.6-C.sub.9 aryl. A C.sub.6-C.sub.9 aryl can be a branched C.sub.6-C.sub.9 aryl, a monocyclic C.sub.6-C.sub.9 aryl, a polycyclic C.sub.6-C.sub.9 aryl, a branched polycyclic C.sub.6-C.sub.9 aryl, a fused polycyclic C.sub.6-C.sub.9 aryl, or a branched fused polycyclic C.sub.6-C.sub.9 aryl. Optionally, C.sub.6-C.sub.12 aryl groups have six carbon atoms, i.e., C.sub.6 aryl. A C.sub.6 aryl can be a branched C.sub.6 aryl or a monocyclic C.sub.6 aryl.

[0034] As used herein, the term heteroaryl refers to univalent groups derived from heteroarenes by removal of a hydrogen atom from a ring atom. Heteroarenes are heterocyclic compounds derived from arenes by replacement of one or more methine (C?) and/or vinylene (CH?CH) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous R-electron system characteristic of aromatic systems and a number of out-of-plane R-electrons corresponding to the Hickel rule (4n+2). In polycyclic heteroaryl groups, the rings can be attached together in a pendant manner or can be fused. Heteroaryl group can have three to 50 carbon atoms, i.e., C.sub.3-C.sub.50 heteroaryl. A C.sub.3-C.sub.50 heteroaryl can be a branched C.sub.3-C.sub.50 heteroaryl, a monocyclic C.sub.3-C.sub.50 heteroaryl, a polycyclic C.sub.3-C.sub.50 heteroaryl, a branched polycyclic C.sub.3-C.sub.50 heteroaryl, a fused polycyclic C.sub.3-C.sub.50 heteroaryl, or a branched fused polycyclic C.sub.3-C.sub.50 heteroaryl. Optionally, heteroaryl groups have six to 30 carbon atoms, i.e., C.sub.6-C.sub.30 heteroaryl. A C.sub.6-C.sub.30 heteroaryl can be a branched C.sub.6-C.sub.30 heteroaryl, a monocyclic C.sub.6-C.sub.30 heteroaryl, a polycyclic C.sub.6-C.sub.30 heteroaryl, a branched polycyclic C.sub.6-C.sub.30 heteroaryl, a fused polycyclic C.sub.6-C.sub.30 heteroaryl, or a branched fused polycyclic C.sub.6-C.sub.30 heteroaryl. Optionally, heteroaryl groups have six to 20 carbon atoms, i.e., C.sub.6-C.sub.20 heteroaryl. A C.sub.6-C.sub.20 heteroaryl can be a branched C.sub.6-C.sub.20 heteroaryl, a monocyclic C.sub.6-C.sub.20 heteroaryl, a polycyclic C.sub.6-C.sub.20 heteroaryl, a branched polycyclic C.sub.6-C.sub.20 heteroaryl, a fused polycyclic C.sub.6-C.sub.20 heteroaryl, or a branched fused polycyclic C.sub.6-C.sub.20 heteroaryl. Optionally, heteroaryl groups have six to twelve carbon atoms, i.e., C.sub.6-C.sub.12 heteroaryl. A C.sub.6-C.sub.12 heteroaryl can be a branched C.sub.6-C.sub.12 heteroaryl, a monocyclic C.sub.6-C.sub.12 heteroaryl, a polycyclic C.sub.6-C.sub.12 heteroaryl, a branched polycyclic C.sub.6-C.sub.12 heteroaryl, a fused polycyclic C.sub.6-C.sub.12 heteroaryl, or a branched fused polycyclic C.sub.6-C.sub.12 heteroaryl. Optionally, C.sub.6-C.sub.12 heteroaryl groups have six to eleven carbon atoms, i.e., C.sub.6-C.sub.11 heteroaryl. A C.sub.6-C.sub.11 heteroaryl can be a branched C.sub.6-C.sub.11 heteroaryl, a monocyclic C.sub.6-C.sub.11 heteroaryl, a polycyclic C.sub.6-C.sub.11 heteroaryl, a branched polycyclic C.sub.6-C.sub.11 heteroaryl, a fused polycyclic C.sub.6-C.sub.11 heteroaryl, or a branched fused polycyclic C.sub.6-C.sub.11 heteroaryl. Optionally, C.sub.6-C.sub.12 heteroaryl groups have six to nine carbon atoms, i.e., C.sub.6-C.sub.9 heteroaryl. A C.sub.6-C.sub.9 heteroaryl can be a branched C.sub.6-C.sub.9 heteroaryl, a monocyclic C.sub.6-C.sub.9 heteroaryl, a polycyclic C.sub.6-C.sub.9 heteroaryl, a branched polycyclic C.sub.6-C.sub.9 heteroaryl, a fused polycyclic C.sub.6-C.sub.9 heteroaryl, or a branched fused polycyclic C.sub.6-C.sub.9 heteroaryl. Optionally, C.sub.6-C.sub.12 heteroaryl groups have six carbon atoms, i.e., C.sub.6 heteroaryl. A C.sub.6 heteroaryl can be a branched C.sub.6 heteroaryl, a monocyclic C.sub.6 heteroaryl, a polycyclic C.sub.6 heteroaryl, a branched polycyclic C.sub.6 heteroaryl, a fused polycyclic C.sub.6 heteroaryl, or a branched fused polycyclic C.sub.6 heteroaryl.

[0035] As used herein, the term substituted, means that the chemical group or moiety contains one or more substituents replacing the hydrogen atoms in the chemical group or moiety. The substituents include, but are not limited to: [0036] a halogen atom, an alkyl group, a cycloalkyl group, a heteroalkyl group, a cycloheteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, a heteroaryl group, a polyaryl group, a polyheteroaryl group, OH, SH, NH.sub.2, N.sub.3, OCN, NCO, ONO.sub.2, CN, NC, ONO, CONH.sub.2, NO, NO.sub.2, ONH.sub.2, SCN, SNCS, CF.sub.3, CH.sub.2CF.sub.3, CH.sub.2C.sub.1, CHCl.sub.2, CH.sub.2NH.sub.2, NHCOH, C HO, COCl, COF, COBr, COOH, SO.sub.3H, CH.sub.2SO.sub.2CH.sub.3, PO.sub.3H.sub.2, OPO.sub.3H.sub.2, P(?O)(OR.sup.T1)(OR.sup.T2), OP(?O)(OR.sup.T1)(OR.sup.T2), BR.sup.T1(OR.sup.T2), B(OR.sup.T1)(OR.sup.T2), or -GR.sup.T1 in which -T is O, S, NR.sup.T2, C(?O), S(?O), SO.sub.2, C(?O)O, C(?O)NR.sup.T2, OC(?O), NR.sup.T2C(?O), OC(?O)O, OC(?O)NR.sup.T2, NR.sup.T2C(?O)O, NR.sup.T2C(?O)NR.sup.T3, C(?S), C(?S)S, SC(?S), SC(?S)S, C(?NR.sup.T2), C(?NR.sup.T2)O, C(?NR.sup.T2)NR.sup.T3, OC(?NR.sup.T2), NR.sup.T2C(?NR.sup.T3), NR.sup.T2SO.sub.2, C(?NR.sup.T2)NR.sup.T3, OC(?NR.sup.T2), NR.sup.T2C(?NR.sup.T3), NR.sup.T2SO.sub.2, NR.sup.T2SO.sub.2NR.sup.T3, NR.sup.T2C(?S), SC(?S)NR.sup.T2, NR.sup.T2C(?S)S, NR.sup.T2C(?S)NR.sup.T3, SC(?NR.sup.T2), C(?S)NR.sup.T2, OC(?S)NR.sup.T2, NR.sup.T2C(?S)O, SC(?O)NR.sup.T2, NR.sup.T2C(?O)S, C(?O)S, SC(?O), SC(?O)S, C(?S)O, OC(?S), OC(?S)O, SO.sub.2NR.sup.T2, BR.sup.T2, or PR.sup.T2; where each occurrence of R.sup.T1, R.sup.T2, and R.sup.T3 is, independently, a hydrogen atom, a halogen atom, an alkyl group, a heteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, or a heteroaryl group.

[0037] In some instances, substituted also refers to one or more substitutions of one or more of the carbon atoms in a carbon chain (e.g., alkyl, alkenyl, alkynyl, and aryl groups) by a heteroatom, such as, but not limited to, nitrogen, oxygen, and sulfur.

[0038] It is understood that substitution or substituted includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, i.e. a compound that does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc.

[0039] Use of the term about is intended to describe values either above or below the stated value in a range of approx. +/?10%; in other embodiments the values may range in value either above or below the stated value in a range of approx. +/?5%. The preceding ranges are intended to be made clear by context, and no further limitation is implied.

[0040] Numerical ranges disclosed in the present application of any type, disclose individually each possible number that such a range could reasonably encompass, as well as any sub-ranges and combinations of sub-ranges encompassed therein.

II. Compositions

[0041] Bicyclic heterocyclic compounds and their derivatives (together also referred to therein as compounds) having antiviral properties and low toxicity have been developed. These have broad antiviral properties and should be suitable for use in the prophylaxis and/or treatment of multiple classes of viruses.

[0042] Generally, the compounds mimic RNA and/or DNA bases through base pairing with RNA and/or DNA nucleosides, becoming incorporated into the viral RNA and/or DNA strand, resulting in viral mutagenesis (Strombaugh et al., Nucleic Acids Research, 37(7):2294-2312 (2009); Jin et al., POLS one, 8(7):e68347 (2013)). Compounds that are structurally comparable to RNA and/or DNA nucleosides (also referred to herein as nucleoside analogue prodrugs) act as competitive enzymatic inhibitors when incorporated into newly synthesized viral RNA and/or DNA. It is known that nucleoside analogue prodrugs can be converted to active metabolite drugs, 5 ribose triphosphate (RTP) (see, e.g., Good, et al., Antimicrobial Agents and Chemotherapy, 65(4):e02479-20, 2021). The nucleoside analogue prodrugs can accelerate the absorption of these prodrugs into cells and the formation of the active metabolite drug, 5 ribose triphosphate (RTP), which base-pairs with RNA and/or DNA bases and gets incorporated into the viral RNA and/or DNA strand, resulting in viral mutagenesis (see, for example, U.S. Pat. No. 7,018,989 to McGuigan et al.). The overall structure of these compounds for base pairing may render them useful in treating medical conditions in addition to viruses.

[0043] Typically, the compounds can form at least two hydrogen bonds with RNA nucleosides and hence show high potential to mimic RNA and/or DNA bases. Additionally, the compounds eliminate the free rotation of the amide group of the currently approved antivirals (e.g., Ribavirin and Favipiravir), thereby lowering the toxicity (e.g. teratogenicity and embryo toxicity) of these compounds. In one embodiment, the compounds possess enhanced antiviral activity and reduced toxicity (e.g. teratogenicity and embryo toxicity) compared with the currently approved antivirals, such as Ribavirin and Favipiravir.

[0044] Pharmaceutical compositions and formulations containing the compounds are also disclosed.

[0045] A. Compounds

[0046] 1. Bicyclic Heterocyclic Compounds and Derivatives Thereof

[0047] The compounds can have the structures of Formula I.

##STR00001## [0048] where A and A are independently an unsubstituted heterocyclic group or a substituted heterocyclic group; and [0049] where X is a carbon or a nitrogen, [0050] where the substituents are independently a phosphoramidate, a heterocyclic group, a halogen, a sulfonic acid, an azide group, a cyanate group, an isocyanate group, a nitrate group, a nitrile group, an isonitrile group, a nitrosooxy group, a nitroso group, a nitro group, an aldehyde group, an alkoxy group, an acyl halide group, a carboxylic acid group, a carboxylate group, an alkyl group, a heteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, a heteroaryl group, polyaryl group, a heteropoly aryl group, a alkyl aryl group, an amino group, a hydroxyl group, a thiol group, a sulfonyl group, an ester group, an aliphatic ester group, an amide group, an aliphatic amide group, an azo group, an acyl group, a carbonyl group, a carbonate ester group, an ether group, an oxo, an aminooxy group, or a hydroxyamino group.

[0051] In some embodiments, A and A are independently an unsubstituted heterocyclic group. In some embodiments, A and A are independently a substituted heterocyclic group.

[0052] In some embodiments, A and A are independently an unsubstituted or substituted pyrrolyl group, an unsubstituted or substituted imidazolyl group, an unsubstituted or substituted pyrazolyl group, an unsubstituted or substituted triazolyl group, an unsubstituted or substituted thiazolyl group, an unsubstituted or substituted isothiazolyl group, an unsubstituted or substituted oxazolyl group, an unsubstituted or substituted oxazinyl group, an unsubstituted or substituted pyrrolidinyl group, an unsubstituted or substituted pyrrolinyl group, an unsubstituted or substituted imidazolidinyl group, an unsubstituted or substituted imidazolinyl group, an unsubstituted or substituted pyrazolidinyl group, an unsubstituted or substituted tetrahydrofuranyl group, an unsubstituted or substituted pyranyl group, an unsubstituted or substituted pyronyl group, an unsubstituted or substituted pyridyl group, an unsubstituted or substituted pyrazinyl group, an unsubstituted or substituted pyridazinyl group, an unsubstituted or substituted piperidyl group, an unsubstituted or substituted piperazinyl group, an unsubstituted or substituted morpholinyl group, an unsubstituted or substituted benzofuranyl group, an unsubstituted or substituted isobenzofuryl group, an unsubstituted or substituted indolyl group, an unsubstituted or substituted oxyindolyl group, an unsubstituted or substituted isoindolyl group, an unsubstituted or substituted indazolyl group, an unsubstituted or substituted indolinyl group, an unsubstituted or substituted 7-azaindolyl group, an unsubstituted or substituted isoindazolyl group, an unsubstituted or substituted benzopyranyl group, an unsubstituted or substituted coumarinyl group, an unsubstituted or substituted isocoumarinyl group, an unsubstituted or substituted quinolyl group, an unsubstituted or substituted iso-quinolyl group, an unsubstituted or substituted naphthridinyl group, an unsubstituted or substituted cinnolinyl group, an unsubstituted or substituted quinazolinyl group, an unsubstituted or substituted pyridopyridyl group, an unsubstituted or substituted benzoxazinyl group, an unsubstituted or substituted quinoxadinyl group, an unsubstituted or substituted chromenyl group, an unsubstituted or substituted chromanyl group, an unsubstituted or substituted isochrcmanyl group, or an unsubstituted or substituted carbolinyl group.

