Inhibitors for targeting flaviviruses

Abstract

The present invention relates to methods for identifying candidate therapeutics for a disease caused by a viral envelope protein. In particular, the method can include contacting a test envelope protein with the candidate and determining its activity.

Claims

1. A method for identifying a candidate therapeutic for a disease caused by a viral envelope protein, the method comprising: contacting a test envelope protein with a compound, wherein the test protein comprises a first sequence having at least 80% sequence identity to any one of SEQ ID NOs:35-104 or having any one of SEQ ID NOs:105, 106, 179, 181, 182, 185, 187, and 188; wherein the test protein comprises a second sequence having at least 80% sequence identity to any one of SEQ ID NOs: 107-176 or having any one of SEQ ID NOs: 177, 178, 180, 183, 184, 186, and 189-191; and wherein the second sequence comprises a lysine at position 9 and/or position 10; and determining an activity of the compound with the test protein, wherein the activity indicates greater inhibition of viral entry, as compared to a control.

2. The method of claim 1, further comprising, after the determining step: contacting a mutant viral envelope protein with the compound, wherein the mutant protein comprises the sequence of the test protein with a mutation in the second sequence at position 9 and/or position 10; determining an activity of the compound with the mutant protein; and comparing the activity of the compound with the test protein and the mutant protein, wherein the activity of the test protein indicates greater inhibition, as compared to the mutant protein.

3. The method of claim 1, wherein the second sequence of the test protein comprises a lysine at positions 9 and 10.

4. The method of claim 1, wherein the mutation in the second sequence at position 9 and/or 10 comprises a glycine, alanine, valine, leucine, isoleucine, methionine, aspartic acid, glutamic acid, asparagine, or glutamine.

5. The method of claim 2, wherein the first sequence of the test protein comprises an arginine at position 30, and wherein the first sequence of the mutant protein comprises a mutation at position 30.

6. The method of claim 5, wherein the mutation in the first sequence at position 30 comprises a glycine, alanine, valine, leucine, isoleucine, methionine, aspartic acid, glutamic acid, asparagine, or glutamine.

7. The method of claim 1, wherein the test protein comprises an arginine at position 30 of the first sequence, a lysine at position 9 of the second sequence, and a lysine at position 10 of the second sequence.

8. The method of claim 2, wherein the mutant protein comprises a mutation at position 30 of the first sequence, at position 9 of the second sequence, and at position 10 of the second sequence.

9. A method for identifying a candidate therapeutic for a disease caused by a viral envelope protein, the method comprising: contacting a test envelope protein with a compound, wherein the test protein comprises a sequence having at least 80% sequence identity to SEQ ID NO: 192, wherein the sequence comprises an arginine at position 73, an arginine at position 99, a lysine at position 246, and/or a lysine at position 247; and determining an activity of the compound with the test protein, wherein the activity indicates greater inhibition of viral entry, as compared to a control.

10. The method of claim 9, further comprising, after the determining step: determining an activity of the compound with the test protein; contacting a mutant viral envelope protein with the compound, wherein the mutant protein comprises the sequence of the test protein with at position 73, 99, 246, and/or 247; determining an activity of the compound with the mutant protein; and comparing the activity of the compound with the test protein and the mutant protein, wherein the activity of the test protein indicates greater inhibition, as compared to the mutant protein.

11. The method of claim 9, wherein the mutation at position 73, 99, 246, and/or 247 comprises a glycine, alanine, valine, leucine, isoleucine, methionine, aspartic acid, glutamic acid, asparagine, or glutamine.

12. The method of claim 9, wherein the test protein comprises a lysine at position 246 and a lysine at position 247.

13. The method of claim 9, wherein the test protein comprises an arginine at position 99.

14. The method of claim 10, wherein the mutant protein comprises a mutation at positions 99, 246, and 247.

15. A method of treating a viral infection in a subject, the method comprising: administering an effective amount of a lysine inhibitor and/or an arginine inhibitor to the subject, thereby treating the viral infection, wherein the infection arises from a flavivirus.

16. The method of claim 15, wherein the flavivirus is a mosquito-borne virus.

17. The method of claim 15, wherein the flavivirus is an Alkhumra hemorrhagic fever virus, Bussuquara virus, Chaoyang virus, Dengue virus, Donggang virus, Ilheus virus, Japanese encephalitis virus, Kedougou virus, Kokobera virus, Kunjin virus, Kyasanur Forest disease virus, Langat virus, Layer flavivirus, Louping ill virus, Murray Valley encephalitis virus, Omsk hemorrhagic fever virus, Powassan virus, Rocio virus, St. Louis encephalitis virus, tick-borne encephalitis virus, Usutu virus, West Nile virus, and Zika virus.

18. The method of claim 15, wherein the lysine inhibitor is selected from the group consisting of manoalide, seco-manoalide, wortmannin, myriocin, carbaglucose-6-phosphate, an aldehyde terpenoid, a wortmannin analogue, a pyrrole-5-carboxaldehyde inhibitor, an alkyl 6-(N-substituted sulfamoyl)cyclohex-1-ene-1-carboxylate compound, a fluorosulfonyl compound, a sulfonyl fluoride probe, a purine-based cyclin-dependent kinase inhibitor, a stilbene compound, an 8-N-benzyl adenosine reversible inhibitor, an adenosine-derived ATP-competitive inhibitor, an indole-based inhibitor, a peptide inhibitor including an unnatural amino acid with aryl sulfonyl fluoride, an iminoboronate compound, and salts thereof.

19. The method of claim 15, wherein the arginine inhibitor is selected from the group consisting of phenylglyoxal, p-azidophenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione, 5,6,9,10-tetrahydro[1,10]phenanthrolino[2,3-b][1,10]phenanthroline-2,13-dicarboxylic acid, 5,6,9,10-tetrahydrodinaphtho[1,2-b2′,1′-g][1,8]-naphthyridine-2,13-dicarboxylic acid, 5,6,9,10-tetrahydrobenzo[7,8]quino[2,3-b][1,10]phenanthroline-2,13-dicarboxylic acid, and salts thereof.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 shows an exemplary schematic of viral entry by a Dengue virus. Provided are the steps of viral entry, including approach of the Dengue virus to a host cell, binding of the virus (e.g., by way of the E protein dimer) to one or more cellular receptors, endocytosis of the virus into an endosome, fusion of the viral cell wall to the endosome (e.g., triggered by low pH, in which fusion occurs by way of the E protein trimer), and release of the capsid including the viral nucleic acid into the cytoplasm of the host cell.

(2) FIG. 2 shows schematics of an exemplary envelope (E) protein for a Dengue virus. Provided is the crystal structure of an E trimer showing the truncated trimer (TT, bottom, ˜45 Å), including the fusion loop (FL).

(3) FIG. 3A-3F shows molecular dynamics simulation data of the TT. Provided are (A) an image of the structure of the tip of the TT showing the location of all lysine (Lys) and arginine (Arg) residues; (B) characterization of hydrogen bonding between Lys residues near the fusion loop (FL) of truncated E trimers and neighboring lipids for the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine:1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine:cholesterol (PC:PE:CHOL) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine:1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-glycerol (PC:PG) systems, in which characterization is provided for two different truncated E trimer structures: a first TT (T1) and a second TT (T2) placed on one side of a lipid membrane; and (C) common hydrogen-bonding configurations of Lys to the phosphate and ester oxygens in the lipid headgroups. Also provided are characterization of hydrogen bonding between positively-charged residues (K246, K247, R73, R99) near the FL of truncated E trimers (T1 and T2) and neighboring lipids for the (D) 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PC:PE) system, (E) PC:PE:CHOL system, and (F) PC:PG system.

(4) FIG. 4 shows a molecular dynamics simulation image of a E protein (in dimer form) on a virus surface, in which K246 and K247 (arrowheads) are shown to interact most strongly with lipids.

(5) FIG. 5 shows alignment of exemplary flavivirus sequences (SEQ ID NOs:1-34) showing the conservation of positively-charged residues R73, R99, K246, and K247, which can form hydrogen bonds with phosphate oxygens of the lipid headgroups.

(6) FIG. 6A-6B shows alignment of exemplary flavivirus sequences in a domain II region of the envelope (E) protein (SEQ ID NOs:35-104) and exemplary consensus sequences (SEQ ID NOs:105-106).

(7) FIG. 7A-7B shows alignment of exemplary flavivirus sequences in another domain II region of the E protein (SEQ ID NOs: 107-176) and exemplary consensus sequences (SEQ ID NOs: 177-178).

(8) FIG. 8 shows alignment of exemplary Dengue virus strain sequences in a domain II region of the E protein and exemplary consensus sequences (SEQ ID NOs: 179-184).

(9) FIG. 9 shows alignment of exemplary flavivirus sequences in two different portions of the domain II regions of the E protein and exemplary consensus sequences (SEQ ID NOs: 185-191).

(10) FIG. 10 shows the amino acid sequence for the E protein of Dengue virus type 2 (strain Thailand/NGS-C/1944) (UniprotKB Acc. No. P14340, position 281-775) (SEQ ID NO: 192) and various domains of the protein, including domain I (red), domain II (yellow), domain III (dark blue), stem region (light blue), and transmembrane region (gray) (SEQ ID NO: 192). Provided are positions of R73, R99, K246, K247, and the fusion loop (position 98-111).

(11) FIG. 11A-11B shows structures of exemplary inhibitors, including (A) exemplary lysine inhibitors and (B) exemplary arginine inhibitors.

