Cell-permeable imaging sensors and uses thereof
10933146 ยท 2021-03-02
Assignee
Inventors
- Alan Pradip Jasanoff (Cambridge, MA, US)
- Ali Barandov (Brookline, MA, US)
- Benjamin B. Bartelle (Cambridge, MA, US)
Cpc classification
A61K49/0002
HUMAN NECESSITIES
G01N33/6872
PHYSICS
International classification
Abstract
The disclosure relates in some aspects to imaging agents, and in particular, imaging agents for sensing of calcium signaling. According to some embodiments of the disclosure, contrast agents for magnetic resonance imaging and related technologies are provided, and methods of making and using the contrast agents.
Claims
1. A sensor comprising the structure, Y-L-Z, wherein: Y is an analyte binding moiety; L is a linker that covalently links Y and Z; and Z is of the formula: ##STR00004## wherein: M is metal ion; X is N; each instance of R.sup.A is independently halogen, unsubstituted C.sub.1-6 alkyl, C.sub.1-6 alkyl substituted with one or more instances of halogen, oxo, or OR.sup.a; each instance of R.sup.a is independently unsubstituted C.sub.1-6 alkyl or C.sub.1-6 alkyl substituted with one or more instances of halogen; k is 0, 1, 2, or 3; each instance of R.sup.B is directly attached to any one of the 3a- to 6a-positions and is independently halogen, unsubstituted C.sub.1-6 alkyl, C.sub.1-6 alkyl substituted with one or more instances of halogen, oxo, or OR.sup.a, or two instances of R.sup.B are joined to form a phenyl ring, wherein the phenyl ring formed by joining two instances of R.sup.B is unsubstituted or substituted with 1, 2, 3, or 4 instances of substituents independently selected from the group consisting of halogen, OR.sup.a, unsubstituted C.sub.1-6 alkyl, and C.sub.1-6 alkyl substituted with one or more instances of halogen; m is 0, 1, 2, 3, or 4; each instance of R.sup.c is independently halogen, unsubstituted C.sub.1-6 alkyl, C.sub.1-6 alkyl substituted with one or more instances of halogen, oxo, or OR.sup.a, or two instances of R.sup.c are joined to form a phenyl ring, wherein the phenyl ring formed by joining two instances of R.sup.c is unsubstituted or substituted with 1, 2, 3, or 4 instances of substituents independently selected from the group consisting of halogen, OR.sup.a, unsubstituted C.sub.1-6 alkyl, and C.sub.1-6 alkyl substituted with one or more instances of halogen; and n is 0, 1, 2, 3, or 4.
2. The sensor of claim 1, wherein the sensor further comprises an additional Y, Z, L, -L-Y, or -L-Z covalently bound to Y or Z.
3. The sensor of claim 1, wherein M is a paramagnetic metal ion.
4. The sensor of claim 1, wherein the analyte is a cell signaling ion.
5. The sensor of claim 4, wherein the cell signaling ion is a cation selected from the group consisting of: Calcium.sup.2+, Sodium.sup.+, Potassium.sup.+, Magnesium.sup.2+, and Zinc.sup.2+.
6. The sensor of claim 1, wherein the analyte binding moiety contains at least one aromatic group.
7. The sensor of claim 1, wherein the analyte binding moiety contains at least one aromatic group selected from the group consisting of monocyclic aryl, bicyclic aryl, monocyclic heteroaryl, and bicyclic heteroaryl.
8. The sensor of claim 1, wherein Z has a planar configuration when chelating a paramagnetic metal ion.
9. The sensor of claim 1, wherein Z is of the formula: ##STR00005##
10. The sensor of claim 1, wherein the analyte binding moiety comprises a selective calcium chelating moiety derived from 1,2-bis(2-aminophenoxy)ethane-N,N, N,N-tetraacetic acid (BAPTA).
11. The sensor of claim 10, wherein the selective calcium chelating moiety derived from BAPTA does not comprise the moiety C(O)OH.