[0053] In some embodiments, A and A are independently an unsubstituted or substituted pyrazinyl group, an unsubstituted or substituted oxazinyl group, an unsubstituted or substituted triazinyl group, an unsubstituted or substituted triazolyl group, an unsubstituted or substituted pyrazolyl group, an unsubstituted or substituted pyrrolyl group, an unsubstituted or substituted pyridazinyl group, an unsubstituted or substituted pyrimidinyl group, an unsubstituted or substituted pyridinyl group, or an unsubstituted or substituted imidazolyl group. In some embodiments, A and A are independently a substituted pyrazinyl group, a substituted oxazinyl group, a substituted triazinyl group, a substituted triazolyl group, a substituted pyrazolyl group, a substituted pyrrolyl group, a substituted pyridazinyl group, a substituted pyrimidinyl group, a substituted pyridinyl group, or a substituted imidazolyl group.

[0054] In some embodiments, the compounds have the structures of Formula IIa or Formula IIIa.

##STR00002## [0055] (a) where A and X are as defined above; (b) where E.sub.1, E.sub.1, P.sub.1, P.sub.1, G.sub.1, G.sub.1, and W.sub.1 are independently CR.sub.20 or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (c) where Q.sub.1 and Q.sub.1 are independently CR.sub.20 and R.sub.20 can be as defined above, for example, R.sub.20 is absent or hydrogen according to valency; and (d) where the substituents are independently a phosphoramidate, a heterocyclic group, a halogen, a sulfonic acid, an azide group, a cyanate group, an isocyanate group, a nitrate group, a nitrile group, an isonitrile group, a nitrosooxy group, a nitroso group, a nitro group, an aldehyde group, an alkoxy group, an acyl halide group, a carboxylic acid group, a carboxylate group, an alkyl group, a heteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, a heteroaryl group, polyaryl group, a heteropoly aryl group, a alkyl aryl group, an amino group, an ester group, a hydroxyl group, a thiol group, a sulfonyl group, an ester group, an aliphatic ester group, an amide group, an aliphatic amide group, an azo group, an acyl group, a carbonyl group, a carbonate ester group, an ether group, an aminooxy group, or a hydroxyamino group.

[0056] In some embodiments, the compounds have the structures of Formula IIa.

##STR00003## [0057] (a) where A, X, P.sub.1, and G.sub.1 are as defined above; (b) where L and M are independently a carbon or a nitrogen; (c) where R.sub.2 is absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; (d) R.sub.3 is absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and (e) where the substituents are as defined above.

[0058] In some embodiments, the compounds have the structures of Formula IIb, IIb, or Formula IIIb.

##STR00004## [0059] (a) where A and X are as defined above; (b) where L, M, L, and M are independently a carbon or a nitrogen; (c) where P.sub.1, P.sub.1 and G.sub.1 are independently CR.sub.20 or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (d) where X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (e) where R.sub.2 and R.sub.2 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; (f) where R.sub.3 and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and (g) where the substituents are as defined above.

[0060] In some embodiments, the compounds have the structures of Formula II, Formula III, Formula II, Formula III, Formula II, or Formula II.

##STR00005## [0061] where X and A are as defined above; [0062] where L, M, L, M, L, L, and L.sub.1-L.sub.3 are independently a carbon or a nitrogen; [0063] where X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0064] where R.sub.1, R.sub.1, R.sub.23, and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; [0065] where R.sub.2, R.sub.2, R.sub.22, R.sub.22, R.sub.22, R.sub.22, and R.sub.25 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; [0066] where R.sub.3 and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0067] where R.sub.8, R.sub.8, R.sub.24, and R.sub.27 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0068] where the substituents are as defined above.

[0069] In some embodiments, A of Formulae I, IIa, IIb, II, II, IIa, IIb, II, II, IIIa, IIIb, III, and/or III is

##STR00006## [0070] (a) where X is as defined above; (b) where E.sub.2, E.sub.2, G.sub.2, G.sub.2, Q.sub.2, Q.sub.2, and W.sub.2 are independently an oxygen, a sulfur, CR.sub.20, or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; (c) where Q.sub.1 and Q.sub.1 are independently CR.sub.20 and R.sub.20 can be as defined above, for example, R.sub.20 is absent; and (d) where the substituents are as defined above.

[0071] In some embodiments, A of Formulae I, IIa, IIb, II, II, IIa, IIb, II, II, IIIa, IIIb, III, and/or III is

##STR00007## [0072] where X is as defined above; where Y, Y, and Z are independently a carbon, an oxygen, a nitrogen, or a sulfur; [0073] where J and J are independently an oxygen, OR.sub.3, a sulfur, a thiol group, an unsubstituted amino group, or a substituted amino group (e.g. a hydroxyl substituted amino group, such as

##STR00008## [0074] where R.sub.3, R.sub.3, and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0075] where R.sub.4, R.sub.5, R.sub.4, R.sub.5, R.sub.6, and R.sub.7, according to valency, are independently absent, a hydrogen, an oxygen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, where the substituents are as defined above.

[0076] In some embodiments of Formula IV or Formula V, Y and Y are nitrogen and Z is a carbon, an oxygen, a nitrogen, or a sulfur. In some embodiments of Formula IV or Formula V, Y and Y are nitrogen and Z is a carbon, an oxygen, or a nitrogen. In some embodiments of Formula IV or Formula V, Y and Y are nitrogen and Z is a carbon or a nitrogen.

[0077] In some embodiments, the compounds of Formulae I, IIa, IIb, II, II, IIa, IIb, II, II, IIIa, IIIb, III, III, IVa, Va, IV, and V contain an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic-aliphatic group, a substituted heterocyclic-aliphatic group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an unsubstituted aryl-aliphatic group, and/or a substituted aryl-aliphatic group, such as R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.22, R.sub.22, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27, where the aliphatic group of the unsubstituted aliphatic group, the substituted aliphatic group, the unsubstituted aliphatic ester group, the substituted aliphatic ester group, the unsubstituted aliphatic ether group, the substituted aliphatic ether group, the unsubstituted heterocyclic-aliphatic group, the substituted heterocyclic-aliphatic group, the unsubstituted aliphatic-amide group, the substituted aliphatic-amide group, the unsubstituted aryl-aliphatic group, and/or the substituted aryl-aliphatic group, is a C.sub.1-C.sub.14 aliphatic group, optionally a C.sub.1-C.sub.6 aliphatic group.

[0078] In some embodiments, the compounds have the structures of Formula IV.

##STR00009## [0079] wherein X, L, G.sub.1, P.sub.1, M, Y, Z, J, R.sub.3, R.sub.3, R.sub.2, and R.sub.4R.sub.7 are as defined above.

[0080] In some embodiments, the compounds have the structures of Formula VIa or VIa.

##STR00010## [0081] wherein X, X, L, G.sub.1, P.sub.1, M, Y, Z, J, R.sub.3, R.sub.3, R.sub.2, and R.sub.4R.sub.7 are as defined above.

[0082] In some embodiments, the compounds have the structures of Formula VI, Formula VI, Formula VI, or Formula VI.

##STR00011## [0083] where X, X, L, L, L.sub.1-L.sub.3, M, Y, Z, J, R.sub.3, R.sub.3, R.sub.1-R.sub.8, R.sub.22R.sub.24, R.sub.22, R.sub.22, and R.sub.22 are as defined above. In some embodiments, the compounds of Formula VI or VI are disclosed where X, L, L, M, and Y are independently a carbon or a nitrogen, and Z is a carbon, an oxygen, or a nitrogen. In some embodiments, the compounds of Formula VI or VI are disclosed where X is carbon, L, L, and M are independently a carbon or a nitrogen, Y is a nitrogen, and Z is an oxygen, a nitrogen, or a carbon. In some embodiments, the compounds of Formula VI or VI are disclosed where X, L.sub.1, L.sub.2, L.sub.3, M, and Y are independently a carbon or a nitrogen, and Z is a carbon, an oxygen, or a nitrogen. In some embodiments, the compounds of Formula VI or VI are disclosed where X is carbon, L.sub.1, L.sub.2, L.sub.3, and M are nitrogen, Y is a nitrogen, and Z is a nitrogen or a carbon.

[0084] In some embodiments, the compounds of Formula VI are disclosed where X is carbon and L, M, Y, and Z are independently a carbon or a nitrogen. In some embodiments, the compounds of Formula VI are disclosed where X is carbon, L, M, and Y are nitrogen, and Z is independently an oxygen, a nitrogen, or a sulfur. In some embodiments, the compounds of Formula VI are disclosed where X is carbon, L, M, and Y are nitrogen, and Z is oxygen.

[0085] In some embodiments, the compounds are pyrazino-oxazine having the structures of Formula VII, Formula VII, or Formula VII.

##STR00012## [0086] where X, R.sub.3, R.sub.3, J, R.sub.1, R.sub.2, R.sub.4, R.sub.5, R.sub.8, and R.sub.22 are as defined above; and where L and L are independently a carbon or a nitrogen.

[0087] In some embodiments, the compounds are pyrazino-oxazine having the structures of Formula VIII, IX, or X.

##STR00013## [0088] where X, R.sub.3, R.sub.3, J, R.sub.1, R.sub.2, R.sub.4, R.sub.5, and R.sub.8 are as defined above.

[0089] In some embodiments, the compounds are triazolo-pyrazine having the structures of Formula XIa.

##STR00014## [0090] wherein X, L, L, M, Z, Y, J, R.sub.2, R.sub.3, R.sub.39, R.sub.8, R.sub.4R.sub.7, and R.sub.25 are as defined above.

[0091] In some embodiments, the compounds are triazolo-pyrazine having the structures of Formula XI or Formula XI.

##STR00015## [0092] where X, L, L, M, Z, Y, J, R.sub.1R.sub.3, R.sub.3, R.sub.8, R.sub.4R.sub.7, and R.sub.25R.sub.27 are as defined above.

[0093] In some embodiments, the compounds of Formula XI or Formula XI are disclosed where M, L, L, X, Y, and Z are independently a carbon or a nitrogen. In some embodiments, the compounds of Formula XI are disclosed where M and L are nitrogen, Z is carbon, and X and Y are independently a carbon or a nitrogen. In some embodiments, the compounds of Formula XI are disclosed where X, M, L, and Y are nitrogen and Z is a carbon or a nitrogen.

[0094] In some embodiments, the compounds are triazolo-pyrazine having the structures of Formula XII or Formula XII.

##STR00016## [0095] where J, R.sub.1R.sub.3, R.sub.8, R.sub.4R.sub.7, and R.sub.25R.sub.27 are as defined above; and where Z is a carbon or a nitrogen.

[0096] In some embodiments, the compounds are triazolo-pyrazine having the structures of Formulae XIII, XIII, XIII, XIV, or XV.

##STR00017## [0097] where J, R.sub.1R.sub.3, R.sub.8, R.sub.4R.sub.7, and R.sub.26 are as defined above.

[0098] In some embodiments, the compounds are triazolo-imidazole having the structures of Formula XVIa.

##STR00018## [0099] where X, L, L, M, Y, J, R.sub.2, R.sub.3, R.sub.3, R.sub.4, R.sub.5, and R.sub.25 are as defined above.

[0100] In some embodiments, the compounds are triazolo-imidazole having the structures of Formula XVI or Formula XVI.

##STR00019## [0101] where X, L, L, M, Y, J, R.sub.2, R.sub.3, R.sub.3, R.sub.4, R.sub.8, and R.sub.25R.sub.27 are as defined above.

[0102] In some embodiments, the compounds of Formula XVI or Formula XVI are disclosed where L, L, and M are independently a carbon or a nitrogen and X and Y are independently an oxygen, a nitrogen, or a sulfur. In some embodiments, the compounds of Formula XVI are disclosed where L and M are nitrogen and X and Y are independently an oxygen, a nitrogen, or a sulfur. In some embodiments, the compounds of Formula XVI are disclosed where X, L, and M are nitrogen and Y is an oxygen, a nitrogen, or a sulfur.

[0103] In some embodiments, the compounds are triazolo-imidazole having the structures of Formula XVII or Formula XVII.

##STR00020## [0104] where J, R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5, R.sub.8 and R.sub.25R.sub.27 are as defined above.

[0105] In some embodiments, the compounds are triazolo-imidazole having the structures of Formula XVIII, XIX, XX, or XX.

##STR00021## [0106] where J, R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5, R.sub.8, and R.sub.26 are as defined above.

[0107] In some embodiments, the compounds of Formulae IV, IV, V, VIa, VI, VIa, VI, VIa, VI, VI, VII, VII, VII, VIII, IX, X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, and XX are disclosed where J and J are independently an oxygen or OR.sub.3, where R.sub.3 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, and where the substituents are as defined above.

[0108] In some embodiments, the compounds have the structures of any one of Formulae 1-24 and 84-102 and tautomer thereof.

##STR00022## ##STR00023## ##STR00024## ##STR00025## ##STR00026## ##STR00027## [0109] where X, R.sub.1-R.sub.8, R.sub.22, R.sub.23, R.sub.25, R.sub.26, R.sub.1R.sub.5, R.sub.8, R.sub.3, and R.sub.3 are as defined above.

[0110] In some embodiments, the aliphatic group of the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 is a C.sub.1-C.sub.14 aliphatic group, a C.sub.1-C.sub.12 aliphatic group, a C.sub.1-C.sub.10 aliphatic group, a C.sub.1-C.sub.8 aliphatic group, or a C.sub.1-C.sub.6 aliphatic group, or a combination thereof.

[0111] Typically, the compounds can form at least two hydrogen bonds with RNA nucleosides and hence show high potential to mimic RNA bases. For example, the compounds can form at least two hydrogen bonds or at least three hydrogen bonds with a RNA nucleoside, such as two hydrogen bonds or three hydrogen bonds. For example, when the compounds are triazolo-pyrazine having the structures of any one of Formulae XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, 7-12, 19-20, 24, and 89-92, the compounds can form at least two hydrogen bonds with cytidine (see, e.g. FIGS. 1A-1B). In some embodiments, when the compounds are pyrazino/pyrimidino/pyridazino oxazin having the structures of any one of Formulae VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, 1-6, 84-88, and 96-102 or are triazolo-imidazole having the structures of any one of Formulae XVIa, XVI, XVI, XVII, XVII, XVIII-XX, and XX, 13-18, 21-23, and 93-95, the compounds can form at least two hydrogen bonds with cytidine. In some embodiments, R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.22, R.sub.22, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 of any one of the Formulae described above is a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, or an azide group. In such embodiments, the compounds can form at least three hydrogen bonds with a RNA nucleoside. For example, when the compounds are triazolo-pyrazine having the structures of any one of Formulae XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, 7-12, 19-20, 24, and 89-92, where R.sub.4 or R.sub.5 is an amino or oxo group, the compounds can form at least three hydrogen bonds with uridine (see, e.g. FIGS. 2A-2B). In some embodiments, when the compounds are pyrazino/pyrimidino/pyridazino oxazin having the structures of any one of Formulae VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, 1-6, and 84-88, where R.sub.4 or R.sub.5 is an amino, an aliphatic-amino, or oxo group or when the compounds are triazolo-imidazole having the structures of any one of Formulae XVIa, XVI, XVI, XVII, XVII, XVIII-XX, and XX, 13-18, 21-23, and 93-95, where R.sub.4 or R.sub.5 is an amino, an aliphatic-amino, or oxo group, the compounds can form at least three hydrogen bonds with cytidine.