DETAILED DESCRIPTION OF THE INVENTION

(12) We have identified several amino acids within a viral envelope protein that contribute to disruption of a lipid layer. In part, one or more of the amino acids (e.g., R73, R99, K246, and/or K247, in reference to the sequence of the E protein, such as SEQ ID NO: 192 or in reference to a polypeptide sequence that is optimally aligned to SEQ ID NO: 192 as the reference sequence) participate in hydrogen bonding to a lipid headgroup, which in turn results in deformation of a lipid layer. This interaction between the E protein and the lipid layer may contribute to fusion of the viral membrane to a host's endosome, in which fusion is a typically required prior to release of the viral capsid into the host's cytoplasm. Thus, these amino acid(s) could be useful targets for developing therapeutic agents that can inhibit viral fusion. Accordingly, the present invention relates, in part, to a method for identifying a candidate therapeutic for a disease caused by a viral envelope protein. In another aspect, the present invention relates, in part, to a method of treating a viral infection in a subject. Additional details follow.

(13) Methods of Identifying a Candidate Therapeutic

(14) The present invention relates to methods for identifying a candidate therapeutic for a disease caused by a viral envelope protein. In particular embodiments, the viral envelope protein includes one or more protein sequences or polypeptide sequences described herein (e.g., one or more of SEQ ID NOs:35-192). In another embodiment, the viral envelope protein includes one or more of R73, R99, K246, and/or K247, in reference to the sequence of the E protein, such as SEQ ID NO: 192 or in reference to a polypeptide sequence that is optimally aligned to SEQ ID NO: 192 as the reference sequence.

(15) In some embodiments, the method includes contacting a viral envelope protein (e.g., any described herein) with the compound (e.g., a candidate therapeutic or any described herein) and determining an activity of the compound with the protein. Activity can include any useful biochemical, chemical, biological, pharmacodynamic, and/or pharmacokinetic assay to determine whether or not the compound provides a decrease or increase in biological effect of the viral protein. In particular embodiment, the biological effect means inhibiting the viral protein from fusion with a lipid layer, as compared to a control. In another embodiment, the biological effect means reducing the efficacy of the viral protein from fusion with a lipid layer, as compared to a control. In yet another embodiment, the biological effect means reduced hydrogen bonding between the viral protein and a lipid layer, as compared to a control. Exemplary activity can include determining binding (e.g., between the compound and a lipid layer, including competitive assays, binding assays, etc.), inhibition (e.g., inhibitory activity, such as determined by IC.sub.50 values, as well as other methods of determining an activity of inhibitors, as described herein), and/or infection (e.g., infection and/or replication activity, as determined by cellular assays to measure cellular infection or replication, including a cytopathic viral assay, a viral replicon assay, a phenotypic assay, or a gene-targeted viral assay).

(16) Additional activity parameters, as well as assays to measure such activity, as described in Green N et al., “Cell-based assays to identify inhibitors of viral disease,” Expert Opin Drug Discov. 2008; 3:671-676; Everts M et al., “Accelerating drug development: antiviral therapies for emerging viruses as a model,” Annu. Rev. Pharmacol. Toxicol. 2017; 57:155-169; Zaitseva E et al., “Dengue virus ensures its fusion in late endosomes using compartment-specific lipids,” PLoS Pathogens 2010; 6:e1001131 (14 pp.); and Leyssen P et al., “Perspectives for the treatment of infections with Flaviviridae,” Clin. Microbiol. Rev. 2000; 13:67-82, each of which is incorporated herein by reference in its entirety.

(17) In some embodiments, the method can further include comparing the activity of the compound with the test protein to a control. In other embodiments, the control includes determining an activity with a mutant protein, and the activity of the test protein indicates greater inhibition, as compared to the mutant protein. In yet other embodiments, the activity of the test protein indicates greater inhibition of viral entry, as compared to the control.

(18) Any useful control can be employed in determining an activity. An exemplary, non-limiting control includes activity of a protein without exposure to the compound. In this mode, activity of the test protein in the presence of the compound can be compared to activity of the test protein in the absence of the compound. Activity parameters can include determining viral infection and/or replication activity in the presence and absence of the compound. Another activity parameters can include determining binding of the protein to a lipid layer (e.g., in a planar lipid layer or in a liposome) in the presence and absence of the compound. Yet other activity parameters can include determining fusogenic activity of the protein, which can be tested by the extent of liposome fusion with the protein and in the presence and absence of the compound.

(19) Another exemplary, non-limiting control includes activity of mutant protein in the presence of the compound. In this mode, the mutant protein can include one or more modifications that would diminish hydrogen bonding between the protein and the lipid layer (e.g., a modification to one or more of R73, R99, K246, and/or K247, in reference to the sequence of the E protein, such as SEQ ID NO: 192 or in reference to a polypeptide sequence that is optimally aligned to SEQ ID NO: 192 as the reference sequence; or a modification to K9 and/or K10, in reference to a second sequence, as described herein, or in reference to a polypeptide sequence that is optimally aligned to one or SEQ ID NOs: 107-176; or a modification to R30, in reference to a first sequence, as described herein, or in reference to a polypeptide sequence that is optimally aligned to one or SEQ ID NOs:35-104). Such modifications can include replacing the arginine (Arg or R) or lysine (Lys K) residue with an amino acid having reduced hydrogen bonding capability, such as a hydrophobic residue, a nucleophilic residue, a small residue, an aromatic residue, an acidic residue, or an amide residue (e.g., glycine (Gly or G), alanine (Ala or A), serine (Ser or S), threonine (Thr or T), cysteine (Cys or C), valine (Val or V), leucine (Leu or L), isoleucine (Ile or I), methionine (Met or M), aspartic acid (Asp or D), glutamic acid (Glu or E), asparagine (Asn or N), or glutamine (Gin or Q)). In some embodiments, the modification includes replacing R or K with G, A, D, or E. Activity parameters can include determining binding in the presence of the protein or in the presence of the mutant protein.

(20) A lipid layer can include any useful composition include one or more lipid compounds and/or components (e.g., sterols) that emulate one or more physical or chemical characteristics (e.g., lipid composition, fluidity, curvature, charge, etc.) of a host lipid layer (e.g., a lipid layer of the host's endosome or host's cell membrane).

(21) Exemplary combinations of lipids include one or more PE (e.g., any described herein) with one or more PS (e.g., any described herein); one or more SM (e.g., any described herein) with cholesterol; one or more PC (e.g., any described herein) with one or more PE (e.g., any described herein) and optionally including one or more sterols; one or more PC (e.g., any described herein) with one or more PG (e.g., any described herein); PC, PE, PI, and BMP (e.g., any of these described herein); one or more PC (e.g., any described herein) with one or more PG (e.g., any described herein); and combinations thereof.

(22) The lipid layer can include any useful lipids and/or lipid-related components, including a phosphocholine (PC), such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-gly cero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), 1-oleoyl-2-[12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]lauroyl]-sn-glycero-3-phosphocholine (18:1-12:0 NBD PC), and 1-palmitoyl-2-{12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]lauroyl}-sn-glycero-3-phosphocholine (16:0-12:0 NBD PC); a phosphatidylethanolamine (PE), such as 1-palmitoyl-2-oleoyl-sn-gly cero-3-phosphoethanolamine (POPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (18:1 PEG-2000 PE), and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (16:0 PEG-2000 PE); a phosphatidylserine (PS), such as 1,2-dipalmitoyl-sn-glycero-3-[phosphor-L-serine] (POPS) and 1,2-dioleoyl-sn-glycero-3-[phosphor-L-serine] (DOPS); a phosphoglycerol (PG), such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-glycerol (POPG), and 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DOPG); an ammonium lipid, such as 1,2-dioleoyl-3-trimethylammonium-propane (18:1 DOTAP); a sterol, such as cholesterol, desmosterol, stigmasterol, sitosterol, a cholesteryl ester, glucosyl stigmasterol, and glucosyl sitosterol; a sphingomyelin (SM), such as N-acyl-sphing-4-enine-1-phosphocholine, N-oleoyl-D-erythro-sphingosylphosphorylcholine (18:1 SM), N-stearoyl-D-erythro-sphingosyl phosphorylcholine (18:0 SM), N-lauroyl-D-erythro-sphingosylphosphorylcholine (12:0 SM), N-myristoyl-D-erythro-sphingosylphosphorylcholine (14:0 SM), N-palmitoyl-D-erythro-sphingosylphosphorylcholine (16:0 SM), N-palmitoleoyl-D-erythro-sphingosyl phosphorylcholine (16:1 SM), and N-heptadecanoyl-D-erythro-sphingosylphosphorylcholine (17:0 SM); a bis(monoacylglycero) phosphate (BMP), such as bis(monooleoylglycero) phosphate, bis(monomyristoylglycero)phosphate, sn-(3-myristoyl-2-hydroxy)-glycerol-1-phospho-sn-3′-(1′,2′-dimyristoyl)-glycerol, sn-[2,3-dioleoyl]-glycerol-1-phospho-sn-1′-[2,3-dioleoyl]-glycerol, sn-(1-oleoyl-2-hydroxy)-glycerol-3-phospho-sn-3′-(1′-oleoyl-2′-hydroxy)-glycerol, sn-(3-oleoyl-2-hydroxy)-glycerol-1-phospho-sn-3′-(1′,2′-dioleoyl)-glycerol, sn-(3-oleoyl-2-hydroxy)-glycerol-1-phospho-sn-1′-(3-oleoyl-2-hydroxy)-glycerol, as well as isomers thereof (e.g., S and/or R isomers) and/or salts thereof; and a phosphatidylinositol (PI), including 1,2-diacyl-sn-glycero-3-phospho-(1-D-myo-inositol), L-α-phosphatidylinositol (from soy), 1,2-dipalmitoyl-sn-glycero-3-phospho-(1′-myo-inositol) (16:0 PI), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol (16:0-18:1 PI), 1,2-distearoyl-sn-glycero-3-phosphoinositol (18:0 PI), 1,2-dioleoyl-sn-glycero-3-phospho-(1′-myo-inositol) (18:1 PI), 1,2-dioleoyl-ST7-glycero-3-phospho-(1′-myo-inositol-3′-phosphate) (18:1 PI(3)P), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-myo-inositol-4′-phosphate) (16:0-18:1 PI(4)P), including salts thereof, as well as combinations thereof. Additional lipids and lipid components are readily available commercially from Avanti Polar Lipids, Inc. (Alabaster, Ala., USA).