12. The sensor of claim 9, wherein the analyte binding moiety is of the formula: ##STR00006## wherein: L.sup.1 is unbranched C.sub.2-8 alkylene, wherein: 0, 1, 2, or 3 methylene units of the unbranched C.sub.2-8 alkylene are independently replaced with O or N(R.sup.F), as valency permits, wherein each instance of R.sup.F is independently H or unsubstituted C.sub.1-6 alkyl; and each methylene unit of the unbranched C.sub.2-8 alkylene is independently unsubstituted or substituted with 1 or 2 instances of substituents independently selected from the group consisting of oxo, OR.sup.a, halogen, unsubstituted C.sub.1-6, and C.sub.1-6 alkyl substituted with one or more instances of halogen; each instance of R.sup.a is independently unsubstituted C.sub.1-6 alkyl or C.sub.1-6 alkyl substituted with one or more instances of halogen; each instance of R.sup.D is independently halogen, unsubstituted .sub.1-6 alkyl, .sub.1-6 alkyl substituted with one or more instances of halogen, or OR.sup.a; p is 0, 1, 2, or 3; each instance of R.sup.E is independently halogen, unsubstituted C.sub.1-6 alkyl, C.sub.1-6 alkyl substituted with one or more instances of halogen, or OR.sup.a; q is 0, 1, 2, 3, or 4; each instance of r is independently 0, 1, 2, or 3; each instance of R is independently H or substituted or unsubstituted C.sub.1-6 alkyl.
13. The sensor of claim 9, wherein the analyte binding moiety is a polyaminocarboxylate chelator.
14. The sensor of claim 13, wherein the polyaminocarboxylate chelator is selected from the group consisting of ethylenediaminetetraacetic acid (EDTA), ethylene glycol-bis(-aminoethyl ether)-N,N,N, N-tetraacetic acid (EGTA), diethylenetriaminepentaacetic acid (DTPA), 2-[(2-amino-5-methylphenoxy)methyl]-6-methoxy-8-aminoquinoline-N,N,N,N-tetraacetic acid (quin-2), 1-(2-nitro-4,5-dimethoxyphenyl)-1,2-diaminoethane-N,N,N,N-tetraacetic acid (DM-nitrophen), and o-aminophenol-N,N,O-triacetic acid (APTRA).
15. The sensor of claim 9, wherein the analyte binding moiety is a metal ion-selective crown ether.
16. The sensor of claim 1, wherein the linker, L, is an unbranched C.sub.4-40 alkylene, unbranched C C.sub.4-40 alkenylene, or unbranched C.sub.4-40 alkynylene, wherein: 0, 1, or more methylene units of the unbranched C.sub.4-40 alkylene, unbranched C.sub.4-40 alkenylene, or unbranched C.sub.4-40 alkynylene are independently replaced with O, N, N(R.sup.F), C(O)O, C(O)NR.sup.F, S, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl as valency permits, wherein each instance of R.sup.F is independently H or unsubstituted C.sub.1-6 alkyl; each methylene unit of the unbranched C.sub.4-40 alkylene, unbranched C.sub.4-40 alkenylene, or unbranched C.sub.4-40 alkynylene is independently unsubstituted or substituted with 1 or 2 instances, as valency permits, of substituents independently selected from the group consisting of oxo, OR.sup.a, halogen, unsubstituted C.sub.1-6 alkyl, and C.sub.1-6 alkyl substituted with one or more instances of halogen; and each instance of R.sup.a is independently unsubstituted C.sub.1-6 alkyl or C.sub.1-6 alkyl substituted with one or more instances of halogen.
17. The sensor of claim 3, wherein M is an ion of iron, nickel, manganese, copper, gadolinium, dysprosium, or europium.
18. The sensor of claim 3, wherein M is Mn.sup.2+.
19. The sensor of claim 1, wherein L is of the formula: ##STR00007## wherein: the position a is directly attached to Z; and the position b is directly attached to the analyte binding moiety.
20. The sensor of claim 1, wherein the sensor is of the formula: ##STR00008##
Description
BRIEF DESCRIPTION OF THE DRAWINGS
(1) The accompanying drawings are not intended to be drawn to scale. In the drawings, each identical or nearly identical component that is illustrated in various figures may be represented by a like numeral. For purposes of clarity, not every component may be labeled in every drawing. In the drawings:
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DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION
(10) Certain ions (e.g., calcium, potassium, sodium) are important for signal transduction in cells, where they help coordinate biological processes ranging from embryonic development to neural function in the brain. Accordingly, in some embodiments, sensors and related methods described herein may be used to detect such ions and other analytes to gain a functional and/or physiological understanding of the biology of major disease areas, e.g., in neuroscience, which may lead to the discovery of addressable functional mechanisms in health and disease.