[0112] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VI a, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where the structures of the compounds are comparable to RNA nucleosides. For example, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.22, R.sub.22, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 is an unsubstituted aliphatic ether or a substituted aliphatic ether, such that the structures of the compounds are comparable to RNA nucleosides. Compounds that are structurally comparable to RNA nucleosides (nucleoside analogue prodrugs) can act as competitive enzymatic inhibitors when incorporated into newly synthesized viral RNA.

[0113] The nucleoside analogue prodrugs may be a nucleoside or a nucleotide. The nucleoside analogue prodrugs can accelerate the absorption of these prodrugs into cells and the formation of the active metabolite drug, 5 ribose triphosphate (RTP), which base-pairs with RNA bases and gets incorporated into the viral RNA strand, resulting in viral mutagenesis.

[0114] In some embodiments, the compounds are nucleoside analogue prodrugs, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 is an unsubstituted aliphatic ether or a substituted aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether, and where the substituents are as defined above.

[0115] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIIa, IIIb, IIa, IIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 is a substituted C.sub.1-C.sub.6 aliphatic ether having the structure of Formula XXI.

##STR00028## [0116] where A.sub.1 and A.sub.2 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, a cyanide group, a nitrile group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0117] where A.sub.7 is a methylene group or an ethylene group; [0118] where R.sub.9 and R.sub.10 are independently a hydrogen, a hydroxyl group, an unsubstituted alkyl group, or a substituted alkyl group, optionally wherein R.sub.9 and R.sub.10 are independently a substituted alkyl group that together form a ring; and [0119] where B.sub.2 is hydrogen or a phosphoramidate, [0120] where the substituents are as defined above.

[0121] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 has the structure of Formula 25 or 25.

##STR00029## [0122] where A.sub.1, A.sub.2, A.sub.7, and B.sub.2 are as defined above.

[0123] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 has the structure of Formula XXII.

##STR00030## [0124] where A.sub.1, A.sub.2, A.sub.7, and B.sub.2 are as defined above; and [0125] wherein A.sub.3, A.sub.4, A.sub.5, and A.sub.6 are independently absent, a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group, [0126] where the substituents are as defined above.

[0127] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 has the structure of Formula 26 or 26.

##STR00031## [0128] where A.sub.7 and B.sub.2 are as defined above. [0129] where A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and [0130] where A.sub.2, A.sub.3, and A.sub.4 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group, [0131] where the substituents are as defined above.

[0132] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.8, R.sub.1, R.sub.2, R.sub.8, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.4, R.sub.5, R.sub.6, R.sub.7, R.sub.22, R.sub.23, R.sub.24, R.sub.25, R.sub.26, and/or R.sub.27 has the structure of Formula 27 or 27.

##STR00032## [0133] where A.sub.7 and B.sub.2 are as defined above. [0134] where A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; [0135] where A.sub.2-A.sub.6 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0136] optionally where A.sub.2, A.sub.4, and A.sub.6 are hydrogen, or A.sub.1 is cyanide, or A.sub.3 and/or A.sub.6 are hydroxyl, or a combination thereof; [0137] where the substituents are as defined above.

[0138] In some forms, Formula 27 is

##STR00033##

[0139] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-24, and 84-102 are disclosed, where R.sub.1, R.sub.2, R.sub.1, R.sub.2, R.sub.23, R.sub.26, R.sub.22, or R.sub.25 has the structure of Formula XXI, Formula XXII, Formula 25, Formula 25, Formula 26, Formula 26, Formula 27, or Formula 27.

[0140] In some embodiments, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VI a, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-27, and 84-102 are disclosed, where the structures of the compounds are comparable to RNA nucleotides. Compounds that are structurally comparable to RNA nucleosides can accentuate the antiviral activity of such compounds. For example, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VIa, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-27, and 84-102 are disclosed, where B.sub.2 is hydrogen. For example, the compounds of any one of Formulae II, IIa, IIb, IIa, IIb, IIIa, IIIb, II, II, II, II, III, III, IVa, Va, IV, IV, V, VIa, VI a, VI, VI, VI, VI, VII, VII, VII, VIII-X, XIa, XI, XI, XII, XII, XIII, XIII, XIII, XIV, XV, XVIa, XVI, XVI, XVII, XVII, XVIII-XX, XX,1-27, and 84-102 are disclosed, where B.sub.2 is a phosphoramidate having the structure of Formula 28.

##STR00034## [0141] wherein B.sub.1 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, or a substituted aryl group; [0142] wherein Q is an oxygen or a sulfur; [0143] wherein T is an oxygen, a sulfur, NR.sub.11, CR.sub.11R.sub.12, CR.sub.11W.sub.1, or CW.sub.1W.sub.2, wherein R.sub.11 and R.sub.12 are independently a hydrogen, an unsubstituted alkyl group, a substituted alkyl group, an unsubstituted aryl group, a substituted aryl group, and wherein W.sub.1 and W.sub.2 are independently a heteroatom; [0144] wherein Y is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; and [0145] wherein A is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an alkoxy, CM.sub.1alkyl, CM.sub.1aryl, or -CM.sub.1heterocyclic, wherein M.sub.1 is an oxygen or a methylene group.

[0146] In some forms, A is O-alkyl, where the alkyl can be a substituted or unsubstituted alkyl, such as an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.6 alkyl, an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.4 alkyl, or an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.3 alkyl.

[0147] In some forms, B.sub.1 is an unsubstituted aryl group or a substituted aryl group, such as an unsubstituted phenyl. In some forms, A-C(O)Y-T- is

##STR00035##

[0148] In some embodiments, the compounds of any one of Formulae VI, VI, VI and VIare disclosed, where R.sub.1 or R.sub.2 of Formula VI, R.sub.22 or R.sub.23 of Formula VI, R.sub.23 or R.sub.1 of Formula VI, and R.sub.23, R.sub.22, or R.sub.22 of Formula VI has the structure of Formula XXI, Formula XXII, Formula 25, Formula 25, Formula 26, Formula 26, Formula 27, or Formula 27; X and the other R groups are absent, hydrogen, substituted or unsubstituted aliphatic group, substituted or unsubstituted amino group, substituted or unsubstituted aliphatic-amino group, or oxo group (for example, R.sub.4 or R.sub.5 is an oxo or a substituted or unsubstituted amino or aliphatic-amino group and the rest of the R groups and X are independently substituted or unsubstituted aliphatic group, hydrogen or absent according to valency); and optionally B.sub.2 has the structure of Formula 28. In some embodiments, the compounds of any one of Formulae XI and XI are disclosed, where R.sub.1 or R.sub.2 of Formula XI and R.sub.25 or R.sub.26 of Formula XI has the structure of Formula XXI, Formula XXII, Formula 25, Formula 25, Formula 26, Formula 26, Formula 27, or Formula 27; the other R groups are absent, hydrogen, substituted or unsubstituted aliphatic group, substituted or unsubstituted amino group, substituted or unsubstituted aliphatic-amino group, or oxo group (for example, R.sub.4 or R.sub.5 is an oxo or a substituted or unsubstituted amino or aliphatic-amino group and the rest of the R groups are independently substituted or unsubstituted aliphatic group, hydrogen or absent according to valency); and optionally where B.sub.2 has the structure of Formula 28. In some embodiments, the compounds of any one of Formulae XVI and XVI are disclosed, where R.sub.1 or R.sub.2 of Formula XVI and R.sub.25 or R.sub.26 of Formula XVI has the structure of Formula XXI, Formula XXII, Formula 25, Formula 25, Formula 26, Formula 26, Formula 27, or Formula 27; the other R groups are absent, hydrogen, substituted or unsubstituted aliphatic group, substituted or unsubstituted amino group, substituted or unsubstituted aliphatic-amino group, or oxo group (for example, R.sub.4 or R.sub.5 is an oxo or a substituted or unsubstituted amino or aliphatic-amino group and the rest of the R groups are independently substituted or unsubstituted aliphatic group, hydrogen or absent according to valency); and optionally where B.sub.2 has the structure of Formula 28. When these embodiments of Formulae VI, VI, VI, VI, XI, XI, XVI and XVI are disclosed, J and J of any one of these Formulae can be independently an oxygen or OR.sub.3, where R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group. The compounds may contain one or more chiral centers or may otherwise be capable of existing as multiple stereoisomers. These may be pure (single) stereoisomers or mixtures of stereoisomers, such as enantiomers, diastereomers, and enantiomerically or diastereomerically enriched mixtures. The compounds may be capable of existing as geometric isomers. Accordingly, it is to be understood that the present invention includes pure geometric isomers or mixtures of geometric isomers.

[0149] 2. Exemplary Nucleoside Analogue Prodrugs and Nucleotides

[0150] Exemplary nucleoside analogue prodrugs can be prepared using three alternative C.sub.1-C.sub.6 aliphatic ethers of Formulae 26, 27, and 25 as R.sub.1, R.sub.2, R.sub.1, or R.sub.2 in compounds having the structures of Formulae 1-18. Exemplary nucleotides can be prepared by using phosphoramidates of Formula 28 as B.sub.2 in the exemplary nucleoside analogue prodrugs.

[0151] It is understood that the exemplary compounds shown herein can exist in alternative stereoisomer forms. For example, the atoms/substituents attached to any one of the stereocenters of any one of the Formulae described in Table 1 below and the Examples below can have a different spatial configuration than those shown. For example, the aliphatic ether is attached to the bicyclic rings in an R configuration (see, e.g., Formulae 25, 26, and 27). For example, the substituents on the cyclic ether have an R,R,S,R configuration. Preferably, when the bicyclic ring moiety of the disclosed compounds is a 6,6-bicyclic ring, the substituents on the cyclic ether attached to the 6,6-bicyclic ring have an R,R,S,R configuration.

[0152] It is also understood that the exemplary compounds shown herein can exist in alternative tautomer forms. For example, the bicyclic ring structure of each of the exemplary compounds described herein can present in the form of a tautomer or a mixture of two or three different forms of tautomer, such as a keto-keto form, a keto-enol form, an amino-enol form, an amino-keto form, or an enol-enol form, or a mixture thereof.

[0153] A summary of exemplary nucleoside analogue prodrugs and nucleotides that can be prepared is presented in Table 1. Although not illustrated in Table 1 below, it is understood that additional exemplary nucleoside analogue prodrugs and nucleotides can be prepared using the three alternative C.sub.1-C.sub.6 aliphatic ethers of Formulae 26, 27, and 25 as R.sub.1, R.sub.2, R.sub.2, R.sub.22, R.sub.23, R.sub.25, R.sub.26 in compounds having any of the structures of Formulae 19-24 and 84-102.

TABLE-US-00001 TABLE 1 Exemplary nucleosides and nucleotides Nucleoside Analogue prodrug (R.sub.1 or R.sub.1 is the Nucleotide aliphatic ether (B.sub.2 is a R.sub.1, R.sub.2, R.sub.1, or R.sub.2 is a C.sub.1-C.sub.6 unless noted phosphor- Formula Aliphatic Ether otherwise) amidate) [00036] [00037] 29a 29b [00038] 30a 30b [00039] 31a 31b [00040] [00041] 32a 32b [00042] 33a 33b [00043] 34a 34b [00044] [00045] 35a 35b [00046] 36a (R.sub.2) 36b (R.sub.2) [00047] 37a 37b [00048] [00049] 38a 38b [00050] 39a 39b [00051] 40a 40b [00052] [00053] 41a 41b [00054] 42a 42b [00055] 43a 43b [00056] [00057] 44a 44b [00058] 45a 45b [00059] 46a 46b [00060] [00061] 47a 47b [00062] 48a 48b [00063] 49a 49b [00064] [00065] 50a 50b [00066] 51a (R.sub.2) 51b (R.sub.2) [00067] 52a 52b [00068] [00069] 53a 53b [00070] 54a (R.sub.2) 54b (R.sub.2) [00071] 55a 55b [00072] [00073] 56a 56b [00074] 57a 57b [00075] 58a 58b [00076] [00077] 59a 59b [00078] 60a 60b [00079] 61a 61b [00080] [00081] 62a 62b [00082] 63a (R.sub.2) 63b (R.sub.2) [00083] 64a (R.sub.2) 64b (R.sub.2) [00084] [00085] 65a 65b [00086] 66a 66b [00087] 67a 67b [00088] [00089] 68a 68b [00090] 69a (R.sub.2) 69b (R.sub.2) [00091] 70a 70b [00092] [00093] 71a (R.sub.2) 71b (R.sub.2) [00094] 72a 72b [00095] 73a 73b [00096] [00097] 74a 74b [00098] 75a 75b [00099] 76a 76b [00100] [00101] 77a 77b [00102] 78a (R.sub.2) 78b (R.sub.2) [00103] 79a 79b [00104] [00105] 80a (R.sub.2) 80b (R.sub.2) [00106] 81a 81b [00107] 82a 82b [00108]

[0154] Specific exemplary compounds 29a-33b, 36a, 36b, 47a, 47b, 51a, 51b, 54a, 54b, 57a, 57b, 63a-65b, 69a, 69b, 71a, 71b, 75a, 75b, 78a, 78b, 81a, and 81b in Table 1 and additional exemplary compounds are described in the Examples section below.

[0155] In some embodiments, the compound has the structure of Formula 83 (also referred to therein as T-101) or Formula 83 (also referred to therein as T-101).

##STR00109##

[0156] 3. Pharmaceutically Acceptable Salts

[0157] The compounds may be neutral or may be one or more pharmaceutically acceptable salts, crystalline forms, non-crystalline forms, hydrates, or solvates, or a combination thereof. References to the compounds may refer to the neutral molecule, and/or those additional forms thereof collectively and individually from the context. Pharmaceutically acceptable salts of the compounds include the acid addition and base salts thereof.