(23) Any useful compound or candidate therapeutic can be tested. Exemplary, non-limiting candidate therapeutics include any described (e.g., a lysine inhibitor and/or arginine inhibitor, as well as combinations thereof).

(24) Methods of Treating an Infection

(25) The present invention also relates to methods of treating a viral infection in a subject. In some embodiment, the viral infection is caused, at least in part, by a viral envelope protein. In another embodiment, the viral infection is exacerbated, at least in part, by entry of the viral envelope protein into a host cell. In yet another embodiment, the viral infection is exacerbated, at least in part, by fusion of the viral envelope protein to a lipid membrane of a host cell (e.g., a cellular membrane or an endosomal membrane). In particular embodiments, the viral envelope protein includes one or more protein sequences or polypeptide sequences described herein (e.g., one or more of SEQ ID NOs:35-192). In another embodiment, the viral envelope protein includes one or more of R73, R99, K246, and/or K247, in reference to the sequence of the E protein, such as SEQ ID NO: 192 or in reference to a polypeptide sequence that is optimally aligned to SEQ ID NO: 192 as the reference sequence.

(26) The viral infection can be caused by a virus characterized by a viral envelope protein (e.g., including one or more protein sequences or polypeptide sequence described herein). In particular embodiments, the viral infection is caused by a flavivirus (e.g., a mosquito-borne flavivirus). Additional flaviviruses are described herein.

(27) Proteins and Polypeptide Sequences

(28) The methods herein employ an envelope protein, as described herein, which can be employed as a target protein for identifying a candidate therapeutic or can be the protein intended to be targeted for a method of treatment. The envelope protein can be characterized in any useful manner. In one non-limiting instance, the envelope protein includes a sequence having at least 80% sequence identity (e.g., at least about 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity) to SEQ ID NO: 192 (see, e.g., FIG. 10), where the sequence includes an arginine at position 73, an arginine at position 99, a lysine at position 246, and/or a lysine at position 247, e.g., in reference to a polypeptide sequence that is optimally aligned to SEQ ID NO: 192 as the reference sequence.

(29) In another non-limiting instance, the envelope protein includes a first sequence, as described herein (see, e.g., FIG. 6A-6B, 8, or 9). In some embodiments, the first sequence has at least 80% sequence identity (e.g., at least about 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity) to any one of SEQ ID NOs:35-104 (e.g., having one or more conservative amino acid substitutions for one or more amino acids in any of positions 1 to 31). In yet other embodiments, the first sequence includes or is any one of SEQ ID NOs:105, 106, 179, 181, 182, 185, 187, and 188.

(30) FIG. 6A-6B provides exemplary regions of a viral envelope protein (e.g., a first sequence of a viral envelope protein) for various flaviviruses (see, e.g., SEQ ID NOs:35-104, including any of these having one or more conservative amino acid substitutions for one or more amino acids in any of positions 1 to 31). These regions can include an arginine at position 30 and an optional arginine at position 4, in which the position is determined in reference to a polypeptide sequence that is optimally aligned to one or more of SEQ ID NOs:35-104 as the reference sequence. A skilled artisan would understand how to determine such an optimal alignment.

(31) In some embodiments, the first sequence includes a consensus sequence, such as the following:

(32) TABLE-US-00001 (SEQ ID NO: 105) CX.sub.2X.sub.3X.sub.4X.sub.5X.sub.6X.sub.7RG,
in which X.sub.2 can be K or R; X.sub.3 can be H, K, Q, R, or S; X.sub.4 can be D, G, L, S, or T; X.sub.5 can be F, L, M, Q, V, or Y; X.sub.6 can be S, T, or V; and X.sub.7 can be D or N.

(33) In other embodiments, the first sequence includes a consensus sequence, such as the following:

(34) TABLE-US-00002 (SEQ ID NO: 106) X.sub.1X.sub.2X.sub.3X.sub.4CP,
in which X.sub.1 can be A, I, S, T, or V; X.sub.2 can be A, D, E, K, N, Q, R, S, T, or V; X.sub.3 can be A, D, G, S, or T; and X.sub.4 can be A, K, N, or R.

(35) In yet other embodiments, the first sequence includes a consensus sequence, such as the following:

(36) TABLE-US-00003 (SEQ ID NO: 179) TX.sub.2X.sub.3RCPX.sub.7X.sub.8GEX.sub.11X.sub.12LX.sub.14EEQDX.sub.19X.sub.20X.sub.21X.sub.22CX.sub.24X.sub.25X.sub.26X.sub.27VDRG,
in which X.sub.2 can be A, D, or E; X.sub.3 can be S or T; X.sub.7 can be I or T; X.sub.8 can be L or Q; X.sub.11 can be A or P; X.sub.12 can be I, S, T, V, or Y; X.sub.14 can be K, N, P, or V; X.sub.19 can be A, K, Q, or T; X.sub.20 can be N, Q, or R; X.sub.21 can be F, L or Y; X.sub.22 can be L, I, or V; X.sub.24 can be K or R; X.sub.25 can be H or R; X.sub.26 can be D, S, or T; and X.sub.27 can be F, M, V, or Y.

(37) In some embodiments, the first sequence includes a consensus sequence, such as the following:

(38) TABLE-US-00004 (SEQ ID NO: 181) CX.sub.2X.sub.3X.sub.4X.sub.5VDRG,
in which X.sub.2 can be K or R; X.sub.3 can be H or R; X.sub.4 can be D, S, or T; and X.sub.5 can be F, M, V, or Y.

(39) In other embodiments, the first sequence includes a consensus sequence, such as the following:

(40) TABLE-US-00005 (SEQ ID NO: 182) TX.sub.2X.sub.3RCP,
in which X.sub.2 can be A, D, or E; and X.sub.3 can be S or T.

(41) In some embodiments, the first sequence includes a consensus sequence, such as the following:

(42) X.sub.1X.sub.2X.sub.3X.sub.4CPX.sub.7X.sub.8X.sub.9X.sub.10X.sub.11X.sub.12X.sub.13X.sub.14X.sub.15X.sub.16X.sub.17X.sub.18X.sub.19X.sub.20X.sub.21X.sub.22CX.sub.24X.sub.25X.sub.26X.sub.27X.sub.28X.sub.29RG (SEQ ID NO: 185), in which X.sub.1 can be I, S, T, or V; X.sub.2 can be A, D, E, K, R, S, or V; X.sub.3 can be A, S, or T; X.sub.4 can be A, N, or R; X.sub.7 can be A, I, or T; X.sub.8 can be L, M, Q, T, or V; X.sub.9 can be G or Q; X.sub.10 can be E, L, or P; X.sub.11 can be A, P, S, or T; X.sub.12 can be A, E, H, I, S, T, V, or Y; X.sub.13 can be L or N; X.sub.14 can be A, D, E, K, N, P, S, T, or V; X.sub.15 can be E or K; X.sub.16 can be A, E, Q, R, or S; X.sub.17 can be A, H, Q, L, R, S, or T; X.sub.18 can be D, E, or Q; X.sub.19 can be A, D, G, H, I, K, P, Q, S, or T; X.sub.20 can be A, G, N, Q, R, S, or T; X.sub.21 can be F, L, M, T, or Y; X.sub.22 can be I, L, or V; X.sub.24 can be K or R; X.sub.25 can be H, K, Q, R, or S; X.sub.26 can be D, G, S, or T; X.sub.27 can be F, L, M, Q, V, or Y; X.sub.28 can be S, T, or V; and X.sub.29 can be D or N.

(43) In other embodiments, the first sequence includes a consensus sequence, such as the following:

(44) TABLE-US-00006 (SEQ ID NO: 187) CX.sub.2X.sub.3X.sub.4X.sub.5X.sub.6X.sub.7RG,
in which X.sub.2 can be K or R; X.sub.3 can be H, K, Q, R, or S; X.sub.4 can be D, G, S, or T; X.sub.5 can be F, L, M, Q, V, or Y; X.sub.6 can be S, T, or V; and X.sub.7 can be D or N.

(45) In yet other embodiments, the first sequence includes a consensus sequence, such as the following:

(46) TABLE-US-00007 (SEQ ID NO: 188) X.sub.1X.sub.2X.sub.3RCP,
in which X.sub.1 can be I, S, T, or V; X.sub.2 can be A, D, E, K, R, S, or V; and X.sub.3 can be A, S, or T.

(47) In another non-limiting instance, the envelope protein includes a second sequence, as described herein (see, e.g., FIG. 7A-7B, 8, or 9). In some embodiments, the second sequence has at least 80% sequence identity (e.g., at least about 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity) to any one of SEQ ID NOs: 107-176 (e.g., having one or more conservative amino acid substitutions for one or more amino acids in any of positions 1 to 28). In other embodiments, the second sequence includes or is any one of SEQ ID NOs: 177, 178, 180, 183, 184, 186, and 189-191.