(11) In some embodiments, sensors and related methods provided herein facilitate drug development by providing new tools for pharmacological screening and characterization. In some embodiments, using the ion response (e.g., calcium signaling as a readout facilitates the study of drug or physiological effects.
(12) In some embodiments, sensors and related methods provided herein may be used for clinical diagnostic imaging. In some embodiments, sensors may be used, for example, to visualize cell signaling for diagnosis in numerous conditions, including neurological and muscular disorders, as well as immunological and endocrine conditions and others.
Sensors
(13) In some embodiments, sensors provided herein comprise the structure Y-L-Z, wherein: Y is an analyte binding moiety; Z is a lipophilic, branched chelating moiety; and L is a linker that covalently links Y and Z. Accordingly, in some embodiments, the sensor comprises an organic or an organometallic compound. In some embodiments, the sensor further comprises an additional Y, Z, L, -L-Y, or -L-Z covalently bound to Y or Z. In some embodiments, the sensor further comprises an additional L-Z covalently bound to Y (e.g., Z-L-Y-L-Z). In some embodiments, the sensor further comprises an additional -L-Y covalently bound to Z (e.g., Y-L-Z-L-Y).
(14) Various analytes that may be detected using the sensors described herein include metal ions, nitric oxide, or other species associated with normal biological function. The analyte may be present within a subject (e.g., a human), and, in some cases, may be present within a cell. In some cases, the analyte may be present within a subject in a location exterior to a cell. In some cases, the analyte is a metal ion, such as a toxic metal ion. Examples of metal ions include, but are not limited to, Zn.sup.2+, Ca.sup.2+, Hg.sup.2+, Cd.sup.2+, Pb.sup.2+, Na.sup.+, Mg.sup.2+, Mn.sup.2+, Fe.sup.2+, Co.sup.2+, Ni.sup.2+, and Cu.sup.2+. In some cases, the analyte is Zn.sup.2+, Ca.sup.2+, Mg.sup.2+, Hg.sup.2+, Cd.sup.2+, or Pb.sup.2+. In some embodiments, the analyte may be a zinc ion or calcium ion. In certain embodiments, the analyte may be a magnesium ion.
(15) In some embodiments, the analyte may be a calcium ion. Calcium is a component of cellular signaling systems and participates in brain function among other processes. Muscles (including the heart) may also depend on regulation of calcium, and calcium has been implicated in myocardial dysfunction. In one embodiment, a sensor may be useful in the determination of calcium ions within a cell, such as a muscle cell or neuronal cell.
(16) In some embodiments, the analyte binding moeity contains at least one aromatic group. In some embodiments, contains at least one aromatic group selected from the group consisting of monocyclic aryl (e.g., phenyl), bicyclic aryl (e.g., naphthyl), monocyclic heteroaryl (e.g., pyridyl, pyrimidyl, pyrrolyl, imidazolyl), and bicyclic heteroaryl (e.g., quinolyl, indolyl).
(17) In certain embodiments, the analyte binding moiety is a polyaminocarboxylate chelator. In certain embodiments, the analyte binding moiety is a polyaminocarboxylate chelator selected from the group consisting of polyaminocarboxylate chelator is selected from the group consisting of ethylenediaminetetraacetic acid (EDTA), ethylene glycol-bis(-aminoethyl ether N,N,N,N-tetraacetic acid (EGTA), diethylenetriaminepentaacetic acid (DTPA), 2-[(2-amino-5-methylphenoxy)methyl]-6-methoxy-8-aminoquinoline-N,N,N,N-tetraacetic acid (quin-2), 1-(2-nitro-4,5-dimethoxyphenyl)-1,2-diaminoethane-N,N,N,N-tetraacetic acid (DM-nitrophen), and o-aminophenol-N,N,O-triacetic acid (APTRA). In some embodiments, the analyte binding moiety selectively chelates metal ions. In some embodiments, the analyte binding moiety is ethylenediaminetetraacetic acid (EDTA). In certain embodiments, the analyte binding moiety is ethylene glycol-bis(-aminoethyl ether)N,N,N,N-tetraacetic acid (EGTA). In certain embodiments, the analyte binding moiety is a metal ion-selective crown ether.