[0158] Suitable acid addition salts are formed from acids which form non-toxic salts. Examples include the acetate, aspartate, benzoate, besylate, bicarbonate/carbonate, bisulphate/sulphate, borate, camsylate, citrate, edisylate, esylate, formate, fumarate, gluceptate, gluconate, glucuronate, hexafluorophosphate, hibenzate, hydrochloride/chloride, hydrobromide/bromide, hydroiodide/iodide, isethionate, lactate, malate, maleate, malonate, mesylate, methylsulphate, naphthylate, 2-napsylate, nicotinate, nitrate, orotate, oxalate, palmitate, pamoate, phosphate/hydrogen phosphate/dihydrogen phosphate, saccharate, stearate, succinate, tartrate, tosylate and trifluoroacetate salts.

[0159] Suitable base salts are formed from bases which form non-toxic salts. Examples include the aluminium, arginine, benzathine, calcium, choline, diethylamine, diolamine, glycine, lysine, magnesium, meglumine, olamine, potassium, sodium, tromethamine and zinc salts.

[0160] Hemisalts of acids and bases may also be formed, for example, hemisulphate and hemicalcium salts.

[0161] 4. Effective Doses

[0162] Effective doses of the present compounds depend on many factors, including the indication being treated, the route of administration, co-administration of other therapeutic compositions, and the overall condition of the patient.

[0163] In general, treatment regimens utilizing compounds comprise administration of from about 0.1 mg to about 300 mg of the compounds per kilogram body weight of the recipient per day in multiple doses or in a single dose. In some embodiments, a suitable dose may be in the range of 0.1 to 300 mg per kilogram body weight of the recipient per day, optionally in the range of 6 to 150 mg per kilogram body weight per day, and optionally in the range 15 to 100 mg per kilogram body weight per day. The desired dose may be presented as two, three, four, five or six or more sub-doses administered at appropriate intervals throughout the day. These sub-doses may be administered in unit dosage forms, for example, containing 10 to 1500 mg, optionally 20 to 1000 mg, and optionally 50 to 700 mg of the compounds per unit dosage form.

[0164] B. Pharmaceutical Compositions

[0165] Pharmaceutical compositions and pharmaceutical formulations in unit dosage form suitable for the delivery of the compounds thereof and their preparation are disclosed. Generally, the pharmaceutical composition or formulation contains the compounds and/or the pharmaceutically acceptable salts of the compounds described herein, and a pharmaceutically acceptable excipient. The term pharmaceutically acceptable excipient is used herein to describe any ingredient in the formulation other than the compounds described herein. The pharmaceutical compositions or formulations can include an effective amount of one or more compounds of any of the formulae described herein and/or their pharmaceutically acceptable salts, including any one or any combination of compounds of the formulae described herein and/or their pharmaceutically acceptable salts, for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in a subject. In some embodiments, the pharmaceutical composition or formulation can further contain one or more active agents in addition to the compounds, such as antiviral agents and/or anti-inflammatory agents. Antiviral agents and anti-inflammatory agents that can be included in the pharmaceutical compositions or formulations are known, for example, see Erik De Clercq, Medmicro, Chapter 52 (2000).

[0166] It is to be understood that combinations and/or mixtures of the compounds and/or their pharmaceutically acceptable salts may be included in the composition or formulation. In some embodiments, the pharmaceutical composition or formulation includes an effective amount of the compounds and/or their pharmaceutically acceptable salts for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in a subject in a patient in need of relief.

[0167] Any one of more of the compounds provided herein can be expressly included or expressly excluded from the pharmaceutical compositions, dosage units, and/or methods of use or treatment disclosed herein.

[0168] 1. Oral Formulations

[0169] The compounds and/or their pharmaceutically acceptable salts may be administered orally. Oral administration may involve swallowing, so that the compound enters the gastrointestinal tract, or buccal or sublingual administration may be employed by which the compound enters the blood stream directly from the mouth.

[0170] Formulations suitable for oral administration include solid formulations such as tablets, capsules containing particulates, liquids, powders, lozenges (including liquid-filled lozenges), chews, multi- and nano-particulates, gels, solid solutions, liposomes, films, ovules, sprays and liquid formulations.

[0171] Liquid formulations include suspensions, solutions, syrups and elixirs. Such formulations may be employed as fillers in soft or hard capsules and typically comprise a carrier, for example, water, ethanol, polyethylene glycol, propylene glycol, methylcellulose or a suitable oil, and one or more emulsifying agents and/or suspending agents. Liquid formulations may also be prepared by the reconstitution of a solid, for example, from a sachet.

[0172] The compounds and/or their pharmaceutically acceptable salts may also be used in fast-dissolving, fast-disintegrating dosage forms such as those described in Expert Opinion in Therapeutic Patents, 11 (6), 981-986, by Liang and Chen (2001).

[0173] For tablet or capsule dosage forms, depending on dose, the compounds and/or their pharmaceutically acceptable salts may make up from 1 weight % to 80 weight % of the dosage form, more typically from 5 weight % to 60 weight % of the dosage form. In addition to the compounds described herein, tablets generally contain a disintegrant. Examples of disintegrants include sodium starch glycolate, sodium carboxymethyl cellulose, calcium carboxymethyl cellulose, croscarmellose sodium, crospovidone, polyvinylpyrrolidone, methyl cellulose, microcrystalline cellulose, lower alkyl-substituted hydroxypropyl cellulose, starch, pregelatinised starch and sodium alginate. Generally, the disintegrant will comprise from 1 weight % to 25 weight %, preferably from 5 weight % to 20 weight % of the dosage form.

[0174] Binders are generally used to impart cohesive qualities to a tablet formulation. Suitable binders include microcrystalline cellulose, gelatin, sugars, polyethylene glycol, natural and synthetic gums, polyvinylpyrrolidone, pregelatinised starch, hydroxypropyl cellulose and hydroxypropyl methylcellulose. Tablets may also contain diluents, such as lactose (as, for example, the monohydrate, spray-dried monohydrate or anhydrous form), mannitol, xylitol, dextrose, sucrose, sorbitol, microcrystalline cellulose, starch and dibasic calcium phosphate dihydrate.

[0175] Tablets or capsules may also optionally contain surface active agents, such as sodium lauryl sulfate and polysorbate 80, and glidants such as silicon dioxide and talc. When present, surface active agents may comprise from 0.2 weight % to 5 weight % of the tablet, and glidants may comprise from 0.2 weight % to 1 weight % of the tablet.

[0176] Tablets or capsules also generally contain lubricants such as magnesium stearate, calcium stearate, zinc stearate, sodium stearyl fumarate, and mixtures of magnesium stearate with sodium lauryl sulphate. Lubricants generally comprise from 0.25 weight % to 10 weight %, preferably from 0.5 weight % to 3 weight % of the tablet.

[0177] Other possible ingredients include glidants (e.g. Talc or colloidal anhydrous silica at about 0.1 weight % to about 3 weight %), anti-oxidants, colourants, flavouring agents, preservatives and taste-masking agents.

[0178] Exemplary tablets contain up to about 80% of one or more of the compounds described herein, from about 10 weight % to about 90 weight % binder, from about 0 weight % to about 85 weight % diluent, from about 2 weight % to about 10 weight % disintegrant, and from about 0.25 weight % to about 10 weight % lubricant.

[0179] Tablet or capsule blends may be compressed directly or by roller to form tablets. Tablet or capsule blends or portions of blends may alternatively be wet-, dry-, or melt-granulated, melt congealed, or extruded before tableting. The final formulation may contain one or more layers and may be coated or uncoated; it may even be encapsulated.

[0180] Solid formulations for oral administration may be formulated to be immediate and/or modified release. Modified release formulations include delayed, sustained, pulsed, controlled, targeted and programmed release formulations.

[0181] 2. Parenteral Formulations

[0182] The compounds and/or their pharmaceutically acceptable salts may also be administered directly into the blood stream, into muscle, or into an internal organ. Suitable routes for such parenteral administration include intravenous, intraarterial, intraperitoneal, intrathecal, epidural, intracerebroventricular, intraurethral, intrasternal, intracranial, intramuscular, and subcutaneous delivery. Suitable means for parenteral administration include needle (including microneedle) injectors, needle-free injectors, and infusion techniques.

[0183] Parenteral formulations are typically aqueous solutions which may contain excipients such as salts, carbohydrates and buffering agents (preferably at a pH of from 3 to 9), but, for some applications, they may be more suitably formulated as a sterile non-aqueous solution or as a dried form to be used in conjunction with a suitable vehicle such as sterile, pyrogen-free water.

[0184] The preparation of parenteral formulations under sterile conditions, for example, by lyophilisation, may readily be accomplished using standard pharmaceutical techniques well known to those skilled in the art.

[0185] The solubility of the compounds used in the preparation of a parenteral formulation may be increased by the use of appropriate formulation techniques, such as the incorporation of solubility-enhancing agents.

[0186] Formulations for parenteral administration may be formulated to be immediate and/or modified release. Modified release formulations include delayed, sustained, pulsed, controlled, targeted and programmed release formulations. Thus, the compounds may be formulated as a solid, semi-solid, or thixotropic liquid for administration as an implanted depot providing modified release of the active compound. Examples of such formulations include drug-coated stents and poly(dl-lactic-coglycolic)acid (PGLA) microspheres.

[0187] 3. Pulmonary and Mucosal Formulations

[0188] The compounds and/or their pharmaceutically acceptable salts can be formulated for pulmonary or mucosal administration. The administration can include delivery of the composition to the lungs, nasal, oral (sublingual, buccal), vaginal, or rectal mucosa.

[0189] For example, the compounds can also be administered intranasally or by oral inhalation, typically in the form of a dry powder (either alone, as a mixture, for example, in a dry blend with lactose, or as a mixed component particle, for example, mixed with phospholipids, such as phosphatidylcholine) from a dry powder inhaler or as an aerosol spray from a pressurised container, pump, spray, atomiser (preferably an atomiser using electrohydrodynamics to produce a fine mist), or nebuliser, with or without the use of a suitable propellant, such as water, ethanol-water mixture, 1,1,1,2-tetrafluoroethane or 1,1,1,2,3,3,3-heptafluoropropane. For intranasal or oral inhalation use, the powder may comprise a bioadhesive agent, for example, chitosan or cyclodextrin. The term aerosol as used herein refers to any preparation of a fine mist of particles, which can be in solution or a suspension, whether or not it is produced using a propellant. Aerosols can be produced using standard techniques, such as ultrasonication or high-pressure treatment.

[0190] The pressurized container, pump, spray, atomizer, or nebuliser contains a solution or suspension of one or more of the compounds including, for example, ethanol, aqueous ethanol, or a suitable alternative agent for dispersing, solubilising, or extending release of the active, a propellant(s) as solvent and an optional surfactant, such as sorbitan trioleate, oleic acid, or an oligolactic acid.

[0191] Prior to use in a dry powder or suspension formulation, a drug product is micronised to a size suitable for delivery by inhalation (typically less than 5 microns). This may be achieved by any appropriate comminuting method, such as spiral jet milling, fluid bed jet milling, supercritical fluid processing to form nanoparticles, high pressure homogenisation, or spray drying.

[0192] Capsules (made, for example, from gelatin or hydroxypropylmethylcellulose), blisters and cartridges for use in an inhaler or insufflator may be formulated to contain a powder mix of the compounds described herein, a suitable powder base such as lactose or starch and a performance modifier such as 1-leucine, mannitol, or magnesium stearate. The lactose may be anhydrous or in the form of the monohydrate, preferably the latter. Other suitable excipients include dextran, glucose, maltose, sorbitol, xylitol, fructose, sucrose, and trehalose.

[0193] A suitable solution formulation for use in an atomizer using electrohydrodynamics to produce a fine mist may contain from 1 ?g to 20 mg of one or more of the compounds per actuation and the actuation volume may vary from 1 ?l to 100 ?l. A typical formulation may contain one or more of the compounds described herein, propylene glycol, sterile water, ethanol and sodium chloride. Alternative solvents that may be used instead of propylene glycol include glycerol and polyethylene glycol.

[0194] Suitable flavors, such as menthol and levomenthol, or sweeteners, such as saccharin or saccharin sodium, may be added to those formulations intended for inhaled/intranasal administration.

[0195] Formulations for inhaled/intranasal administration may be formulated to be immediate and/or modified release using, for example, PGLA. Modified release formulations include delayed, sustained, pulsed, controlled, targeted, and programmed release formulations.

[0196] In the case of dry powder inhalers and aerosols, the dosage unit is determined by means of a valve which delivers a metered amount. Units in accordance with the compounds are typically arranged to administer a metered dose or puff. The overall daily dose will be administered in a single dose or, more usually, as divided doses throughout the day.

[0197] In some embodiments, the compounds and/or their pharmaceutically acceptable salts can be formulated for pulmonary delivery, such as intranasal administration or oral inhalation. Carriers for pulmonary formulations can be divided into those for dry powder formulations and for administration as solutions. Aerosols for the delivery of therapeutic agents to the respiratory tract are known in the art. For administration via the upper respiratory tract, the formulation can be formulated into an aqueous solution, e.g., water or isotonic saline, buffered or un-buffered, or as an aqueous suspension, for intranasal administration as drops or as a spray. Such aqueous solutions or suspensions may be isotonic relative to nasal secretions and of about the same pH, ranging e.g., from about pH 4.0 to about pH 7.4 or, from pH 6.0 to pH 7.0. Buffers should be physiologically compatible and include, simply by way of example, phosphate buffers. One skilled in the art can readily determine a suitable saline content and pH for an innocuous aqueous solution for nasal and/or upper respiratory administration.

[0198] In some embodiments, the aqueous solution is water, physiologically acceptable aqueous solutions containing salts and/or buffers, such as phosphate buffered saline (PBS), or any other aqueous solution acceptable for administration to an animal or human. Such solutions are well known to a person skilled in the art and include, but are not limited to, distilled water, de-ionized water, pure or ultrapure water, saline, phosphate-buffered saline (PBS). Other suitable aqueous vehicles include, but are not limited to, Ringer's solution and isotonic sodium chloride. Aqueous suspensions may include suspending agents such as cellulose derivatives, sodium alginate, polyvinyl-pyrrolidone and gum tragacanth, and a wetting agent such as lecithin. Suitable preservatives for aqueous suspensions include ethyl and n-propyl p-hydroxybenzoate.