(48) FIG. 7A-7B provides exemplary regions of a viral envelope protein (e.g., a first sequence of a viral envelope protein) for various flaviviruses (see, e.g., SEQ ID NOs: 107-176, including any of these having one or more conservative amino acid substitutions for one or more amino acids in any of positions 1 to 28). In some embodiments, these regions can include a lysine at position 9 and/or a lysine or an arginine at position 10, in which the position is determined in reference to a polypeptide sequence that is optimally aligned to one or more of SEQ ID NOs: 107-176 as the reference sequence. A skilled artisan would understand how to determine such an optimal alignment.

(49) In some embodiments, the second sequence includes a consensus sequence, such as the following:

(50) TABLE-US-00008 (SEQ ID NO: 177) FX.sub.2X.sub.3X.sub.4HX.sub.6X.sub.7X.sub.8X.sub.9X.sub.10,
in which X.sub.2 can be E, G, K, Q, or T; X.sub.3 can be A, D, E, K, N, P, T, or V; X.sub.4 can be A, P, or T; X.sub.6 can be A or V; X.sub.7 can be A, K, T, or V; X.sup.8 can be K, R, or T; X.sub.9 can be I, M, Q, R, or V; and X.sub.10 can be D, E, K, R, S, or T.

(51) In other embodiments, the second sequence includes a consensus sequence, such as the following:

(52) TABLE-US-00009 (SEQ ID NO: 178) LX.sub.2X.sub.3QX.sub.5X.sub.6,
in which X.sub.2 can be A or G; X.sub.3 can be A, D, N, P, or S; X.sub.5 can be E or T; and X.sub.6 can be A or G.

(53) In yet other embodiments, the second sequence includes a consensus sequence, such as the following:

(54) TABLE-US-00010 (SEQ ID NO: 180) VTFKX.sub.5X.sub.6HAKX.sub.10QX.sub.12VX.sub.14VLGSQEGAMX.sub.24X.sub.25ALX.sub.28,
in which X.sub.5 can be N, T, or V; X.sub.6 can be A or P; X.sub.10 can be K or R; X.sub.12 can be D or E; X.sub.14 can be T or V; X.sub.24 can be H or Q; X.sub.25 can be S or T; and X.sub.28 can be A or T.

(55) In some embodiments, the first sequence includes a consensus sequence, such as the following:

(56) TABLE-US-00011 (SEQ ID NO: 183) VTFKX.sub.5X.sub.6HAKX.sub.10QX.sub.12,
in which X.sub.5 can be N, T, or V; X.sub.6 can be A or P; X.sub.10 can be K or R; and X.sub.12 can be D or E.

(57) In other embodiments, the first sequence includes a consensus sequence, such as the following:

(58) TABLE-US-00012 (SEQ ID NO: 184) LGSQEG.

(59) In some embodiments, the second sequence includes a consensus sequence, such as the following:

(60) X.sub.1X.sub.2FX.sub.4X.sub.5X.sub.6HX.sub.8X.sub.9X.sub.10X.sub.11X.sub.12X.sub.13X.sub.14X.sub.15LX.sub.17X.sub.18QX.sub.20X.sub.21X.sub.22X.sub.23X.sub.24X.sub.25X.sub.26LX.sub.28 (SEQ ID NO: 186), in which X.sub.1 can be I, L, M, or V; X.sub.2 can be E or T; X.sub.4 can be E, G, K, or Q; X.sub.5 can be A, D, E, K, N, P, T, or V; X.sub.6 can be A, P, or T; X.sub.8 can be A or V; X.sub.9 can be K, T, or V; X.sub.10 can be K or R; X.sub.11 can be M, Q, or R; X.sub.12 can be D, E, S, or T; X.sub.13 can be I or V; X.sub.14 can be F, I, L, T, V, or Y; X.sub.15 can be A, N, or V; X.sub.17 can be A or G; X.sub.18 can be A, D, N, or S; X.sub.20 can be E or T; X.sub.21 can be A or G; X.sub.22 can be A, E, G, I, T, or V; X.sub.23 can be L, M, or V; X.sub.24 can be H, L, or Q; X.sub.25 can be I, K, Q, R, S, T, or V; X.sub.26 can be A, S, or V; and X.sub.28 can be A or T.

(61) In other embodiments, the second sequence includes a consensus sequence, such as the following:

(62) TABLE-US-00013 (SEQ ID NO: 189) X.sub.1X.sub.2FX.sub.4X.sub.5X.sub.6HX.sub.8X.sub.9X.sub.10X.sub.11X.sub.12,
in which X.sub.1 can be I, L, M, or V; X.sub.2 can be E or T; X.sub.4 can be E, G, K, or Q; X.sub.5 can be A, D, E, K, N, P, T, or V; X.sub.6 can be A, P, or T; X.sub.8 can be A or V; X.sub.9 can be K, T, or V; X.sub.10 can be K or R; X.sub.11 can be M, Q, or R; and X.sub.12 can be D, E, S, or T.

(63) In yet other embodiments, the second sequence includes a consensus sequence, such as the following:

(64) TABLE-US-00014 (SEQ ID NO: 190) X.sub.1HX.sub.3X.sub.4X.sub.5,
in which X.sub.1 can be A, P, or T; X.sub.3 can be A or V; X.sub.4 can be K, T, or V; and X.sub.5 can be K or R.

(65) In other embodiments, the second sequence includes a consensus sequence, such as the following:

(66) TABLE-US-00015 (SEQ ID NO: 191) LX.sub.2X.sub.3QX.sub.5X.sub.6,
in which X.sub.2 can be A or G; X.sub.3 can be A, D, N, or S; X.sub.5 can be E or T; and X.sub.6 can be A or G.

(67) Any envelope protein can include a first sequence (e.g., any described herein), a second sequence (e.g., any described herein), or a combination of a first sequence and a second sequence (e.g., any first and second sequences described herein). FIG. 8 provides exemplary combinations of first and second sequences that may be present in a viral envelope protein (e.g., a combination of SEQ ID NOs: 179 and 180; or a combination of SEQ ID NOs: 181 or 182 with one of SEQ ID NOs: 183 or 184). FIG. 9 provides further exemplary combinations of first and second sequences that may be present in a viral envelope protein (e.g., a combination of SEQ ID NOs: 185 and 186; or a combination of SEQ ID NOs: 187 or 188 with one of SEQ ID NOs: 189-191).

(68) Lysine and Arginine Inhibitors

(69) The present invention relates, in part, to use of one or more inhibitors (e.g., any described herein). Such inhibitors can bind (e.g., through one or more covalent or non-covalent bonds) to any useful portion (e.g., one or more amino acid residues, such as arginine or lysine) of a virus (e.g., any virus herein). In particular embodiments, the portion is in proximity to tip region of a viral envelope protein, in which the tip region interfaces with a potential host cell.