(18) In some embodiments, an analyte binding moiety comprises a selective metal ion chelating moiety. In some embodiments, the selective metal ion chelating moiety is cell permeable. In some embodiments, the selective metal ion chelating moiety comprises a selective calcium chelating moiety derived from 1,2-bis(2-aminophenoxy)ethane-N,N,N,N-tetraacetic acid (BAPTA). In some embodiments, BAPTA, which is highly polar and membrane-impermeant in its Ca.sup.2+-binding acidic form, may be modified with modifying groups (e.g., with acetomethoxyl (AM) ester groups) to produce a neutral, inactive complex that is readily internalized inside cells. In certain embodiments, the selective calcium chelating moiety derived from BAPTA does not comprise carboxyl moieties. In certain embodiments, in the selective calcium chelating moiety derived from BAPTA, each of the moieties C(O)OH of BAPTA is replaced with the moiety C(O)OR, wherein each instance of R is independently substituted or unsubstituted C.sub.1-6 alkyl. In certain embodiments, each instance of R is C.sub.1-6 alkyl or C.sub.3-10 cycloalkyl, wherein R is unsubstituted or substituted with OR.sup.1, C(O)R.sup.1, OC(O)R.sup.1, C(O)OR.sup.1, NR.sup.1C(O)R.sup.1, or C(O)N(R.sup.1).sub.2 wherein each R.sup.1 is independently H, substituted or unsubstituted C.sub.1-6 alkyl (e.g., methyl, ethyl, propyl, butyl), or substituted or unsubstituted C.sub.3-10 cycloalkyl (e.g., cyclopentyl, cyclobutyl, cyclopentyl, cyclohexyl). In certain embodiments, each instance of R is CH.sub.2OC(O)CH.sub.3. In some embodiments, after internalization, the modifying groups (e.g., AM esters) undergo hydrolysis (e.g., catalyzed by intracellular esterases). In some embodiments, this process may activate the sensor (also referred to herein as an indicator) and trap it in the cell cytosol, where it functions as a cytosolic [Ca.sup.2+] imaging agent.
(19) In some embodiments, the lipophilic, branched chelating moiety is capable of binding a metal ion, such as a paramagnetic metal ion (e.g., Mn.sup.3+, Fe.sup.3+). In some embodiments, the analyte binding moiety is capable of binding an analyte such that an MRI and/or optical property of the sensor is shifted upon binding the analyte. As described herein, the presence or absence of a metal ion bound to the chelating moiety (chelator group), or, the type of metal ion bound to the chelating moiety, may affect one or more properties of the sensor, such as an MRI or optical property. In some cases, the sensor comprises a chelating moiety which binds a paramagnetic metal ion, such that the sensor exhibits an MRI signal upon exposure to MRI conditions, e.g., exposure to a magnetic field. In some cases, the sensor comprises a chelating moiety which does not bind a metal ion or binds a diamagnetic metal ion, such that the sensor exhibits a luminescence emission or absorption upon exposure to electromagnetic radiation.
(20) As used herein, the term paramagnetic metal ion refers to a metal ion having unpaired electrons, causing the metal ion to have a measurable magnetic moment in the presence of an externally applied field. Examples of suitable paramagnetic metal ions, include, but are not limited to, ions of iron, nickel, manganese, copper, gadolinium, dysprosium, europium, and the like. Mn.sup.2+, Mn.sup.3+, Fe.sup.2+, and Fe.sup.3+ are non-limiting examples of paramagnetic metal ions. In some embodiments, a sensor or composition of the disclosure comprises a chelator group bound to a paramagnetic metal ion, wherein the paramagnetic ion is an ion of iron or manganese.