[0199] In some embodiments, solvents that are low toxicity organic (i.e. non-aqueous) class 3 residual solvents, such as ethanol, acetone, ethyl acetate, tetrahydrofuran, ethyl ether, and propanol may be used for the formulations. The solvent is selected based on its ability to readily aerosolize the formulation. The solvent should not detrimentally react with the compounds. An appropriate solvent should be used that dissolves the compounds or forms a suspension of the compounds. The solvent should be sufficiently volatile to enable formation of an aerosol of the solution or suspension. Additional solvents or aerosolizing agents, such as freons, can be added as desired to increase the volatility of the solution or suspension.

[0200] In some embodiments, the pharmaceutical compositions may contain minor amounts of polymers, surfactants, or other excipients well known to those of the art. In this context, minor amounts means no excipients are present that might affect or mediate uptake of the compounds by cells and that the excipients that are present in amount that do not adversely affect uptake of compounds by cells.

[0201] Dry lipid powders can be directly dispersed in ethanol because of their hydrophobic character. For lipids stored in organic solvents such as chloroform, the desired quantity of solution is placed in a vial, and the chloroform is evaporated under a stream of nitrogen to form a dry thin film on the surface of a glass vial. The film swells easily when reconstituted with ethanol. To fully disperse the lipid molecules in the organic solvent, the suspension is sonicated. Non-aqueous suspensions of lipids can also be prepared in absolute ethanol using a reusable PARI LC Jet+ nebulizer (PARI Respiratory Equipment, Monterey, CA).

[0202] 4. Topical Formulations

[0203] The compounds and/or their pharmaceutically acceptable salts may be administered directly to the external surface of the skin or the mucous membranes (including the surface membranes of the nose, lungs and mouth), such that the compounds and/or their pharmaceutically acceptable salts cross the external surface of the skin or mucous membrane and enters the underlying tissues.

[0204] Formulations for topical administration generally contain a dermatologically acceptable carrier that is suitable for application to the skin, has good aesthetic properties, is compatible with the active agents and any other components, and will not cause any untoward safety or toxicity concerns.

[0205] The carrier can be in a wide variety of forms. For example, emulsion carriers, including, but not limited to, oil-in-water, water-in-oil, water-in-oil-in-water, and oil-in-water-in-silicone emulsions, are useful herein. These emulsions can cover a broad range of viscosities, e.g., from about 100 cps to about 200,000 cps. These emulsions can also be delivered in the form of sprays using either mechanical pump containers or pressurized aerosol containers using conventional propellants. These carriers can also be delivered in the form of a mousse or a transdermal patch. Other suitable topical carriers include anhydrous liquid solvents such as oils, alcohols, and silicones (e.g., mineral oil, ethanol isopropanol, dimethicone, and cyclomethicone); aqueous-based single phase liquid solvents (e.g., hydro-alcoholic solvent systems, such as a mixture of ethanol and/or isopropanol and water); and thickened versions of these anhydrous and aqueous-based single phase solvents (e.g. where the viscosity of the solvent has been increased to form a solid or semi-solid by the addition of appropriate gums, resins, waxes, polymers, salts, and the like). Examples of topical carrier systems useful in the present formulations are described in the following references: Sun Products Formulary Cosmetics & Toiletries, vol. 105, pp. 122-139 (December 1990); Sun Products Formulary, Cosmetics & Toiletries, vol. 102, pp. 117-136 (March 1987); U.S. Pat. No. 5,605,894 to Blank et al., and U.S. Pat. No. 5,681,852 to Bissett.

[0206] Formulations for topical administration may be formulated to be immediate and/or modified release. Modified release formulations include delayed, sustained, pulsed, controlled, targeted and programmed release formulations. Thus, the compounds may be formulated as a solid, semi-solid, or thixotropic liquid for administration as an implanted depot providing modified release of the active compound. Examples of such formulations include drug-coated stents and poly(dl-lactic-coglycolic)acid (PGLA) microspheres.

III. Methods of Use

[0207] A. Preventing, Treating, or Ameliorating Symptom(s) Associated with a Viral Infection

[0208] Methods of using the compounds for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in a subject are disclosed.

[0209] Generally, the method includes (i) administering to the subject an effective amount of the compound(s) to prevent, treat, or ameliorate one or more symptoms associated with the viral infection in the subject. The subject can be a mammal. The compound(s) can be administered by a medical professional or the subject being treated (e.g. self-administration).

[0210] In some embodiments, the compounds and/or their pharmaceutically acceptable salts can be administered in the form of a pharmaceutical composition or formulation in association with one or more pharmaceutically acceptable excipients, such as the pharmaceutical composition or formulation described above. The choice of the pharmaceutically acceptable excipients will to a large extent depend on factors such as the particular mode of administration, the effect of the excipient on solubility and stability, and the nature of the dosage form.

[0211] Generally, the administered compounds can mimic DNA and/or RNA bases through base pairing with RNA and/or DNA nucleosides, thereby get incorporated into the viral RNA and/or DNA strand, resulting in viral mutagenesis (Strombaugh et al., Nucleic Acids Research, 37(7):2294-2312 (2009); Jin et al., POLS one, 8(7):e68347 (2013)). In particular, compounds that are structurally comparable to DNA and/or RNA nucleosides (also referred to herein as nucleoside analogue prodrugs) can act as competitive enzymatic inhibitors when incorporated into newly synthesized viral RNA and/or viral DNA. The nucleoside analogue prodrugs disclosed herein may be a nucleoside or a nucleotide. The nucleoside analogue prodrugs can accelerate the absorption of these prodrugs into cells and the formation of the active metabolite drug, 5 ribose triphosphate (RTP), which base-pairs with DNA and/or RNA bases and gets incorporated into the viral DNA and/or viral RNA strand, resulting in viral mutagenesis (U.S. Pat. No. 7,018,989 to McGuigan et al.). For example, the exemplary compound T-101 can accelerate the absorption of T-101 into cells and the conversion of T-101 to T-101-5-Ribosyl Triphosphate, which is the active metabolite.

[0212] 1. Administration Routes

[0213] The compound(s) and/or their pharmaceutically acceptable salts or pharmaceutical composition or formulation containing the compound(s) and/or their pharmaceutically acceptable salts can be administered to the subject by oral administration, parenteral administration, inhalation, mucosal, topical administration, or a combination thereof.

[0214] For example, the compound(s) and/or their pharmaceutically acceptable salts or the pharmaceutical composition or formulation containing the compound(s) and/or their pharmaceutical acceptable slats can be orally administered to a subject by a medical professional or the subject being treated (e.g. self-administration). The compound(s) or the pharmaceutical composition or formulation containing the compound(s) and/or their pharmaceutical acceptable slats can be administered as tablets, capsules containing particulates, granules, powders, lozenges (including liquid-filled lozenges), chews, multi- and nano-particulates, gels, or liquids (e.g. solution or suspensions in aqueous or non-aqueous solvent).

[0215] Optionally, the compound(s) and/or their pharmaceutically acceptable salts or the pharmaceutical composition or formulation containing the compound(s) and/or their pharmaceutical acceptable slats can be administered to the subject by intravenous injection or intraperitoneal injection. The intravenous injection or intraperitoneal injection can be performed by a medical professional or the subject being treated (e.g. self-injection).

[0216] Alternatively, the compound(s) and/or their pharmaceutically acceptable salts or the pharmaceutical composition or formulation containing the compound(s) and/or their pharmaceutical acceptable slats can be administered to the subject by inhalation, such as mouth inhalation and/or nasal inhalation.

[0217] Optionally, the compound(s) and/or their pharmaceutically acceptable salts or the pharmaceutical composition or formulation containing the compound(s) and/or their pharmaceutical acceptable slats can be administered to the subject by topically applying the compound(s) or the pharmaceutical composition or formulation on one or more of the exposed surfaces of the subject.

[0218] 2. Optional Steps

a. Administering Additional Active Agent(s)

[0219] One or more active agents in addition to the compounds may be administered to the subject throughout the method or at different intervals during the method. For example, the one or more additional active agents is administered to the subject prior to, during, and/or subsequent to step (i). In some embodiments, the one or more additional active agents is included in a pharmaceutical composition or formulation containing the compound(s) and is administered to the subject simultaneously with the compound(s) in the pharmaceutical composition or formulation in association with one or more pharmaceutically acceptable excipients.

[0220] In some embodiments, the one or more additional active agents are one or more antiviral agents and/or one or more anti-inflammatory agents. Antiviral agents and anti-inflammatory agents are known in the art. The amount of the one or more antiviral agents and/or one or more anti-inflammatory agents required will vary from subject to subject according to their need.

[0221] 3. Viruses Causing Viral Infections

[0222] The compounds will have broad antiviral properties and will be suitable for use in the prophylaxis and/or treatment of all classes of viruses.

[0223] For example, the compounds can be administered to a subject for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in the subject caused by different classes of viruses. The viral infection in the subject to be treated may be caused by double stranded DNA viruses, single stranded DNA viruses, double stranded RNA viruses, single stranded positive sense RNA viruses, single stranded negative sense RNA viruses, positive sense single stranded RNA viruses that replicate through a DNA intermediate, double stranded DNA viruses that replicate through a single stranded RNA intermediate, single stranded RNA viruses with reverse transcriptase, or double stranded DNA viruses with reverse transcriptase, or a combination thereof. Exemplary viruses that can cause the viral infection in a subject include, but are not limited to, adenoviruses, herpesviruses, poxviruses, parvoviruses, SARS, Coronaviruses, Picornaviruses, Togaviruses, Influenza A viruses, Influenza B viruses, Influenza C viruses, Influenza D viruses, Retroviruses, Hepatitis B viruses, Hepatitis C viruses, or a combination thereof.

[0224] The amount of the compound(s) required will vary from subject to subject according to their need. Typically, the amount of the compound(s) is effective to prevent, treat, or ameliorate at least one of the one or more symptoms associated with the viral infection caused by any one of or a combination of the viruses described above.

[0225] Table 2 below summarizes the different viruses where the compounds can be used as prophylactic or treatment of viral infections.

TABLE-US-00002 TABLE 2 Viruses where the compounds can be used as prophylactic or treatment of viral infections Class Type of Virus Examples of Viruses I dsDNA viruses Adenoviruses, Herpesviruses, Poxviruses II ssDNA viruses parvoviruses III dsRNA viruses adenovirus IV (+) ssRNA viruses [+strand or SARS (e.g., SARS-CoV-2), sense] Coronaviruses, Picornaviruses, Togaviruses V (?) ssRNA viruses [?strand or Influenza A (e.g., H1N1, antisense] H3N2), B, C and D viruses VI ssRNA-RT viruses (+) sense Retroviruses (e.g., HIV) RNA with DNA intermediate in lifecycle VII dsDNA-RT viruses Hepatitis B and C viruses

a. Adenoviruses

[0226] In some embodiments, the subject being treated may have one or more symptoms associated with adenoviruses infection.

[0227] Adenoviruses are medium-sized (90-100 nm), non-enveloped icosahedral viruses with double-stranded DNA (dsDNA). More than 50 types of immunologically distinct adenoviruses can cause infections in humans. Most commonly adenoviruses cause respiratory illness, ranging from common cold to pneumonia, croup, and bronchitis. Depending on the type, adenoviruses can also cause other illnesses such as gastroenteritis, conjunctivitis, cystitis, and, less commonly, neurological disease. Immunosuppressed subjects are more susceptible and likely to develop more severe illness.

b. Herpes Simplex Virus

[0228] In some embodiments, the subject being treated may have one or more symptoms associated with Herpes Simplex Virus (HSV) infection.

[0229] HSV is an infection that causes herpes. HSV is a common viral infection and affects all ages. Herpes can appear in various parts of the body, most commonly on the genitals or mouth. Two types of the herpes simplex virus exist, namely HSV-1, that primarily causes oral herpes, and is generally responsible for cold sores, fever blisters around the mouth and face and HSV-2 responsible for genital herpes outbreaks is primarily sexually transmitted.

c. Poxviruses

[0230] In some embodiments, the subject being treated may have one or more symptoms associated with poxviruses infection.

[0231] Poxviruses are large double-stranded DNA (dsDNA) genomes. Variola virus (smallpox virus) emerged and began causing illness and deaths in human populations several thousand years ago, with smallpox outbreaks occurring occasionally.

d. Parvovirus B19

[0232] In some embodiments, the subject being treated may have one or more symptoms associated with Parvovirus B19 infection.

[0233] Parvovirus B19 infects only humans. The infected human can have a range of symptoms depending on your age and overall health. Parvovirus B19 infection spreads through respiratory secretions, such as saliva, sputum, or nasal mucus, when an infected person coughs or sneezes, and can also spread through blood or blood products. Parvovirus B19 crosses the placenta and an infected pregnant woman can pass the virus to her baby.

e. Severe Acute Respiratory Syndrome

[0234] In some embodiments, the subject being treated may have one or more symptoms associated with Severe acute respiratory syndrome (SARS).

[0235] SARS is a viral respiratory illness caused by a Coronavirus called SARS-associated coronavirus (SARS-CoV). Coronaviruses are (+) ssRNA associated with a nucleoprotein within a capsid comprised of matrix protein. The envelope bears club-shaped glycoprotein projections. Thought to originate from bats, these viruses are spread to humans through other animals. SARS-COV2 or COVID-19 is a recent pandemic infection that is now global and resulting in increased morbidity and mortality. The COVID-19 virus is known to affect the respiratory tract severely. The SARS -CoV-2the virus behind the COVID-19 pandemicenters the lungs, typically triggers an immune response, attracting immune cells to the region to attack the virus, resulting in localized inflammation. In some patients, excessive or uncontrolled levels of cytokines are released which then activate more immune cells, resulting in hyperinflammation-Cytokine storm, that can seriously harm or even kill the patient. Cytokine storms are a common complication not only of COVID-19 and flu but also other respiratory diseases caused by coronaviruses such as SARS and MERS. They are also associated with non-infectious diseases such as multiple sclerosis and pancreatitis. Favipiravir and Remdesivir two experimental viral polymerase inhibitors anecdotally are known to be effective in treating early-late stage coronavirus infections.

f. Influenza Virus

[0236] In some embodiments, the subject being treated may have one or more symptoms associated with influenza virus infection.