(70) Exemplary, non-limiting inhibitors (e.g., lysine inhibitors) include manoalide; seco-manoalide; wortmannin; an aldehyde terpenoid (see, e.g., 3-(E)-methoxycarbonyl-2,4,6-trienal; methyl (E,E)-4-oxo-2-[(2,6,6-trimethylcyclohex-1-enyl)vinyl]but-2-enoate; methyl (E,E)-4-oxo-2-[(2-methyl-1-propenyl)vinyl]but-2-enoate; methyl (E,E,E)-4-oxo-2-[(2,6-dimethyl-1,5-heptadienyl)vinyl]but-2-enoate; methyl (E,E)-4-oxo-2-[(2,5,5,8a-tetramethyl-trans-3,4,4a,5,6,7,8,8a-octahydronaphthyl)vinyl]but-2-enoate; or salts thereof); a wortmannin analogue (see, e.g., sonolisib (PX-866, [(3aR,6E,9S,9aR,10R,11aS)-6-[[bis(prop-2-enyl)amino]methylidene]-5-hydroxy-9-(methoxymethyl)-9a,11a-dimethyl-1,4,7-tri oxo-2,3,3a,9,10,11-hexahydroindeno[4,5-h]isochromen-10-yl] acetate) or salts thereof); carbaglucose-6-phosphate; myriocin; 4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid; a pyrrole-5-carboxaldehyde inhibitor (e.g., 2,4-ethyl-3-methyl-5-formyl-1H-pyrrole-2,4-dicarboxylate; 2,4-ethyl-3-ethyl-5-formyl-1H-pyrrole-2,4-dicarboxylate; 2,4-ethyl-3-methyl-5-hydroxymethyl-1H-pyrrole-2,4-dicarboxylate; 2-tert-butyl-4-ethyl-3-ethyl-5-formyl-1H-pyrrole-2,4-dicarboxylate; ethyl 5-[(tert-butylamino)carbonyl]-4-ethyl-2-formyl-1H-pyrrole-3-carboxylate; 2-tert-butyl-4-ethyl-3-ethyl-5-formyl-1-methyl-1H-pyrrole-2,4-dicarboxylate; or salts thereof); a fungal alkaloid (e.g., K-252a ((9S-(9α, 10β, 12α))-2,3,9,10,11,12-hexahydro-10-hydroxy-10-(m ethoxy carbonyl)-9-methyl-9,12-epoxy-1H-diindolo[1,2,3-fg:3′,2′,1′-kl]pyrrolo[3,4-i][1,6]benzodiazocin-1-one)); an alkyl 6-(N-substituted sulfamoyl)cyclohex-1-ene-1-carboxylate compound (e.g., ethyl 6-[N-(2-chlorophenyl)sulfamoyl]yclohex-1-ene-1-carboxylate; ethyl 6-[N-(2,4-difluorophenyl) sulfamoyl]cyclohex-1-ene-1-carboxylate; ethyl 6-[N-(2,4,5-trifluorophenyl)sulfamoyl]cyclohex-1-ene-1-carboxylate; ethyl 6-[N-(2-chloro-4-fluorophenyl)sulfamoyl]cyclohex-1-ene-1-carboxylate; TAK-242 (ethyl (6R)-6-[N-(2-chloro-4-fluorophenyl)sulfamoyl]cyclohex-1-ene-1-carboxylate); and salts thereof); a fluorosulfonyl compound (e.g., such as fluorosulfonylbenzoate compounds, (2-aminoethyl)benzenesulfonyl fluoride (AEBSF), 5′-p-fluorosulfonylbenzoyl adenosine (FSBA), and compound 1 ([(2R,3R,4R,5R)-5-[4-amino-5-(4-methylphenyl) pyrrolo[2,3-d]pyrimidin-7-yl]-3-hydroxy-4-prop-2-ynoxyoxolan-2-yl]methyl 4-fluorosulfonylbenzoate) from Gushwa N N et al., “Selective targeting of distinct active site nucleophiles by irreversible Src-family kinase inhibitors,” J. Am. Chem. Soc. 2012; 134:20214-20217; or salts thereof); a sulfonyl fluoride probe (e.g., compounds 1-4 from Zhao Q et al., “Broad-spectrum kinase profiling in live cells with lysine-targeted sulfonyl fluoride probes,” J. Am. Chem. Soc. 2017; 139:680-685; or salts thereof); a purine-based cyclin-dependent kinase inhibitor (see, e.g., NU6102 (4-[[6-(cyclohexylmethoxy)-9H-purin-2-yl]amino]-benzene sulfonamide), NU2058 (6-(cyclohexylmethoxy)-9H-purin-2-amine), NU6094 (6-(cyclohexyl methoxy)-N-[4-phenyl]-9H-purin-2-amine), NU6086 (4-[[6-(cyclohexylmethoxy)-7H-purin-2-yl]amino]phenol), NU6300 (6-(cyclohexylmethoxy)-N-[4-(vinylsulfonyl)phenyl]-9H-purin-2-amine), NU6310 (6-(cyclohexylmethoxy)-N-[4-(ethylsulfonyl)phenyl]-9H-purin-2-amine), NU6155 (6-(cyclohexylmethoxy)-N-[4-(methylsulfonyl)phenyl]-9H-purin-2-amine), NU6483 (6-(cyclohexylmethoxy)-N-[4-(2-hydroxyethylsulfonyl)phenyl]-9H-purin-2-amine), or salts thereof); a stilbene compound (see, e.g., compounds 1-4 (S-phenyl 3-[2-(3,5-dibromo-4-hydroxyphenyl)ethenyl]benzenecarbothioate; S-phenyl 3-[2-(3,5-dimethyl-4-hydroxyphenyl) ethenyl]benzenecarbothioate; (2-nitrophenyl) 3-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzoate; and (4-fluorophenyl) 3-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzoate) from Choi S et al., “Chemoselective Small molecules that covalently modify one Lys in a non-enzyme protein in plasma,” Nat. Chem. Biol. 2010; 6:133-139; and compounds 1a-1d (2-(3,5-dimethylphenyl)-2,3-dihydro-1,3-benzoxazole; 2-(3,5-dibromophenyl)-2,3-dihydro-1,3-benzoxazole; 2-(4-hydroxyl-3,5-dimethylphenyl)-2,3-dihydro-1,3-benzoxazole; and 2-(4-hydroxyl-3,5-dibromophenyl)-2,3-dihydro-1,3-benzoxazole), 3d (3,5-dibromobiphenyl-4-ol), 4d (2,6-dibromo-4-(2-phenylethyl)phenol), 5d (4-anilino-2,6-dibromophenol), 3c (3,5-dimethyl biphenyl-4-ol), 4c (2,6-dimethyl-4-(2-phenylethyl)phenol), 7d (1-(3,5-dibromo-4-methylphenyl)-3-phenyl-urea), and 9d (N-(3,5-dibromo-4-hydroxyl-phenyl)benzamide) from Johnson S M et al., “Toward optimization of the linker substructure common to transthyretin amyloidogenesis inhibitors using biochemical and structural studies,” J. Med Chem. 2008; 51:6348-6358; and salts thereof); an 8-N-benzyl adenosine reversible inhibitor (e.g., ((2R,3R,4S,5R)-2-(6-amino-8-((4-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol)); an 8-N-benzyl adenosine covalent inhibitor (e.g., 3-((2R,3S,4R,5R)-5-(6-amino-8-((4-chlorobenzyl) amino)-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)propyl acrylate); an adenosine-derived ATP-competitive inhibitor (e.g., tubercidin, sangivamycin, 8-aminosangivamycin, 8-aminotoyocamycin, benzyltoyocamycin, 8-N-benzyladenosine, compounds 3 (8-amino adenosine), 4 (2-[6-amino-8-(methylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol), 7 (2-[6-amino-8-(methylamino)purin-9-yl]-5-(methyl)oxolane-3,4-diol), 10 (sangivamycin), 12-15 (4-amino-6-(methylamino)-7-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile; 4-amino-7-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-(methylamino)pyrrolo[2,3-d]pyrimidine-5-carboxamide; 4-amino-6-(benzylamino)-7-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile; and 2-[6-amino-8-(benzylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol), and 17-21 (2-[6-amino-8-(quinoline-4-ylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol; 2-[6-amino-8-(4-chlorobenzylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol; 2-[6-amino-8-(4-fluorobenzylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol; 2-[6-amino-8-(4-methylbenzylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol; and 2-[6-amino-8-(3,4-dichlorobenzylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol) from Cheeseman M D et al., “Exploiting protein conformational change to optimize adenosine-derived inhibitors of HSP70,” J. Med. Chem. 2016; 59:4625-4636; a peptide inhibitor including an unnatural amino acid with aryl sulfonyl fluoride (e.g, peptides 2-5 (Ac-QSQQTF*NLWRLL #QN-NH.sub.2, Ac-QSQQTF*NX.sup.1WRLL #QN-NH.sub.2, AC-QSQQTF*NX.sup.2WRLL #QN-NH2, and Ac-QSQQTA*NX.sup.2WRLL #QN-NH.sub.2, where a bridge —(CH.sub.2).sub.6(CH═CH)(CH.sub.2).sub.3— extends from * to #, X.sup.1 is an unnatural amino acid of 2-amino-3-[(4-fluorosulfonylbenzoyl)amino]propanoic acid, and X.sup.2 is an unnatural amino acid of 2-amino-3-[(3-fluorosulfonylbenzoyl)amino]propanoic acid) from Hoppmann C et al., “Proximity-enabled bioreactivity to generate covalent peptide inhibitors of p53-Mdm4,” Chem. Commun. 2016; 52:5140-5143; or salts thereof); an indole-based inhibitor (e.g., 3-(3-(naphthalen-1-yloxy)propyl)-1H-indole-2-carboxylic acid; 7-(3-((4-borono-3-formylphenoxy)methyl)-1,5-dimethyl-1H-pyrazol-4-yl)-3-(3-(naphthalen-1-yloxy)propyl)-1H-indole-2-carboxylic acid; 7-(3-((4-borono-3-formylphenoxy)methyl)-1,5-dimethyl-1H-pyrazol-4-yl)-1-methyl-3-(3-(naphthalen-1-yloxy)propyl)-1H-indole-2-carboxylic acid; 7-(3-((3-acetyl-4-boronophenoxy) methyl)-1,5-dimethyl-1H-pyrazol-4-yl)-3-(3-(naphthalen-1-yloxy)propyl)-1H-indole-2-carboxylic acid; 7-(3-((3-acetylphenoxy)methyl)-1,5-dimethyl-1H-pyrazol-4-yl)-3-(3-(naphthalen-1-yloxy)propyl)-1H-indole-2-carboxylic acid; or salts thereof); or an iminoboronate compound (e.g., 1-butylamine and 2-formylbenzeneboronic acid; compounds 4-9 from Cal PMSD et al., “Iminoboronates: a new strategy for reversible protein modification,” J. Am. Chem. Soc. 2012; 134:10299-10305; or salts thereof).

(71) Further exemplary inhibitors (e.g., lysine inhibitors) include an organic moiety including one or more aryl sulfonyl fluoride groups (e.g., —Ar—SO.sub.2F, where Ar is an optionally substituted aryl group, as defined herein, in which the —SO.sub.2F group is in the para, meta, or ortho position); an organic moiety including one or more aryl boronic acid groups (e.g., —Ar—B(OH).sub.2, where Ar is an optionally substituted aryl group, as defined herein, in which the —B(OH).sub.2 group is in the para, meta, or ortho position) or aryl boronic acid carbonyl groups (e.g., —Ar*—B(OH).sub.2, where Ar* is an optionally substituted aryl group, as defined herein, having a carbonyl substitution, in which the —B(OH).sub.2 group is in the para, meta, or ortho position); an organic moiety include one or more ester groups (e.g., —C(O)—OAr, where Ar is an optionally substituted aryl group, as defined herein, such as, e.g., an Ar including one or more halo, carbonyl, carboxyaldehyde, carboxyl, and alkoxy (e.g., as defined herein); an organic moiety including one or more aldehyde groups (e.g., one or more carboxyaldehyde groups, such as an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, or heterocyclyl group having one or more carboxyaldehyde groups (—C(O)H); or R′-Lk-R′, where Lk is a linker, such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy having one or more carboxyaldehyde groups, and where each of R′ is an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, or heterocyclyl); or an organic moiety include one or more optionally substituted triazine groups (e.g., -Het, where Het is an optionally substituted 1,3,5-triazine, 1,2,3-triazine, or 1,2,4-triazine group having one or more optional substitutions described herein for aryl, such as, e.g., halo, alkyl, alkoxy, etc.), as well as salts thereof.