(21) In certain embodiments, the lipophilic, branched chelating moiety comprises an aromatic group. In some embodiments, the lipophilic, branched chelating moiety comprises one or more cyclic moieties. In some embodiments, the lipophilic, branched chelating moiety is independently selected from the group consisting of optionally substituted monocyclic carbocyclyl (e.g., cyclopentyl, cyclohexyl), optionally substituted bicyclic carbocyclyl (e.g., decahydronaphtalenyl, bicyclo[2.2.1]heptanyl), optionally substituted monocyclic heterocyclyl (e.g., tetrahydrofuranyl, tetrahydropyranyl, pyrrolidinyl, pyrolinyl), and optionally substituted bicyclic heterocyclyl (e.g., decahydroquinolinyl). In some embodiments, the lipophilic, branched chelating moiety is independently selected from the group consisting of optionally substituted monocyclic aryl (e.g., phenyl, anilinyl), optionally substituted bicyclic aryl (e.g., naphthyl), optionally substituted monocyclic heteroaryl (e.g., pyridyl, pyrimidyl, pyrrolyl, imidazolyl), and optionally substituted bicyclic heteroaryl (e.g., quinolyl, indolyl). In certain embodiments, the lipophilic, branched chelating moiety comprises aromatic fluorophore.
(22) In some embodiments, the lipophilic, branched chelating moiety comprises a planar lipophilic ligand (e.g., a planar cell-permeable aromatic fluorophore). In some embodiments, the planar lipophilic ligand belongs to a family of planar phenylenediamido (PDA)-based Mn.sup.3+ complexes (see, e.g.,
(23) In some embodiments, interactions between the selective metal ion chelating moiety (e.g., based on BAPTA) and the planar lipophilic ligand (e.g., an Mn-PDA) of the activated sensor provide a basis for transducing calcium concentration changes into T.sub.1-weighted MRI signals. Accordingly, in embodiments provided herein, magnetic resonance imaging (MRI) provides for wide-field deep-tissue ion imaging (e.g., calcium imaging) in animals and humans. MRI achieves a combination of unlimited depth penetration, relatively high 3D spatial resolution (<100 m in some contexts), and sensitivity to a wide variety contrast mechanisms. In some embodiments, the sensors described herein are used for real-time functional magnetic resonance imaging of a signaling ion (e.g., calcium, for calcium ion signaling) in cells and tissues.
(24) In some embodiments, L, is an unbranched C.sub.4-40 alkylene, unbranched C.sub.4-40 alkenylene, or unbranched C.sub.4-40 alkynylene. In certain embodiments, 0, 1, or more methylene units of the unbranched C,.sub.4-40 alkylene, unbranched C.sub.4-40 alkenylene, or unbranched C.sub.4-40 alkynylene are independently replaced with O, N, N(R.sup.F), C(O)O, C(O)NR.sup.F, S, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl as valency permits. In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is N (e.g., CH.sub.2CH.sub.2CNCH.sub.2). In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is C(O)O. In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is C(O)NR.sup.F. In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is optionally substituted carbocyclyl (e.g., cyclopentyl, cyclobutyl, cyclopentyl, cyclohexyl). In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is optionally substituted heterocyclyl (e.g., tetrahydrofuranyl, tetrahydropyranyl, pyrrolidinyl, pyrolinyl, dioxopyrrolidinyl) In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is optionally substituted aryl (e.g., phenyl
(25) ##STR00001##
anilinyl
(26) ##STR00002##
In certain embodiments, 1 or more methylene units of the unbranched C.sub.4-40 alkylene is optionally substituted heteroaryl (e.g., pyridyl, pyrimidyl, pyrrolyl, imidazolyl, tetrazolyl, triazolyl, quinolyl, indolyl). In certain embodiments, R.sup.F is H. In some embodiments, R.sup.F is unsubstituted C.sub.1-6 alkyl (e.g., methyl, ethyl, propyl, isopropyl, butyl, pentyl, hexyl). In certain embodiments, a methylene unit is independently substituted with oxo. In certain embodiments, a methylene unit is independently substituted with OR.sup.a (OCH.sub.3 or OCH.sub.2CH.sub.3). In some embodiments, a methylene unit is substituted with halogen (e.g., F, Cl, Br, or I. In certain embodiments, a methylene unit is substituted with C.sub.1-6 alkyl (e.g., methyl, ethyl, propyl, isopropyl, butyl, pentyl). In certain embodiments, a methylene unit is substituted with C.sub.1-6 alkyl substituted with one or more instances of halogen (e.g. CF.sub.3, CHF.sub.2, CH.sub.2F, CH.sub.2CF.sub.3).