[0237] Influenza virus includes seven genera and they are Influenza A, B, and C. Influenza A includes subtypes of H.sub.1N1 (Spanish flu, swine flu), H.sub.1N2, H.sub.2N2 (Asian flu), H.sub.3N1, H.sub.3N2 (Hong Kong flu), H.sub.3N8, H.sub.5N1 (Avian or bird flu), H.sub.5N2, H.sub.5N3, H.sub.5N8, H.sub.5N9, H.sub.7N1, H.sub.7N2, H.sub.7N3, H.sub.7N4, H.sub.7N7 (zoonotic potential), H.sub.7N9, H.sub.9N2, H.sub.10N7. While humans are the common hosts of all three influenza viruses, animal avian hosts also are known to cause influenza infections (e.g., Avian flu caused by H.sub.5N1). Influenza A viruses are classified based on the viral surface proteins hemagglutinin (HA or H) and neuraminidase (NA or N). More than sixteen H subtypes (or serotypes) and nine N subtypes of influenza A virus have been identified thus far. Every year new mutations of the influenza viruses are identified, and vaccines are prepared. However, the viral mutations quickly develop resistance and hence treatment becomes a more preferred line of therapy. Influenza A has a high level of morbidity and mortality. The compounds can be used to prevent and/or treat influenza infections in mammals.

g. Retroviruses

[0238] In some embodiments, the subject being treated may have one or more symptoms associated with retroviruses infection.

[0239] Retroviruses are spherical viruses that contain RNA as their genetic material. Examples of retroviruses include human T cell leukemia virus, which causes cancer in humans, and the several types of human immunodeficiency virus (HIV), which is widely acknowledged to be the cause of acquired immunodeficiency syndrome (AIDS). Retroviruses are enveloped viruses with an RNA genome. The name is derived from the fact that the virus particle contains an RNA dependent DNA Polymerase (Reverse transcriptase). This enzyme converts the RNA genome into DNA, which then integrates into the host chromosomal DNA. The reverse transcriptase is highly error prone and rapid genetic variation is a feature of this group of viruses. Six human retroviruses have so far been identified. All of these infect T cells, HTLV 1T-cell leukaemias/lymphomas, Tropical spastic paraparesis, HTLV 2 (unknown pathology), HIV 1 and 2 (AIDS). Two new human retroviruses were identified recently in Central Africa. They are related to HTLV1 and 2 and have been called HTLV 3 and 4.

h. Hepatitis C

[0240] In some embodiments, the subject being treated may have one or more symptoms associated with Hepatitis C virus (HCV) infection.

[0241] HCV leads to serious and chronic liver conditions and/or diseases, such as cirrhosis and hepatocellular carcinoma, in a significant number of infected personnel. About 20% of chronically infected individuals eventually develop liver-destroying cirrhosis or cancer. The viral disease is transmitted parenterally by contaminated blood and blood products, contaminated needles, or sexually and vertically from infected mothers or carrier mothers to their offspring.

[0242] The HCV virion is an enveloped (+) RNA virus with a single oligoribonucleotide genomic sequence of about 9600 bases and which encodes a polyprotein of about 3,010 amino acids. The protein products of the HCV gene consist of the structural proteins C, E1, and E2, and the non-structural (NS) proteins NS2, NS3, NS4A and NS4B, and NS5A and NS5B. The NS proteins are believed to provide the catalytic process for viral replication. The NS3 protease releases NS5B, the RNA-dependent RNA polymerase from the polyprotein chain. HCV NS5B polymerase is required for the synthesis of a double-stranded RNA from a single-stranded viral RNA that serves as a template in the replication cycle of HCV. Therefore, NS5B polymerase is considered to be an essential component in the HCV replication complex (K. Ishi, et al. Hepatology, 29:1227-1235 (1999); V. Lohmann, et al, Virology, 249: 108-118 (1998)). Inhibition of HCV NS5B polymerase prevents formation of the double-stranded HCV RNA and therefore constitutes an attractive approach to the development of HCV-specific antiviral therapies.

[0243] The disclosed compounds and methods can be further understood through the following enumerated paragraphs.

1. A compound having the structure of

##STR00110## [0244] (a) wherein A and A are independently an unsubstituted heterocyclic group or a substituted heterocyclic group; and [0245] (b) wherein X is a carbon or a nitrogen.
2. The compound of paragraph 1, wherein the compound has the structure of

##STR00111## [0246] (a) wherein A are independently an unsubstituted heterocyclic group or a substituted heterocyclic group; [0247] (b) wherein X is a carbon or a nitrogen; [0248] (c) wherein E.sub.1, E.sub.1, P.sub.1, P.sub.1, G.sub.1, G.sub.1, and W.sub.1 are independently CR.sub.20 or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0249] (d) wherein Q.sub.1 and Q.sub.1 are carbon; and [0250] (e) wherein the substituents are independently a phosphoramidate, a heterocyclic group, a halogen, a sulfonic acid, an azide group, a cyanate group, an isocyanate group, a nitrate group, a nitrile group, an isonitrile group, a nitrosooxy group, a nitroso group, a nitro group, an aldehyde group, an alkoxy group, an acyl halide group, a carboxylic acid group, a carboxylate group, an alkyl group, a heteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, a heteroaryl group, polyaryl group, a heteropoly aryl group, a alkyl aryl group, an amino group, an ester group, a hydroxyl group, a thiol group, a sulfonyl group, an ester group, an aliphatic ester group, an amide group, an aliphatic amide group, an azo group, an acyl group, a carbonyl group, a carbonate ester group, an ether group, an aminooxy group, or a hydroxyamino group.
3. The compound of paragraph 1 or 2, wherein the compound has the structure of

##STR00112## [0251] (a) wherein A are independently an unsubstituted heterocyclic group or a substituted heterocyclic group; [0252] (b) wherein X is a carbon or a nitrogen; [0253] (c) wherein L, M, L, and M are independently a carbon or a nitrogen; [0254] (d) wherein P.sub.1, P.sub.1, and G.sub.1 are independently CR.sub.20 or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0255] (e) wherein R.sub.2 and R.sub.2 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; [0256] (f) wherein R.sub.3 and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0257] (g) wherein the substituents are as defined in the base paragraph(s).
4. The compound of any one of paragraphs 1-3, wherein the compound has the structure of

##STR00113## [0258] (a) wherein A are independently an unsubstituted heterocyclic group or a substituted heterocyclic group; [0259] (b) wherein X is a carbon or a nitrogen; [0260] (c) wherein L, M, L, M, L, L, and L.sub.1-L.sub.3 are independently a carbon or a nitrogen; [0261] (d) wherein X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0262] (e) wherein R.sub.1, R.sub.1, R.sub.23, and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; [0263] (f) wherein R.sub.2, R.sub.2, R.sub.22, R.sub.22, R.sub.22, R.sub.22, and R.sub.25 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; [0264] (g) wherein R.sub.3 and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0265] (h) wherein R.sub.8, R.sub.8, R.sub.24, and R.sub.27 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0266] (i) wherein the substituents are as defined in the base paragraph(s).
5. The compound of any one of paragraphs 1-4, wherein A is

##STR00114## [0267] (a) wherein X is a carbon or a nitrogen; [0268] (b) wherein E.sub.2, E.sub.2, G.sub.2, G.sub.2, Q.sub.2, Q.sub.2, and W.sub.2 are independently an oxygen, a sulfur, CR.sub.20, or NR.sub.21, and R.sub.20 and R.sub.21 are independently absent, a hydrogen, a halogen, a nitrile group, a nitro group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0269] (c) wherein Q.sub.1 and Q.sub.1 are carbon; and [0270] (d) wherein the substituents are as defined in the base paragraphs.
6. The compound of any one of paragraphs 1-5, wherein A is

##STR00115## [0271] (a) wherein X is a carbon or a nitrogen; [0272] (b) wherein Y and Y are nitrogen; [0273] (c) wherein Z is a carbon, an oxygen, a nitrogen, or a sulfur; [0274] (d) wherein J and J are independently an oxygen, OR.sub.3, a sulfur, a thiol group, an unsubstituted amino group, or a substituted amino group, [0275] (e) wherein R.sub.3, R.sub.3, and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0276] (f) wherein R.sub.4, R.sub.5, R.sub.4, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0277] (g) wherein the substituents are as defined in the base paragraph(s).
7. The compound of any one of paragraphs 1-6, wherein the compound has the structure of

##STR00116## [0278] (a) wherein X is a carbon or a nitrogen; [0279] (b) wherein L, M, L, and L.sub.1-L.sub.3 are carbon or nitrogen; [0280] (c) wherein X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0281] (d) wherein Y is a nitrogen; [0282] (e) wherein Z is a an oxygen, a nitrogen, or a carbon; [0283] (f) wherein J is an oxygen or OR.sub.3; [0284] (g) wherein R.sub.1 and R.sub.23 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; [0285] (h) wherein R.sub.2, R.sub.22, R.sub.22, R.sub.22, and R.sub.22 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; [0286] (i) wherein R.sub.3, R.sub.3, and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0287] (j) wherein R.sub.8 and R.sub.24 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0288] (k) wherein R.sub.4, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0289] (J) wherein the substituents are as defined in the base paragraph(s).
8. The compound of paragraph 7, wherein R.sub.1 or R.sub.2 of Formula VI, R.sub.22 or R.sub.23 of Formula VI, R.sub.23 or R.sub.1 of Formula VI, and R.sub.23, R.sub.22, or R.sub.22 of Formula VI is a substituted an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group, preferably an unsubstituted or substituted aliphatic ether, such as an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, or an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether.
9. The compound of paragraph 7 or 8, wherein R.sub.4 and R.sub.5 are independently absent, hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, or a substituted aliphatic-amino group.
10. The compound of any one of paragraphs 7-9, wherein when J is OR.sub.3, R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group.
11. The compound of any one of paragraphs 7-10, wherein L, M, L, and L.sub.1-L.sub.3 are nitrogen; X is carbon; Z is a nitrogen or a carbon; and R.sub.6 and R.sub.7 are independently absent or hydrogen.
12. The compound of paragraph 7, wherein the compound has the structure of

##STR00117##

13. The compound of paragraph 11, wherein the compound has the structure of

##STR00118##

14. The compound of any one of paragraphs 1-6, wherein the compound has the structure of

##STR00119## [0290] (a) wherein X is a carbon or a nitrogen; [0291] (b) wherein L, M, and L are independently a carbon or a nitrogen; [0292] (c) wherein Y is a nitrogen; [0293] (d) wherein Z is a an oxygen, a nitrogen, or a carbon; [0294] (e) wherein J is an oxygen or OR.sub.3; [0295] (f) wherein R.sub.1 and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; [0296] (g) wherein R.sub.2 and R.sub.25 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; [0297] (h) wherein R.sub.3, R.sub.3, and R.sub.3 is absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0298] (i) wherein R.sub.8 and R.sub.27 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0299] (j) wherein R.sub.4, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0300] (k) wherein the substituents are as defined in the base paragraph(s).
15. The compound of paragraph 14, wherein R.sub.1 or R.sub.2 of Formula XI and R.sub.25 or R.sub.26 of Formula XI is a substituted an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group, preferably an unsubstituted or substituted aliphatic ether, such as an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, or an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether.
16. The compound of paragraph 14 or 15, wherein R.sub.4 and R.sub.5 are independently absent, hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, or a substituted aliphatic-amino group.
17. The compound of any one of paragraphs 13-16, wherein when J is OR.sub.3, R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group.
18. The compound of paragraph 14, wherein the compound has the structure of

##STR00120##

19. The compound of paragraph 18, wherein the compound has the structure of

##STR00121##

20. The compound of any one of paragraphs 1-6, wherein the compound has the structure of:

##STR00122## [0301] (a) wherein X is a carbon or a nitrogen; [0302] (b) wherein L, M, and L are independently a carbon or a nitrogen; [0303] (c) wherein Y is a nitrogen; [0304] (d) wherein J is an oxygen or OR.sub.3; [0305] (e) wherein R.sub.1 and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; [0306] (f) wherein R.sub.2 and R.sub.25 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group; [0307] (g) wherein R.sub.3, R.sub.3, and R.sub.3 is absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted amide group, a substituted amide group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0308] (h) wherein R.sub.8 and R.sub.27 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0309] (i) wherein R.sub.4 and R.sub.5 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0310] (j) wherein the substituents are as defined in the base paragraph(s).
21. The compound of paragraph 20, wherein R.sub.1 or R.sub.2 of Formula XVI and R.sub.25 or R.sub.26 of Formula XVI is a substituted an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, or a substituted aliphatic ether group, preferably an unsubstituted or substituted aliphatic ether, such as an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, or an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether.
22. The compound of paragraph 20 or 21, wherein R.sub.4 and R.sub.5 are independently absent, hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, or a substituted aliphatic-amino group.
23. The compound of any one of paragraphs 20-22, wherein when J is OR.sub.3, R.sub.3 is a hydrogen, a substituted or unsubstituted aliphatic group, or a substituted or unsubstituted amino group.
24. The compound of paragraph 20, wherein the compound has the structure of

##STR00123##

25. The compound of paragraph 24, wherein the compound has the structure of

##STR00124##

[0311] 26. The compound of any one of paragraphs 7-25, wherein R.sub.1, R.sub.2, R.sub.8, R.sub.22, R.sub.23, R.sub.24, R.sub.22, R.sub.22, R.sub.22, R.sub.1, R.sub.2, R.sub.8, R.sub.25, R.sub.26, and/or R.sub.27 (such as R.sub.1, R.sub.2, and/or R.sub.8 of Formula VI; R.sub.22, R.sub.23, and/or R.sub.24 of Formula VI; R.sub.1, R.sub.8, R.sub.22, R.sub.23, and/or R.sub.24 of Formula VI; R.sub.22, R.sub.22, R.sub.23, and/or R.sub.24 of Formula VI; R.sub.1, R.sub.2, and/or R.sub.8 of Formula XI; R.sub.25, R.sub.26, and/or R.sub.27 of Formula XI; R.sub.1, R.sub.2, and/or R.sub.8 of Formula XVI; and/or R.sub.25, R.sub.26, and/or R.sub.27 of Formula XVI) are(is) an unsubstituted aliphatic ether or a substituted aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether.