(72) Exemplary, non-limiting inhibitors (e.g., arginine inhibitors) include phenylglyoxal, p-azidophenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione, 5,6,9,10-tetrahydro[1,10]phenanthrolino[2,3-b][1,10]phenanthroline-2,13-dicarboxylic acid (e.g., including salts thereof, such as a potassium salt), 5,6,9,10-tetrahydrodinaphtho[1,2-b:2′,1′-g][1,8]naphthyridine-2,13-dicarboxylic acid (e.g., including salts thereof, such as a potassium salt), 5,6,9,10-tetrahydro benzo[7,8]quino[2,3-b][1,10]phenanthroline-2,13-dicarboxylic acid (e.g., including salts thereof, such as a potassium salt), as well as salts thereof.

(73) Further exemplary inhibitors (e.g., arginine inhibitors) include an organic moiety including two or more carbonyl groups (e.g., two or more —C(O)— groups, such as a dione group (or —C(O)—C(O)—), including a cyclodione group in which a cycloalkyl group includes two or more carbon atoms within the ring substituted with an oxo group to form two or more —C(O)— groups, such as 1,2-cyclopentanedione, 1,2-cyclohexanedione, 1,2-cycloheptanedione, or 1,2-cyclooctanedione; or an alkanedione group in which an alkyl group includes two or more carbon atoms within the group substituted with an oxo group to form two or more —C(O)— groups, such as 2,3-butanedione, 2,3-pentanedione, or 2,3-hexanedione); an organic moiety including two or more phosphonate groups (e.g., such as X.sup.1-Lk-X.sup.2, wherein each of X.sup.1 and X.sup.2 is a phosphonate group (e.g., as defined herein) and Lk is a linker, such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy); an organic moiety including two or more carboxyl or carboxylate groups (e.g., such as X.sup.1-Lk-X.sup.2, wherein each of X.sup.1 and X.sup.2 is a carboxyl or carboxylate group (e.g., as defined herein) and Lk is a linker, such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy), as well as salts thereof.

(74) Other exemplary inhibitors include, e.g., Ar—C(O)—C(O)H; Ak-C(O)—C(O)H; Ak-C(O)—C(O)-Ak; and A.sup.1-C(O)—C(O)-A.sup.2, and salts thereof, where Ar is an optionally substituted aryl (e.g., as defined herein), where Ak is an optionally substituted alkyl (e.g., as defined herein), and where A.sup.1 and A.sup.2, taken together, is an optionally substituted alkylene, alkyleneoxy, heteroalkylene, or heteroalkyeneoxy group (e.g., as defined herein) and A.sup.1 and A.sup.2, taken together, form an optionally substituted cycloalkyl or heterocyclyl group (e.g., as defined herein); HO.sub.2C-Lk-CO.sub.2H or .sup.−O.sub.2C-Lk-CO.sub.2.sup.−, where Lk is a linker, such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy), and salts thereof; (R′O)(HO)P(O)-Lk-P(O)(OH)(OR′) or (R′O)(O)P(O)-Lk-P(O)(O.sup.−)(OR′), where Lk is a linker, such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy, as well as salts thereof, and where R′ is optionally substituted alkyl, aryl, alkaryl, or heterocyclyl; or salts of any of these.

(75) FIG. 11A-11B provides schematics of exemplary inhibitors (e.g., lysine inhibitors and/or arginine inhibitors), including compounds having structures (I), (II), (III), (IV), (V), (VI), or (VII) or a salt thereof. Also provided in FIG. 11A-11B are exemplary schematics of a reaction between an amino acid residue (e.g., lysine or arginine) with a compound.

(76) In the compound of structure (I), R′ can be any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein); as well as -Lk-R, in which Lk is a linker (e.g., such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy) and R is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein).

(77) In the compound of structure (II), Ar can be any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted aryl, alkaryl, heterocyclyl, alkheterocyclyl, heteroaryl, or alkheteroaryl (e.g., as defined herein); as well as -Lk-R, in which Lk is a bond or linker (e.g., such as a covalent bond or an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy) and R is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted aryl, alkaryl, heterocyclyl, alkheterocyclyl, heteroaryl, or alkheteroaryl (e.g., as defined herein).

(78) In the compound of structure (III), R′ can be any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein); as well as -Lk-R, in which Lk is a linker (e.g., such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy) and R is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein).

(79) In the compound of structure (IV), R′ can be any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein); as well as -Lk-R, in which Lk is a linker (e.g., such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy) and R is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein); and X can be any useful moiety (e.g., a substitution provided for optionally substituted alkyl or aryl, as defined herein), including a leaving group (e.g., halo, alkoxy, haloalkyl, etc.)

(80) In the compound of structure (V) or (VI), Lk can be any useful moiety (e.g., a linker), such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy. In the compound of structure (VI), R is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, alkcycloalkyl, or a leaving group (e.g., halo, alkoxy, haloalkyl, etc.). In other embodiments, R can be -Lk-R′, in which Lk is a linker (e.g., such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy) and R′ is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein).

(81) In the compound of structure (VII), R′ can be any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein); as well as -Lk-R, in which Lk is a linker (e.g., such as an optionally substituted alkylene, alkyleneoxy, heteroalkylene, heteroalkyleneoxy, arylene, or aryleneoxy) and R is any useful moiety (e.g., an organic moiety), including but not limited to an optionally substituted alkyl, heteroalkyl, aryl, alkaryl, heterocyclyl, alkheterocyclyl, cycloalkyl, and alkcycloalkyl (e.g., as defined herein).

(82) Further compounds (e.g., arginine and/or lysine inhibitors) include those disclosed in in Akçay G et al., “Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain,” Nat. Chem. Biol. 2016; 12:931-936; Anderson K E et al., “Chemoproteomics-enabled covalent ligand screening reveals a thioredoxin-caspase 3 interaction disruptor that impairs breast cancer pathogenicity,” ACS Chem. Biol. 2017; 12:2522-2528; Bell I M et al., “Biochemical and structural characterization of a novel class of inhibitors of the type 1 insulin-like growth factor and insulin receptor kinases,” Biochemistry 2005; 44:9430-9440; Bell T W et al., “Role of pyridine hydrogen-bonding sites in recognition of basic amino acid side chains,” J. Am. Chem. Soc. 2002; 124:14092-14103; Bell T W et al., “A small-molecule guanidinium receptor: the arginine cork,” Angew. Chem. Int. Ed. 1999; 38:2543-2547; Cal PMSD et al., “Iminoboronates: a new strategy for reversible protein modification,” J. Am. Chem. Soc. 2012; 134:10299-10305; Cheeseman M D et al., “Exploiting protein conformational change to optimize adenosine-derived inhibitors of HSP70,” J. Med. Chem. 2016; 59:4625-4636; Choi S et al., “Chemoselective small molecules that covalently modify one Lys in a non-enzyme protein in plasma,” Nat. Chem. Biol. 2010; 6:133-139; Davies T G et al., “Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor,” Nature Struct. Biol. 2002; 9:745-749; Gushwa N N et al., “Selective targeting of distinct active site nucleophiles by irreversible Src-family kinase inhibitors,” J. Am. Chem. Soc. 2012; 134:20214-20217; Hacker S M et al., “Global profiling of lysine reactivity and ligandability in the human proteome,” Nat. Chem. 2017; 9:1181-1190; Hoppmann C et al., “Proximity-enabled bioreactivity to generate covalent peptide inhibitors of p53-Mdm4,” Chem. Commun. 2016; 52:5140-5143; Johnson S M et al., “Toward optimization of the linker substructure common to transthyretin amyloidogenesis inhibitors using biochemical and structural studies,” J. Med. Chem. 2008; 51:6348-6358; Lonsdale R et al., “Structure-based design of targeted covalent inhibitors,” Chem. Soc. Rev. 2018; 47:3816-3830; Morgan H P et al., “A new family of covalent inhibitors block nucleotide binding to the active site of pyruvate kinase,” Biochem. J. 2012; 448:67-72; Narayanan A et al., “Sulfonyl fluorides as privileged warheads in chemical biology,” Chem. Sci. 2015; 6:2650-2659; Pal P K et al., “Affinity labeling of the inhibitory DPNH site of bovine liver glutamate dehydrogenase by 5′-fluorosulfonyl benzoyl adenosine,” J. Biol. Chem. 1975; 250:8140-8147; Pettinger J et al., “Lysine-targeting covalent inhibitors,” Angew. Chem. Int. Ed. 2017; 26:15200-15209; Pettinger J et al., “An irreversible inhibitor of HSP72 that unexpectedly targets lysine-56,” Angew. Chem. Int. Ed. 2017; 56(13):3536-3540; Shannon D A et al., “Investigating the proteome reactivity and selectivity of aryl halides,” J. Am. Chem. Soc. 2014; 136:3330-3333; Takahashi K, “The reaction of phenylglyoxal with arginine residues in proteins,” J. Biol. Chem. 1968; 243:6171-6179; Tanaka K et al., “The inhibitory mechanism of bovine pancreatic phospholipase A.sub.2 by aldehyde terpenoids,” Tetrahedron 1999; 55:1657-1686; Tanaka K et al., “Synthesis of anew phospholipase A.sub.2 inhibitor of an aldehyde terpenoid and its possible inhibitory mechanism,” Tetrahedron Lett. 1998; 39:1185-1188; Toi K et al., “Studies on the chemical modification of arginine: 1. The reaction of 1,2-cyclohexanedione with arginine and arginyl residues of proteins,” J. Biol. Chem. 1967; 242:1036-1043; Volz T J et al., “Covalent and noncovalent chemical modifications of arginine residues decrease dopamine transporter activity,” Synapse 2004; 52:272-282; Yamada M et al., “Discovery of novel and potent small-molecule inhibitors of NO and cytokine production as antisepsis agents: synthesis and biological activity of alkyl 6-(N-substituted sulfamoyl)cyclohex-1-ene-1-carboxylate,” J. Med. Chem. 2005; 48:7457-7467; Zhao Q et al., “Broad-spectrum kinase profiling in live cells with lysine-targeted sulfonyl fluoride probes,” J. Am. Chem. Soc. 2017; 139:680-685; Int. Pub. No. WO 2003/024183; U.S. Pat. Pub. No. US 2014/275234; U.S. Pat. No. 8,586,626, each of which is incorporated herein by reference in its entirety.