(27) In some embodiments, methods of making a sensor are provided (See, e.g., Examples and
(28) In some embodiments, methods of using the sensor are provided. In some embodiments, the sensor is used to monitor changes in intracellular metal ion (e.g., calcium ion) levels by MRI (e.g., proton MRI).
Chemical Definitions
(29) The term alkyl refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (C.sub.1-20 alkyl). In some embodiments, an alkyl group has 1 to 12 carbon atoms (C.sub.1-12 alkyl). In some embodiments, an alkyl group has 1 to 10 carbon atoms (C.sub.1-10 alkyl). In some embodiments, an alkyl group has 1 to 8 carbon atoms (C.sub.1-8 alkyl). In some embodiments, an alkyl group has 1 to 7 carbon atoms (C.sub.1-7 alkyl), in some embodiments, an alkyl group has 1 to 6 carbon atoms (C.sub.1-6 alkyl). In some embodiments, an alkyl group has 1 to 5 carbon atoms (C.sub.1-5 alkyl). In some embodiments, an alkyl group has 1 to 4 carbon atoms (C.sub.1-4 alkyl). In some embodiments, an alkyl group has 1 to 3 carbon atoms (C.sub.1-3 alkyl). In some embodiments, an alkyl group has 1 to 2 carbon atoms (C.sub.1-2 alkyl). In some embodiments, an alkyl group has 1 carbon atom (C.sub.1 alkyl). In some embodiments, an alkyl group has 2 to 6 carbon atoms (C.sub.2-6 alkyl). Examples of C.sub.1-6 alkyl groups include methyl (C.sub.1), ethyl (C.sub.2), propyl (C.sub.3) (e.g., n-propyl, isopropyl), butyl (C.sub.4) (e.g., n-butyl, tert-butyl, sec-butyl, iso-butyl), pentyl (C.sub.5) (e.g., n-pentyl, 3-pentanyl, amyl, neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C.sub.6) (e.g., n-hexyl). Additional examples of alkyl groups include n-heptyl (C.sub.7), n-octyl (C.sub.8), and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an unsubstituted alkyl) or substituted (a substituted alkyl) with one or more substituents (e.g., halogen, such as F). In certain embodiments, the alkyl group is an unsubstituted C.sub.1-12 alkyl (such as unsubstituted C.sub.1-6 alkyl, e.g., CH.sub.3 (Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstituted n-propyl (n-Pr), unsubstituted isopropyl (i-Pr)), unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (n-Bu), unsubstituted tert-butyl (tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu or s-Bu), unsubstituted isobutyl (i-Bu)). In certain embodiments, the alkyl group is a substituted C.sub.1-12 alkyl (such as substituted C.sub.1-6 alkyl, e.g., CH.sub.2F, CHF.sub.2, CF.sub.3, CH.sub.2CH.sub.2F, CH.sub.2CHF.sub.2, CH.sub.2CF.sub.3, or benzyl (Bn)).
(30) The term haloalkyl is a substituted alkyl group, wherein one or more of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. Perhaloalkyl is a subset of haloalkyl, and refers to an alkyl group wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In some embodiments, the haloalkyl moiety has 1 to 8 carbon atoms (C.sub.1-8 haloalkyl). In some embodiments, the haloalkyl moiety has 1 to 6 carbon atoms (C.sub.1-6 haloalkyl). In some embodiments, the haloalkyl moiety has 1 to 4 carbon atoms (C.sub.1-4 haloalkyl). In some embodiments, the haloalkyl moiety has 1 to 3 carbon atoms (C.sub.1-3 haloalkyl). In some embodiments, the haloalkyl moiety has 1 to 2 carbon atoms (C.sub.1-2 haloalkyl). In some embodiments, all of the haloalkyl hydrogen atoms are replaced with fluoro to provide a perfluoroalkyl group. In some embodiments, all of the haloalkyl hydrogen atoms are replaced with chloro to provide a perchloroalkyl group. Examples of haloalkyl groups include CF.sub.3, CF.sub.2CF.sub.3, CF.sub.2CF.sub.2CF.sub.3, CCl.sub.3, CFCl.sub.2, CF.sub.2Cl, and the like.