27. The compound of paragraph 26, wherein R.sub.1, R.sub.2, R.sub.8, R.sub.22, R.sub.23, R.sub.24, R.sub.22, R.sub.22, R.sub.22, R.sub.1, R.sub.2, R.sub.8, R.sub.25, R.sub.26, and/or R.sub.27 are(is) a substituted C.sub.1-C.sub.6 aliphatic ether having the structure of

##STR00125## [0312] (a) wherein A.sub.1 and A.sub.2 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, a cyanide group, a nitrile group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0313] (b) wherein A.sub.7 is a methylene group or an ethylene group; [0314] (c) wherein R.sub.9 and R.sub.10 are independently a hydrogen, a hydroxyl group, an unsubstituted alkyl group, or a substituted alkyl group, optionally wherein R.sub.9 and R.sub.10 are independently a substituted alkyl group that together form a ring; and [0315] (d) wherein B.sub.2 is hydrogen or a phosphoramidate, wherein the substituents are as defined in the base paragraph(s).
28. The compound of paragraph 27, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00126##

29. The compound of paragraph 27, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00127## [0316] wherein A.sub.3, A.sub.4, A.sub.5, and A.sub.6 are independently absent, a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group
30. The compound of paragraph 29, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00128## [0317] (a) wherein A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and [0318] (b) wherein A.sub.2 is a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group.
31. The compound of paragraph 29, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00129## [0319] (a) wherein A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and [0320] (b) wherein A.sub.2 is a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0321] (c) optionally wherein A.sub.2, A.sub.4, and A.sub.6 are hydrogen, or A.sub.1 is cyanide, or A.sub.3 and/or A.sub.6 are hydroxyl, or a combination thereof; and [0322] (d) optionally wherein Formula 27 is

##STR00130##

32. The compound of any one of paragraphs 27-31, wherein B.sub.2 is a phosphoramidate having the structure of

##STR00131## [0323] (a) wherein B.sub.1 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, or a substituted aryl group; [0324] (b) wherein Q is an oxygen or a sulfur; [0325] (c) wherein T is an oxygen, a sulfur, NR.sub.11, CR.sub.11R.sub.12, CR.sub.11W.sub.1, or CW.sub.1W.sub.2, wherein R.sub.11 and R.sub.12 are independently a hydrogen, an unsubstituted alkyl group, a substituted alkyl group, an unsubstituted aryl group, a substituted aryl group, and wherein W.sub.1 and W.sub.2 are independently a heteroatom; [0326] (d) wherein Y is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; and [0327] (e) wherein A is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an alkoxyl, CM.sub.1alkyl, CM.sub.1aryl, or CM.sub.1heterocyclic, wherein M.sub.1 is an oxygen or a methylene group, optionally wherein A is O-alkyl, wherein the alkyl can be a substituted or unsubstituted alkyl, such as an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.6 alkyl, an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.4 alkyl, or an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.3 alkyl.
33. The compound of any one of paragraphs 1-6, wherein the compound has the structure of

##STR00132## ##STR00133##

a tautomer thereof, [0328] (a) wherein X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0329] (b) wherein R.sub.1, R.sub.1, R.sub.2, R.sub.2, R.sub.22, R.sub.23, R.sub.25, and R.sub.26 are independently a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, an unsubstituted aliphatic amide group, a substituted aliphatic amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an ether group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; [0330] (c) wherein R.sub.3, R.sub.3, R.sub.3, and R.sub.3 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0331] (d) wherein R.sub.8 and R.sub.8 are independently absent, a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic amino group, a substituted aliphatic amino group, an amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0332] (e) wherein R.sub.4, R.sub.4, R.sub.5, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, a halogen, a nitrile group, an oxo group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0333] (f) wherein the substituents are as defined in the base paragraph(s). 34. The compound of paragraph 33, wherein R.sub.1 of Formulae 1-6; R.sub.1 of Formulae 7-24; R.sub.2 of Formulae 86 and 88; R.sub.22 of Formula 85; R.sub.23 of Formulae 84, 87, and 96-102; R.sub.25 of Formulae 92 and 95; and/or R.sub.26 of Formulae 89-91, 93, and 94 are(is) an unsubstituted aliphatic ether or a substituted aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.14 aliphatic ether or a substituted C.sub.1-C.sub.14 aliphatic ether, optionally an unsubstituted C.sub.1-C.sub.6 aliphatic ether or a substituted C.sub.1-C.sub.6 aliphatic ether.
35. The compound of paragraph 34, wherein R.sub.1 of Formulae 1-6; R.sub.1 of Formulae 7-24; R.sub.2 of Formulae 86 and 88; R.sub.22 of Formula 85; R.sub.23 of Formulae 84, 87, and 96-102; R.sub.25 of Formulae 92 and 95; and/or R.sub.26 of Formulae 89-91, 93, and 94 are(is) a substituted C.sub.1-C.sub.6 aliphatic ether having the structure of

##STR00134## [0334] (a) wherein A.sub.1 and A.sub.2 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, a cyanide group, a nitrile group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0335] (b) wherein A.sub.7 is a methylene group or an ethylene group; [0336] (c) wherein R.sub.9 and R.sub.10 are independently a hydrogen, a hydroxyl group, an unsubstituted alkyl group, or a substituted alkyl group, optionally wherein R.sub.9 and R.sub.10 are independently a substituted alkyl group that together form a ring; and [0337] (d) wherein B.sub.2 is hydrogen or a phosphoramidate, [0338] wherein the substituents are as defined in the base paragraph(s).
36. The compound of paragraph 35, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00135##

37. The compound of paragraph 35, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00136## [0339] wherein A.sub.3, A.sub.4, A.sub.5, and A.sub.6 are independently absent, a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group
38. The compound of paragraph 37, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00137## [0340] (a) wherein A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and [0341] (b) wherein A.sub.2 is a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group.
39. The compound of paragraph 37, wherein the substituted C.sub.1-C.sub.6 aliphatic ether has the structure of

##STR00138## [0342] (a) wherein A.sub.1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; and [0343] (b) wherein A.sub.2 is a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0344] (c) optionally wherein A.sub.2, A.sub.4, and A.sub.6 are hydrogen, or A.sub.1 is cyanide, or A.sub.3 and/or A.sub.6 are hydroxyl, or a combination thereof; and

##STR00139## [0345] (d) optionally wherein Formula 27 is OH
40. The compound of any one of paragraphs 35-39, wherein B.sub.2 is a phosphoramidate having the structure of

##STR00140## [0346] (a) wherein B.sub.1 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, or a substituted aryl group; [0347] (b) wherein Q is an oxygen or a sulfur; [0348] (c) wherein T is an oxygen, a sulfur, NR.sub.11, CR.sub.11R.sub.12, CR.sub.11W.sub.1, or CW.sub.1W.sub.2, wherein R.sub.11 and R.sub.12 are independently a hydrogen, an unsubstituted alkyl group, a substituted alkyl group, an unsubstituted aryl group, a substituted aryl group, and wherein W.sub.1 and W.sub.2 are independently a heteroatom; [0349] (d) wherein Y is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; and [0350] (e) wherein A is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an alkoxyl, CM.sub.1alkyl, CM.sub.1aryl, or CM.sub.1heterocyclic, wherein M.sub.1 is an oxygen or a methylene group, optionally wherein A is O-alkyl, where the alkyl can be a substituted or unsubstituted alkyl, such as an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.6 alkyl, an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.4 alkyl, or an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.3 alkyl.
41. The compound of any one of paragraphs 34-40, wherein X is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted heterocyclic group, or a substituted heterocyclic group; [0351] wherein R.sub.3, R.sub.3, R.sub.3, R.sub.3, R.sub.8, and R.sub.8 are independently absent, a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, or a substituted heterocyclic group; and/or [0352] wherein R.sub.4, R.sub.4, R.sub.5, R.sub.5, R.sub.6, and R.sub.7 are independently absent, a hydrogen, an oxo group, an unsubstituted amino group, a substituted amino group, an unsubstituted aliphatic-amino group, a substituted aliphatic-amino group, an amide group, an unsubstituted aliphatic-amide group, a substituted aliphatic-amide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group.
42. A pharmaceutical composition or dosage unit comprising [0353] the compound of any one of paragraphs 1-41; and [0354] a pharmaceutically acceptable excipient, [0355] wherein the compound is in an effective amount to prevent, treat, or ameliorate one or more symptoms associated with a viral infection in a subject.
43. The pharmaceutical composition or dosage unit of paragraph 42 further comprising a second active agent, optionally more than one second active agent.
44. The pharmaceutical composition or dosage unit of paragraph 43, wherein the second active agent is an antiviral agent or an anti-inflammatory agent.
45. A method for preventing, treating, or ameliorating one or more symptoms associated with a viral infection in a subject comprising [0356] (i) administering to the subject an effective amount of the compound of paragraphs 1-41 to prevent, treat, or ameliorate one or more symptoms associated with the viral infection in the subject.
46. The method of paragraph 45, wherein the subject is a mammal.
47. The method of paragraph 45 or paragraph 46, wherein the compound is administered by oral administration, parenteral administration, inhalation, mucosal administration, topical or a combination thereof.
48. The method of any one of paragraphs 45-47 further comprising administering to the subject a second active agent, optionally more than one active agent, prior to, during, and/or subsequent to step (i).
49. The method of paragraph 48, wherein the second active agent is an antiviral agent or an anti-inflammatory agent.
50. The method of any one of paragraphs 45-49, wherein the viral infection is caused by double stranded DNA viruses, single stranded DNA viruses, double stranded RNA viruses, single stranded positive sense RNA viruses, single stranded negative sense RNA viruses, positive sense single stranded RNA viruses that replicate through a DNA intermediate, double stranded DNA viruses that replicate through a single stranded RNA intermediate, single stranded RNA viruses with reverse transcriptase, or double stranded DNA viruses with reverse transcriptase, or a combination thereof.
51. The method of any one of paragraphs 45-50, wherein one or more functional groups of the compound form one or more hydrogen bonds with a first nucleoside in a RNA or a DNA of the subject, optionally at least two hydrogen bonds with the first nucleoside in the RNA or the DNA of the subject, and wherein the compound is recognized as a second nucleoside or nucleotide in the RNA or the DNA of the subject.

[0357] The present invention will be further understood by reference to the following non-limiting examples.

EXAMPLES

Example 1. Formula 29

[0358] ##STR00141##

[0359] X is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0360] R.sub.3 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0361] R.sub.4 and R.sub.5 are independently a hydrogen, an oxygen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; [0362] A1 is an unsubstituted alkyl group, a substituted alkyl group, a cyanide group, a nitrile group, a hydroxyl group, or a halogen; [0363] A.sub.2, A.sub.3, and A.sub.4 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; [0364] A.sub.7 is a methylene group or an ethylene group; [0365] B.sub.1 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, or a substituted aryl group; [0366] Q is an oxygen or a sulfur; [0367] T is an oxygen, a sulfur, NR.sub.11, CR.sub.11R.sub.12, CR.sub.11W.sub.1, or CW.sub.1W.sub.2, wherein R.sub.11 and R.sub.12 are independently a hydrogen, an unsubstituted alkyl group, a substituted alkyl group, an unsubstituted aryl group, a substituted aryl group, and wherein W.sub.1 and W.sub.2 are independently a heteroatom; [0368] Y is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group; and [0369] A is an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an alkoxyl, CM.sub.1alkyl, CM.sub.1aryl, or CM.sub.1heterocyclic, wherein M.sub.1 is an oxygen or a methylene group, optionally wherein A is O-alkyl, where the alkyl can be a substituted or unsubstituted alkyl, such as an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.6 alkyl, an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.4 alkyl, or an unsubstituted liner, branched, or cyclic C.sub.1-C.sub.3 alkyl; [0370] the substituents are independently a phosphoramidate, a heterocyclic group, a halogen, a sulfonic acid, an azide group, a cyanate group, an isocyanate group, a nitrate group, a nitrile group, an isonitrile group, a nitrosooxy group, a nitroso group, a nitro group, an aldehyde group, an alkoxy group, an acyl halide group, a carboxylic acid group, a carboxylate group, an alkyl group, a heteroalkyl group, an alkenyl group, a heteroalkenyl group, an alkynyl group, a heteroalkynyl group, an aryl group, a heteroaryl group, polyaryl group, a heteropoly aryl group, a alkyl aryl group, an amino group, an ester group, a hydroxyl group, a thiol group, a sulfonyl group, an ester group, an aliphatic ester group, an amide group, an aliphatic amide group, an azo group, an acyl group, a carbonyl group, a carbonate ester group, an ether group, an aminooxy group, or a hydroxyamino group.

Example 2. Formula 30

[0371] ##STR00142##

[0372] X, R.sub.3, R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; and [0373] A.sub.5 and A.sub.6 are independently a hydrogen, a halogen, a hydroxyl group, a thiol group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted aryl group, or a substituted aryl group, [0374] where the substituents are as described in Example 1.

Example 3. Formula 31

[0375] ##STR00143## [0376] X, R.sub.3, R.sub.4, R.sub.5, A.sub.1, A.sub.2, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1.

Example 4. Formula 32

[0377] ##STR00144##

[0378] X, R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; and [0379] R.sub.3 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, [0380] where the substituents are as described in Example 1.

Example 5. Formula 33

[0381] ##STR00145## [0382] X, R.sub.4, R.sub.5, A1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0383] A.sub.5 and A.sub.6 are as described in Example 2; and [0384] R.sub.3 is as described in Example 4.

Example 6. Formula 36

[0385] ##STR00146## [0386] X, R.sub.3, R.sub.4, R.sub.5, A.sub.1, A.sub.2, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0387] A.sub.5 and A.sub.6 are as described in Example 2; [0388] R.sub.1 is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, .an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted amide group, a substituted amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; and [0389] R.sub.8 is a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, [0390] where the substituents are as described in Example 1.

Example 7. Formula 47

[0391] ##STR00147##

[0392] R.sub.3, R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; and [0393] R.sub.6 and R.sub.7 are independently a hydrogen, an oxygen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, [0394] where the substituents are as described in Example 1.

Example 8. Formula 51

[0395] ##STR00148## [0396] R.sub.3, R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0397] R.sub.6 and R.sub.7 are as described in Example 7; [0398] A.sub.5 and A.sub.6 are as described in Example 2; [0399] R.sub.1 is a hydrogen, a halogen, a nitrile group, a nitro group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, .an unsubstituted amino group, a substituted amino group, an amide group, an unsubstituted amide group, a substituted amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group; and [0400] R.sub.8 is a hydrogen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group, [0401] where the substituents are as described in Example 1.

Example 9. Formula 54

[0402] ##STR00149## [0403] R.sub.3, R.sub.4, R.sub.5, A1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0404] R.sub.1 is as described in Example 8; [0405] R.sub.6 and R.sub.7 are as described in Example 7; and [0406] A.sub.5 and A.sub.6 are as described in Example 2.

Example 10. Formula 57

[0407] ##STR00150## [0408] R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0409] R.sub.3 is as described in Example 4; [0410] R.sub.6 and R.sub.7 are as described in Example 7; and [0411] A.sub.5 and A.sub.6 are as described in Example 2.