(83) Activity of Inhibitors

(84) The present invention relates, in part, to determining an activity of a candidate compound with a protein (e.g., a viral envelope E protein, such as any described herein; a protein including a sequence having at least 80% sequence identity to any one of SEQ ID NOs:35-104 or 192; a protein including a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 107-176; a protein having any one of SEQ ID NOs: 105, 106, 179, 181, 182, 185, 187, and 188; and/or a protein having any one of SEQ ID NOs: 177, 178, 180, 183, 184, 186, and 189-191, including any polypeptide sequence described herein). Activity of the candidate compound can be determined by measuring whether or not the compound binds (e.g., reversibly binds or irreversibly binds) to the protein or polypeptide, such as by way of mass spectrometry, electrospray ionization mass spectrometry, radioligand binding assay, fluorescence polarization, fluorescence binding assay (e.g., by use of fluorescence resonance energy transfer), and/or surface plasmon spectroscopy or by determining the binding association constant K.sub.a, a binding dissociation constant K.sub.d, or the inhibitor constant K.sub.i; by determining the structure of a complex including the compound bound to the protein or polypeptide, such as by way of x-ray crystallography, electron spectroscopy, and/or nuclear magnetic resonance (NMR) spectroscopy; by determining the pharmacodynamic or pharmacokinetic effects of the compound with the protein or polypeptide, such as by determining the half maximal inhibitory concentration (IC.sub.50) and/or half maximal effective concentration (EC.sub.50).

(85) The activity of the test protein can be compared to activity of a mutant protein having one or more mutations identified in the present application to be relevant to lipid binding (e.g., R73, R99, K246, and/or K247 of SEQ ID NO: 192). If these relevant sites are important to viral fusion, then mutation at one or more of those sites should provide a mutant with reduced viral fusion and, ultimately, reduced viral infection. Thus, efficacy of a candidate therapeutic compound can be determined by comparing the activity of the compound with the test protein and the mutant protein, in which an efficacious candidate compound will provide indicate greater inhibition with the test protein, as compared to the mutant protein. Greater inhibition can be characterized by, e.g., an IC.sub.50 value with the test protein that is lower than an IC.sub.50 value for the mutant protein; an inhibitor constant K.sub.i value with the test protein that is lower than a K.sub.i value for the mutant protein; and/or an equilibrium dissociation constant K.sub.d value with the test protein that is lower than a K.sub.d value with the mutant protein.

(86) Combination Therapy

(87) The inhibitors herein (e.g., lysine and/or arginine inhibitors) can be combined with one or more other agents for combination therapy. Exemplary other agents include, e.g., chloroquine; geneticin; amodiaquine; hydroxychloroquine; celgosivir; castanospermine; N-nonyl-deoxynojirimycin; sodium oxamate; 2-deoxy-D-glucose; D-like isoneplanocin; balapiravir; sofosbuvir; UV-4B (2-(hydroxymethyl)-1-(9-methoxynonyl)piperidine-3,4,5-triol, HCl salt); anthraquinone; BP13944 (N-ethyl-N,N-bis(hydroxymethyl)hexadecan-1-aminium bromide); ZINC04321905 (2-[3-(7-fluoro-1,2-dihydronaphthalene)]-6-fluoro-3,4-dihydro-1H-naphthalen-2-one); biliverdin; ARDP0006 (1,8-dihydroxy-4,5-dinitroanthracene-9,10-dione); policresulen; SK-12 (2-{[1-hydroxy-4-(4-methyl-3-nitro-benzenesulfonamido)naphthalen-2-yl]sulfanyl}acetic acid); NSC135618 ((3E)-3-[(2-chloro-4-nitrophenyl)hydrazinylidene]-N-(3-chlorophenyl)-6-oxocyclohexa-1,4-diene-1-carboxamide); 4-(1,3-dioxoisoindolin-2-yl)-N-(4-ethylphenyl) benzenesulphonamide; 4-(1,3-dioxoisoindolin-2-yl)-N-(naphthalen-1-yl)benzenesulphonamide; 1-(2-(4-fluorophenyl)-2-oxoethyl)-3,5-bis(4-nitrobenzylidene)piperidin-4-one; 1-(2-(4-methoxyphenyl)-2-oxoethyl)-3,5-bis(4-nitrobenzylidene)piperidin-4-one; ST-610 (1-[2-(1,3-benzoxazol-2-ylsulfanyl)acetyl]-4-piperidin-1-ylpiperidine-4-carboxamide); suramin; ivermectin; 4-[5-(4-chlorophenyl)thiophen-2-yl]-N-(pyridin-3-ylmethyl)quinazolin-2-amine; 1662G07 (N-(3-chloroanilino)-2-(furan-2-yl)-2-oxoethanimidoyl cyanide); 3-110-22 (N-(3-trifluoromethylanilino)-2-(2,3-dihydrobenzofuran-2-yl)-2-oxoethanimidoyl cyanide); ST-148 (3-amino-N-(5-phenyl-1,3,4-thiadiazol-2-yl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]thieno[3,2-e]pyridine-2-carboxamide); NITD-1 (N-(2-carboxyphenyl)-4-(3-methyl-5-oxo-4H-pyrazol-1-yl)benzenesulfonamide); NITD-2 (N-(2-carboxyphenyl)-4-(1-[(2-methylphenyl)methyl]pyrazol-4-yl)benzenesulfonamide); HeE1-2Tyr (-{[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazol-4-yl]carbonyl}-L-tyrosinate); DMB220 (5-(benzenesulfonylmethyl)-N,3-dihydroxy-4-(hydroxymethyl)pyridine-2-carboxamide); 66E2 (1-(5-ethyl-1H-pyrido[4,3-b]indol-8-yl)-3-(2-methyl-4-nitro-phenyl)urea); (3R)-5-chloro-1′-[(4-chlorophenyl)methyl]spiro[1H-indole-3,4′-5H-pyrazolo[3,4-b]pyridine]-2,6′-dione; (3R)-5-chloro-1′-[(4-chloropyridinyl)methyl]spiro[1H-indole-3,4′-5H-pyrazolo[3,4-b]pyridine]-2,6′-dione; 10-allyl-7-chloro-9(10H)-acridone; celastrol; 4-HPR (N-(4-hydroxyphenyl)retinamide); lactimidomycin (LTM); PF-429242 (4-[(diethylamino)methyl]-N-[2-(2-methoxyphenyl)ethyl]-N-(3R)-3-pyrrolidinylbenzamide); QL47 (1-(1-acryloylin-6-yl)-9-(1-methyl-1H-pyrazol-4-yl)benzo[h][1,6]) naphthyridin-2(1H)-one); YKL-04-085 ((E)-4-(dimethylamino)-N-(2-methyl-5-(9-(1-methyl-1H-pyrazol-4-yl)-2-oxobenzo[h]quinolin1(2H)-yl)phenyl)but-2-enamide); 5-(3,4-dichlorophenyl)-N-[2-(p-tolyl)benzotriazol-5-yl]furan-2-carboxamide (26124033); saracatinib (AZD0530); dasatanib; sinefungin; S-adenosyl-L-homocysteine; ribavirin; brequinar; mycophenolic acid; EICAR (5-ethynyl-1-ribofuranosylimidazole-4-carboxamide or 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-ethynylimidazole-4-carboxamide); hymeglusin; lovastatin; zaragozic acid; cerulenin; lanatoside C; andrographolide; cobalt protoporphyrin (CoPP); bromocriptine (BRC); eriodictyol 7-O-glucuronide; luteolin 8-C-beta-glucopyranoside; [−]-epicatechin-3-O-gallate; 6-O-trans-p-coumaroylgeniposide; luteolin-7-O-glucoside; octyl-2-O-sulfo-β-D-glucose; 1-acetyllycorine; lycorine; N-desmethylclozapine; fluoxetine; salmeterol; 2-N-methyl-6-N-(3-hydroxylphenyl)-7H-purine-2,6-diamine; 4-guanidinomethylphenylacteyl-Arg-Ala-Arg-4-amidinobenzylamide; 4-guanidinomethylphenylacteyl-Arg-Tle-Arg-4-amidinobenzyl amide, where Tle is t-butylglycine; 4-guanidinomethyl-phenylacteyl-Arg-Tle-Arg-4-amidino benzyl amide (MI-1148); FWFTLIKTQAKQPARYRRFC (SEQ ID NO: 193); MAILGDTAWDFGSLGGVFTSIGKALHQVFGAIY (DN59, SEQ ID NO: 194); Ac-FAAGRR-αketo-SL-CONH.sub.2 (SEQ ID NO: 195); Ac-FAAGRR-CHO (SEQ ID NO: 196); cyclic peptide GKRKSGCA (SEQ ID NO: 197); cyclic peptide CGKRKSC (SEQ ID NO: 198); cyclic peptide .sup.DRRRKA-homoF-1Nal-.sup.DF (SEQ ID NO: 199); Bz-Nle-Lys-Arg-B(OH).sub.2 (SEQ ID NO:200); AWDFGSLGGVFTSIGKALHQVFGAIYGAA (DV2.sup.419-447, SEQ ID NO:201); AWDFGSLGGVFTSIGKALHQVFGWWWGAA (DV2.sup.419-447(www 442-444), SEQ ID NO:202); Glu-Phe (EF); SVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPG (MLH40, SEQ ID NO:203); Ac-RTSKKR-NH2 (SEQ ID NO:204); WYCW-NH.sub.2 (SEQ ID NO:205); Bz-AKRR-H (SEQ ID NO:206); Bz-nKRR-B(OH).sub.2 (SEQ ID NO:207); 7-deaza-2′-C-methyl-adenosine; 2D22 antibody (DENV-2 specific human monoclonal antibody); Ab513 antibody (an-serotype MAb that neutralizes all four serotypes of DENV); compound 35 from Behnam MAM et al., “C-terminal residue optimization and fragment merging: discovery of a potent peptide-hybrid inhibitor of Dengue protease,” ACS Med Chem. Lett. 2014; 5:1037-1042; compounds 42a and 45a from Weigel L F et al., “Phenylalanine and phenylglycine analogues as arginine mimetics in Dengue protease inhibitors,” J. Med Chem. 2015; 58:7719-7733; compound 104 from Behnam M A M et al., “Discovery of nanomolar Dengue and West Nile virus protease inhibitors containing a 4-benzyloxyphenylglycine residue,” J. Med. Chem. 2015; 58:9354-9370; compound 23i (2-((2-(3-bromophenyl)hydrazinylidene)methyl)-N′-(2-phenylethylidene) quinoline-4-carbohydrazide) from Deng J et al., “Discovery of novel small molecule inhibitors of Dengue viral NS2B-NS3 protease using virtual screening and scaffold hopping,” J. Med. Chem. 2012; 55:6278-6293; compound MB21 ((E)-4-(5-(2-(5-chloro-1H-benzo[d]imidazol-2-yl)-2-cyanovinyl) thiophen-2-yl) benzoic acid) from Raut R et al., “A small molecule inhibitor of dengue virus type 2 protease inhibits the replication of all four dengue virus serotypes in cell culture,” Virol. J. 2015; 12:16 (7 pp.); compound 14 from Li L et al., “Structure-guided discovery of a novel non-peptide inhibitor of Dengue virus NS2B-NS3 protease,” Chem. Biol. Drug Des. 2015; 86:255-264; compounds 7 and 8 from Wu H et al, “Novel Dengue virus NS2B/NS3 protease inhibitors,” Antimicrob. Agents Chemother. 2015; 59:1100-1109; as well as salts thereof.