(31) The term heteroalkyl refers to an alkyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkyl group refers to a saturated group having from 1 to 10 carbon atoms and 1 or more heteroatoms within the parent chain (heteroC.sub.1-10 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 9 carbon atoms and 1 or more heteroatoms within the parent chain (heteroC.sub.1-9 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 8 carbon atoms and 1 or more heteroatoms within the parent chain (heteroC.sub.1-8 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 7 carbon atoms and 1 or more heteroatoms within the parent chain (heteroC.sub.1-7 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 6 carbon atoms and 1 or more heteroatoms within the parent chain (heteroC.sub.1-6 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 5 carbon atoms and 1 or 2 heteroatoms within the parent chain (heteroC.sub.1-5 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and 1 or 2 heteroatoms within the parent chain (heteroC.sub.1-4 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 3 carbon atoms and 1 heteroatom within the parent chain (heteroC.sub.1-3 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 to 2 carbon atoms and 1 heteroatom within the parent chain (heteroC.sub.1-2 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 1 carbon atom and 1 heteroatom (heteroC.sub.1 alkyl). In some embodiments, a heteroalkyl group is a saturated group having 2 to 6 carbon atoms and 1 or 2 heteroatoms within the parent chain (heteroC.sub.2-6 alkyl). Unless otherwise specified, each instance of a heteroalkyl group is independently unsubstituted unsubstituted heteroalkyl) or substituted (a substituted heteroalkyl) with one or more substituents. In certain embodiments, the heteroalkyl group is an unsubstituted heteroC.sub.1-10 alkyl. In certain embodiments, the heteroalkyl group is a substituted heteroC.sub.1-10 alkyl.
(32) The term alkenyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon double bonds (e.g., 1, 2, 3, or 4 double bonds). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (C.sub.2-9 alkenyl). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (C.sub.2-8 alkenyl). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (C.sub.2-7 alkenyl). In some embodiments, an alkenyl group has 2 to 6 carbon atoms (C.sub.2-6 alkenyl). In some embodiments, an alkenyl group has 2 to 5 carbon atoms (C.sub.2-5 alkenyl). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (C.sub.2-4 alkenyl). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (C.sub.2-3 alkenyl). In some embodiments, an alkenyl group has 2 carbon atoms (C.sub.2 alkenyl). The one or more carbon-carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples of C.sub.2-4 alkenyl groups include ethenyl (C.sub.2), 1-propenyl (C.sub.3), 2-propenyl (C.sub.3), 1-butenyl (C.sub.4), 2-butenyl (C.sub.4), butadienyl (C.sub.4), and the like. Examples of C.sub.2-6 alkenyl groups include the aforementioned C.sub.2-4 alkenyl groups as well as pentenyl (C.sub.5), pentadienyl (C.sub.5), hexenyl (C.sub.6), and the like. Additional examples of alkenyl include heptenyl (C.sub.7), octenyl (C.sub.8), octatrienyl (C.sub.8), and the like. Unless otherwise specified, each instance of an alkenyl group is independently unsubstituted (an unsubstituted alkenyl) or substituted (a substituted alkenyl) with one or more substituents. In certain embodiments, the alkenyl group is an unsubstituted C.sub.2-10 alkenyl. In certain embodiments, the alkenyl group is a substituted C.sub.2-10 alkenyl. In an alkenyl group, a CC double bond for which the stereochemistry is not specified (e.g., CHCHCH.sub.3,
(33) ##STR00003##
may be in the (E)- or (Z)-configuration.