Example 11. Formula 63

[0412] ##STR00151## [0413] R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0414] R.sub.1 is as described in Example 8; [0415] R.sub.3 is as described in Example 4; [0416] R.sub.6 and R.sub.7 are as described in Example 7; and [0417] A.sub.5 and A.sub.6 are as described in Example 2.

Example 12. Formula 64

[0418] ##STR00152## [0419] R.sub.3, R.sub.4, R.sub.5, A.sub.1, A.sub.2, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0420] R.sub.1 is as described in Example 8; and [0421] R.sub.6 and R.sub.7 are as described in Example 7.

Example 13. Formula 65

[0422] ##STR00153## [0423] A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0424] R.sub.3 is a hydrogen, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, an unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group; and [0425] R.sub.4 and R.sub.5 are independently a hydrogen, an oxygen, a halogen, a nitrile group, an ester group, an unsubstituted aliphatic ester group, a substituted aliphatic ester group, an unsubstituted amino group, a substituted amino group, an amide group, an aliphatic-amide group, an azide group, an unsubstituted aliphatic group, a substituted aliphatic group, an unsubstituted aryl group, a substituted aryl group, an unsubstituted aryl-aliphatic group, a substituted aryl-aliphatic group, an unsubstituted aliphatic ether group, a substituted aliphatic ether group, un unsubstituted heterocyclic group, a substituted heterocyclic group, an unsubstituted heterocyclic-aliphatic group, or a substituted heterocyclic-aliphatic group where the substituents are as described in Example 1.

Example 14. Formula 69

[0426] ##STR00154## [0427] A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0428] R.sub.1 is as described in Example 8; [0429] A.sub.5 and A.sub.6 are as described in Example 2; and [0430] R.sub.3, R.sub.4, and R.sub.5 are as described in Example 13.

Example 15. Formula 71

[0431] ##STR00155## [0432] A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0433] R.sub.1 and R.sub.8 are as described in Example 8; and [0434] R.sub.3, R.sub.4, and R.sub.5 are as described in Example 13.

Example 16. Formula 75

[0435] ##STR00156## [0436] R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0437] R.sub.3 is as described in Example 4; and [0438] As and A.sub.6 are as described in Example 2.

Example 17. Formula 78

[0439] ##STR00157## [0440] R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0441] R.sub.1 is as described in Example 8; [0442] R.sub.3 is as described in Example 4; and [0443] A.sub.5 and A.sub.6 are as described in Example 2.

Example 18. Formula 80

[0444] ##STR00158## [0445] R.sub.4, R.sub.5, A.sub.1-A.sub.4, A.sub.7, Q, T, Y, B.sub.1, and A are as described in Example 1; [0446] R.sub.1 and R.sub.8 are as described in Example 8; and [0447] R.sub.3 is as described in Example 4.

Example 19. Additional Exemplary Compounds

[0448] ##STR00159## ##STR00160## ##STR00161## ##STR00162## ##STR00163## ##STR00164##

Example 20. Molecular Docking, Binding Mode, and Binding Energy Analysis of Exemplary Compounds

[0449] The nucleoside analogue prodrugs described herein can be converted to active metabolites, 5 ribose triphosphate (RTP), which base-pairs with DNA and/or RNA bases and gets incorporated into the viral DNA and/or viral RNA strand, resulting in viral mutagenesis. The structures of exemplary active metabolites and the corresponding exemplary prodrugs from which they are converted (i.e., Formulae 87, 84, 96, 101, 100, 102, 98, 97, 99, 88, and 86, where R.sub.23 and R.sub.2 are as defined above, e.g., paragraph no. 33 (b) on page 91; any one of Formulae XXI, XXII, 25, 25, 26, 26, 27, and 27;

##STR00165##

or the structures in Example 19 above) are shown below.

##STR00166## ##STR00167## ##STR00168## ##STR00169## ##STR00170##

[0450] Although not illustrated above, it is understood that additional tautomer forms of these exemplary compounds and their active RTP metabolites are present. For example, in addition to the keto-keto and enol-enol tautomer shown above, the active RTP metabolites of the compounds of Formula 96, 102, and 99 can also be a keto-enol tautomer:

##STR00171##

[0451] The active RTP metabolites of Formulae 87, 84, 96, 101, 100, 102, 98, 97, 99, 88, and 86, in different tautomer forms, were evaluated using molecular docking, binding mode, and binding energy analysis. The active RTP metabolites of reference compounds Guanosine and its amino-enol tautomer, Bemnifosbuvir and its amino-enol tautomer, Adenosine, and Remdesivir are used for comparison, the structures of which are shown below.

##STR00172## ##STR00173##

[0452] The bonding between the enol form of a triazolo-pyrazine compound and a nucleoside, cytidine, or an imino form the nucleoside are illustrated in FIGS. 1A and 1B, respectively. The bonding between a triazolo-pyrazine compound and the enol or keto form of a nucleoside, uridine, are illustrated in FIGS. 2A and 2B, respectively. The bonding between the amino-keto active RTP metabolite of the compound of Formula 84 and Cytidine MP within the SARS-CoV-2 RdRp, bonding between reference compound Guanosine and Cytidine MP within the SARS-CoV-2 RdRp, and bonding between reference compound Bemnifosbuvir (generated using the active metabolite, i.e., AT-9010) and Cytidine MP within the SARS-CoV-2 RdRp, are illustrated in FIGS. 3A-3C, respectively. The bonding between the amino-enol active RTP metabolite of the compound of Formula 84 and Uridine MP within the SARS-CoV-2 RdRp, bonding between reference compound Adenosine and Uridine MP within the SARS-CoV-2 RdRp, and bonding between reference compound Remdesivir TP (active metabolite) and the SARS-CoV-2 RdRp, are illustrated in FIGS. 4A-4C, respectively. Additionally, the bonding between the keto-enol active RTP metabolite of the compound of Formula 102 and Cytidine MP within the SARS-CoV-2 RdRp, and bonding between the enol-enol active RTP metabolite of the compound of Formula 102 and Uridine MP within the SARS-CoV-2 RdRp, are illustrated in FIGS. 5A and 5B, respectively.

[0453] The molecular docking, binding mode, and binding energy data are summarized in Tables 3-5. The binding energy reflects the affinity of the active metabolite for a target protein. The lower the free energy, the greater the affinity. Thus, the binding energies of the active metabolites of exemplary compounds described herein demonstrate their ability to compete with naturally occurring nucleosides and inflict chain termination.

[0454] As shown in Table 3, 9 out of the 11 active RTP metabolites show docking scores greater than the reference compounds, guanosine and bemnifosbuvir (generated using the active metabolite, i.e., AT-9010). Further, all 11 active RTP metabolites show binding energies exceeding bemnifosbuvir and 4 out of the 11 active RTP metabolites show binding energies greater than guanosine. These data demonstrate that the compounds described herein can mimic guanosine, with base pairing within the RdRp, leading to chain termination.

[0455] As shown in Table 4, 9 out of the 11 active RTP metabolites, in their tautomer forms, show docking scores matching the reference compounds, adenosine and remdesivir TP. Further, 9 out of the 11 active RTP metabolites show binding energies greater than adenosine and remdesivir. These data demonstrate that the compounds described herein, in different tautomer forms, can mimic adenosine, with ambiguous base pairing within the RdRp, leading to chain termination.

[0456] Table 5 shows the docking score and binding energy of the active RTP metabolite of an exemplary compound having a 5,6-cyclic ring structure, and the docking score and binding energy of an active RTP metabolite of an exemplary compound having a 6,6-cyclic ring structure. The active RTP metabolite structures are shown below. Without being bound to any theories, it is believed that the stereochemistry of the carbon atoms may play a role in binding of the 5,6-cyclic compounds to SARS-CoV-2 RdRp. For example, in Table 5, the exemplary 5,6-cyclic compound has a SRSR configuration on the ribose of the compound, which does not match that of Guanosine, and may affect the binding with SARS-CoV-2 RdRp.

##STR00174##

R is triphosphate

[0457] The data generated by different tautomer of a given compound demonstrate that the compounds described herein can mimic both guanosine and adenosine with similar or better binding energies, which can result in lower dose requirement and fewer side effects, and additional benefits, such as providing a barrier to viral resistance, the ability to target the nsp12NIRAN domain that is specific for guanosine (and analogues), and/or further enhanced effectiveness when compared with a protease inhibitor.

[0458] Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of skill in the art to which the disclosed invention belongs. Publications cited herein and the materials for which they are cited are specifically incorporated by reference. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

TABLE-US-00003 TABLE 3 Molecular Docking, Binding Mode and Binding Energy Analysis of Active RTP Metabolites of Exemplary Compounds* Compared to Reference Compounds Guanosine and Bemnifosbuvir as TP (PDB:7UOB) Binding BINDING Docking Energy H-bonds with Amino Acid Score MM/GBSA Structure Base Pair{circumflex over ()} Arg553 Arg555 Asn691 Asp623 Cys622 Lys545 Lys621 Lys798 Ser682 Ser759 Thr687 Ionic Stacking kcal/mol Guanosine C 101 ? ? ? ? x ? x x x x x PO4: Mg.sup.2+, ?-? . . . ?11.12 ?60.1 Arg555, A 102 (T) Lys798 Bemnifosbuvir C 101 x x ? x ? ? x ? x x x PO4: Mg.sup.2+, A 102 (T) ?12.89 ?33.27 Arg553- Arg555, Lys798 RTP of C 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, A 102 (T) ?12.97 ?70.36 Formula 87 Arg553, Lys798 RTP of C 101 ? ? ? ? ? ? ? ? x ? ? PO4: Mg.sup.2+, A 102 (T) ?14.05 ?66.77 Formula 84 Arg555, Lys798 RTP of C 101 x x ? ? x ? ? ? x ? ? PO4: Mg.sup.2+, A102 (T) ?14.64 ?71.87 Formula 96 Arg553, Arg555, Lys798 RTP of C 101 ? ? ? x ? ? ? x ? ? x PO4: Mg.sup.2+, A 102 (T) ?13.55 ?49.24 Formula 101 Arg555, Lys798 RTP of C 101 ? ? ? ? ? ? ? ? x ? ? PO4: Mg.sup.2+, A 102 (T) ?13.79 ?59.35 Formula 100 Arg555, Lys798 RTP of C 101 ? ? ? x ? ? ? x ? ? x PO4: Mg.sup.2+, A 102 (T) ?14.61 ?54.71 Formula 102 Arg555, Lys798 RTP of C 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, A 102 (T) ?11.3 ?68.02 Formula 98 Arg555, Lys798 RTP of C 101 ? ? ? x ? ? ? ? ? ? x PO4: Mg.sup.2+, A 102 (T) ?13.41 ?37.65 Formula 97 Arg555, Lys798 RTP of C 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, A 102 (T) ?14.49 ?55.26 Formula 99 Arg555, Lys798 RTP of C 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, A 102 (T) ?12.27 ?52.19 Formula 88 Arg555, Lys798 RTP of C 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, A 102 (T) ?13.66 ?53.79 Formula 86 Arg555, Lys798 *amino-keto form or keto-keto form {circumflex over ()}C represents Cytidine MP

TABLE-US-00004 TABLE 4 Molecular Docking, Binding Mode and Binding Energy Analysis of Active RTP Metabolites of Exemplary Compounds** Compared to Reference Compounds Guanosine.sup.#, Bemnifosbuvir.sup.#, Adenosine, and Remdesivir as TP (PDB:7UOB) BINDING Binding Docking Energy H-bonds with Amino Acid Ionic Stacking Score MM/GBSA Structure Base Pair{circumflex over ()} Arg553 Arg555 Asn691 Asp623 Cys622 Lys545 Lys621 Lys798 Ser682 Ser759 Thr687 Ionic Stacking kcal/mol Adensosine U 101 x x x ? x ? ? x x x x PO4: Mg.sup.2+, Arg553, A 102 (T) ?13.41 ?37.76 Arg555, Lys798 Remdesivir U 101 ? ? x x x x ? x ? x ? PO4: Mg.sup.2+, Arg555, x ?13.63 ?36.37 Lys798 Guanosine U 101 x ? x ? x ? ? x ? x ? PO4: Mg2+, Arg553, ?-? . . . ?10.94 ?50.3 Arg555 Lys621, A102 (T) Lys798 Bemnifosbuvir U 101 ? x x ? ? ? ? x x x x PO4: Mg2+, Arg553, A 102 (T) ?10.55 ?24.78 Arg555 Lys621, Lys798 RTP of U 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg2+, Arg555, A 102 (T) ?13.36 ?58.5 Formula 87 Lys798 RTP of U 101 ? ? ? ? ? ? ? ? x ? ? PO4: Mg2+, Arg555, A 102 (T) ?15.00 ?58.31 Formula 84 Lys798 RTP of U 101 x x ? ? x ? ? ? x ? ? PO4: Mg.sup.2+, Arg553, A 102 (T) ?15.10 ?60.83 Formula 96 Arg555, Lys798 RTP of U 101 ? ? ? x ? ? ? x ? ? x PO4: Mg.sup.2+, Arg555, A 102 (T) ?13.39 ?36.53 Formula 101 Lys798 RTP of U 101 ? ? ? ? ? ? ? ? x ? ? PO4: Mg.sup.2+, Arg555, A 102 (T) ?14.67 ?54.37 Formula 100 Lys798 RTP of U 101 ? ? ? x ? ? ? x ? ? x PO4: Mg.sup.2+, Arg555, A 102 (T) ?14.46 ?44.35 Formula 102 Lys798 RTP of U 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, Arg555, A 102 (T) ?13.21 ?50.01 Formula 98 Lys798 RTP of U 101 ? ? ? x ? ? ? ? ? ? x PO4: Mg.sup.2+, Arg555, A 102 (T) ?14.40 ?31.79 Formula 97 Lys798 RTP of U 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, Arg555, A 102 (T) ?15.17 ?47.11 Formula 99 Lys798 RTP of U 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, Arg555, A 102 (T) ?14.13 ?48.59 Formula 88 Lys798 RTP of U 101 ? ? ? ? ? ? ? x x ? ? PO4: Mg.sup.2+, Arg555, A 102 (T) ?14.02 ?52.23 Formula 86 Lys798 **amino-enol tautomer or enol-enol tautomer .sup.#amino-enol tautomer {circumflex over ()}U is for the Uridine MP

TABLE-US-00005 TABLE 5 Molecular Docking and Binding Energy Analysis of Monophosphate Metabolite and Active RTP Metabolites of Exemplary Compounds Binding Energy Docking Score MM/GBSA Structure kcal/mol Metabolite P1 ?12.854 ?52.36 Metabolite P2 ?13.529 ?59.16