(88) Further exemplary other agents include a non-structural (NS) protein inhibitor, such as a NS3/NS2B protease inhibitor, a NS3 helicase inhibitor, a methyltransferase (MTase) inhibitor, a RNA-dependent RNA polymerase (RdRp) inhibitor, an NS1 inhibitor, an NS2B inhibitor, or an NS4B inhibitor; an NS5 polymerase inhibitor; as well as a structural protein inhibitor, such as a capsid protein inhibitor, a membrane precursor protein inhibitor, or an envelope protein inhibitor.

(89) Other non-limiting agents include any described in Behnam M A M et al., “The medicinal chemistry of Dengue virus,” J. Med. Chem. 2016; 59:5622-5649; Behnam M A M et al., “Discovery of nanomolar Dengue and West Nile virus protease inhibitors containing a 4-benzyloxyphenylglycine residue,” J. Med Chem. 2015; 58:9354-9370; Behnam M A M et al., “C-terminal residue optimization and fragment merging: discovery of a potent peptide-hybrid inhibitor of Dengue protease,” ACS Med Chem. Lett. 2014; 5:1037-1042; Deng J et al., “Discovery of novel small molecule inhibitors of Dengue viral NS2B-NS3 protease using virtual screening and scaffold hopping,” J. Med. Chem. 2012; 55:6278-6293; Li L et al., “Structure-guided discovery of a novel non-peptide inhibitor of Dengue virus NS2B-NS3 protease,” Chem. Biol. Drug Des. 2015; 86:255-264; Raut R et al., “A small molecule inhibitor of dengue virus type 2 protease inhibits the replication of all four dengue virus serotypes in cell culture,” Virol. J. 2015; 12:16 (7 pp.); Weigel L F et al., “Phenylalanine and phenylglycine analogues as arginine mimetics in Dengue protease inhibitors,” J. Med. Chem. 2015; 58:7719-7733; Tian Y S et al., “Dengue virus and its inhibitors: a brief review,” Chem. Pharm. Bull. 2018; 66:191-206; and Wu H et al, “Novel Dengue virus NS2B/NS3 protease inhibitors,” Antimicrob. Agents Chemother. 2015; 59:1100-1109, each of which is incorporated herein by reference in its entirety.

(90) Flaviviruses

(91) Exemplary flaviviruses include tick-borne viruses, mosquito-borne viruses, non-vertebrate viruses, and other flaviviruses. Further examples of flaviviruses include any in the genus Flavivirus, including, e.g., Alfuy virus, Alkhumra hemorrhagic fever virus (ALKV), Bagaza virus (BAGV), Baiyangdian virus (BYDV), Bamaga virus (BGV), Banzi virus (BANV), Bouboui virus (BOUV), Bussuquara virus (BUSV), Cacipacore virus (CPCV), Chaoyang virus, Culex flavivirus, Culex theileri flavivirus, Dengue virus (DENV), Donggang virus, Duck egg drop syndrome virus (DEDSV), Edge Hill virus (EHV), Fitzroy river virus, Hanko virus, Ilheus virus (ILHV), Israel turkey meningoencephalomyelitis virus (ITV), Japanese encephalitis virus (JEV), Jiangsu virus (JSV), Jugra virus (JUGV), Kedougou virus (KEDV), Kokobera virus (KOKV), Koutango virus (KOUV), Kunjin virus (KUNJ), Kyasanur Forest disease virus (KFDV), Langat virus (LANV), Layer flavivirus, Louping ill virus (LIV), New Mapoon virus (NMV), Murray Valley encephalitis virus (MVEV), Ntaya virus (NTAV), Omsk hemorrhagic fever virus (OHFV), Powassan virus (POWV), Rocio virus (ROCV), Saboya virus (SABV), St. Louis encephalitis virus (SLEV), Sepik virus (SEPV), Sitiawan virus (STWV), Spondweni virus (SPOV), Stratford virus (STRV), Tembusu virus (TMUV), T'Ho virus, tick-borne encephalitis virus (TBEV), Uganda S virus (UGSV), Usutu virus (USUV), Wesselsbron virus (WSLV), West Nile virus (WNV), Yaounde virus (YAOV), Yellow fever virus (YFV), and Zika virus (ZIKV), as well as strains or isolates of any of these.

EXAMPLES

Example 1; New Target for Inhibitors of Dengue Virus and Other Flaviviruses

(92) We have discovered that lysine 246 and lysine 247 of the envelope protein of Dengue virus are critical for binding and anchoring of the virus to host cell endosomal membranes. This is an essential step in the membrane fusion process. Fusion of viral and host endosomal membranes is required for infectivity as it enables the nucleic acid of the virus to enter the cytosol of host cells. The two amino acids listed above are exposed on the surface of the mature virus and therefore are targets for inhibitors of Dengue virus infection.

(93) The envelope (E) protein of Dengue virus forms a dimer on the surface of the mature Dengue virus (FIG. 1). Upon binding to membranes of the host cell, the virus is taken up into endosomes. Acidification within the endosome results in dissociation of the dimer; and the protein rearranges to form a trimer that mediates fusion of viral and host membranes (FIGS. 1-2). Insertion of the tip of E into host membranes is essential to the process, serving to anchor E into the membrane. We examined the interactions between E and lipid membranes by experiments and simulations. Our results show that two important interactions are hydrogen bonds formed between lysines located on the sides of the trimer close to the tip (K246 and K247) and nearby lipid headgroups (FIG. 3A-3F). An arginine (R73 near the fusion loop) also contributes significant hydrogen bonding. Taken together, K246, K247, and R73 establish about 25% of all hydrogen bonds with the lipids. Such strong hydrogen bonding interactions (between lysine or arginine and lipid headgroups) can be more influential and stronger than hydrophobic interactions between the fusion loop and the lipid headgroups.

(94) Prior to our work, other researchers had focused on the fusion loop, a hydrophobic region at the tip of the protein and located as position 98-111 of the Dengue virus E protein (see, e.g., position 98-111 of SEQ ID NO: 192 in FIG. 10). Early researchers had postulated that insertion of the fusion loop into the lipid tails anchors the protein into the membrane. In contrast, our work establishes that K246 and K247 are exposed at the surface of the E dimer in the mature virus (FIG. 4) and, therefore, that these amino acids could be a viable drug target to inhibit fusion and, consequently infection, of the virus. Exemplary drugs to inhibit the target can include, e.g., any inhibitors described herein. Either or both lysine at position 246 (K246) and lysine at position 247 (K247) are conserved among other flaviviruses (see, e.g., FIGS. 5-9). Thus, without wishing to be limited by mechanism, such a target could be applicable to a broad range of viruses expected to these conserved residues (e.g., as in flaviviruses, such as any described herein, and including West Nile, Zika, tick-borne encephalitis virus, yellow fever, etc.).

(95) Further methods and data are described in Vanegas J M et al., “Insertion of Dengue E into lipid bilayers studied by neutron reflectivity and molecular dynamics simulations,” BBA Biomembranes 2018; 1860:1216-1230, which is incorporated herein by reference in its entirety.

OTHER EMBODIMENTS

(96) All publications, patents, and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.

(97) While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.

(98) Other embodiments are within the claims.