(34) The term heteroalkenyl refers to an alkenyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkenyl group refers to a group having from 2 to 10 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-10 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 9 carbon atoms at least one double bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-9 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 8 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-8 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 7 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-7 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-6 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 5 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain (heteroC.sub.2-5 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 4 carbon atoms, at least one double bond, and for 2 heteroatoms within the parent chain (heteroC.sub.2-4 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 3 carbon atoms, at least one double bond, and 1 heteroatom within the parent chain (heteroC.sub.2-3 alkenyl). In some embodiments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain (heteroC.sub.2-6 alkenyl). Unless otherwise specified, each instance of a heteroalkenyl group is independently unsubstituted (an unsubstituted heteroalkenyl) or substituted (a substituted heteroalkenyl) with one or more substituents. In certain embodiments, the heteroalkenyl group is an unsubstituted heteroC.sub.2-10 alkenyl. In certain embodiments, the heteroalkenyl group is a substituted heteroC.sub.2-10 alkenyl.
(35) The term alkynyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon triple bonds (e.g., 1, 2, 3, or 4 triple bonds) (C.sub.2-10 alkynyl). In some embodiments, an alkynyl group has 2 to 9 carbon atoms (C.sub.2-9 alkynyl). In some embodiments, an alkynyl group has 2 to 8 carbon atoms (C.sub.2-8 alkynyl). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (C.sub.2-7 alkynyl). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (C.sub.2-6 alkynyl). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (C.sub.2-5 alkynyl). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (C.sub.2-4 alkynyl). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (C.sub.2-3 alkynyl). In some embodiments, an alkynyl group has 2 carbon atoms (C.sub.2 alkynyl). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples of C.sub.2-4 alkynyl groups include ethynyl (C.sub.2), 1-propynyl (C.sub.3), 2-propynyl (C.sub.3), 1-butynyl (C.sub.4), 2-butynyl (C.sub.4), and the like. Examples of C.sub.2-6 alkenyl groups include the aforementioned C.sub.2-4 alkynyl groups as well as pentynyl (C.sub.5), hexynyl (C.sub.6), and the like. Additional examples of alkynyl include heptynyl (C.sub.7) octynyl (C.sub.8), and the like. Unless otherwise specified, each instance of an alkynyl group is independently unsubstituted (an unsubstituted alkynyl) or substituted (a substituted alkynyl) with one or more substituents. In certain embodiments, the alkynyl group is an unsubstituted C.sub.2-10 alkynyl. In certain embodiments, the alkynyl group is a substituted C.sub.2-10 alkynyl.
(36) The term heteroalkynyl refers to an alkynyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkynyl group refers to a group having from 2 to 10 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-10 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 9 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-9 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-8 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-7 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (heteroC.sub.2-6 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 5 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain (heteroC.sub.2-5 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain (heteroC.sub.2-4 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 3 carbon atoms, at least one triple bond, and 1 heteroatom within the parent chain (heteroC.sub.2-3 alkynyl). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain (heteroC.sub.2-6alkynyl). Unless otherwise specified, each instance of a heteroalkynyl group is independently unsubstituted (an unsubstituted heteroalkynyl.) or substituted (a substituted heteroalkynyl) with one or more substituents. In certain embodiments, the heteroalkynyl group is an unsubstituted heteroC.sub.2-10 alkynyl. In certain embodiments, the heteroalkynyl group is a substituted heteroC.sub.2-10 alkynyl.
(37) The term carbocyclyl or carbocyclic refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 14 ring carbon atoms (C.sub.3-14 carbocyclyl) and zero heteroatoms in the non-aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 10 ring carbon atoms (C.sub.3-10 carbocyclyl). In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms (C.sub.3-8 carbocyclyl). In some embodiments, a carbocyclyl group has 3 to 7 ring carbon atoms (C.sub.3-7 carbocyclyl). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (C.sub.3-6 carbocyclyl). In some embodiments, a carbocyclyl group has 4 to 6 ring carbon atoms (C.sub.4-6 carbocyclyl). In some embodiments, a carbocyclyl group has 5 to 6 ring carbon atoms (C.sub.5-6 carbocyclyl). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms (C.sub.5-10 carbocyclyl). Exemplary C.sub.3-6 carbocyclyl groups include cyclopropyl (C.sub.3), cyclopropenyl (C.sub.3), cyclobutyl (C.sub.4), cyclobutenyl (C.sub.4), cyclopentyl (C.sub.5), cyclopentenyl (C.sub.5), cyclohexyl (C.sub.6), cyclohexenyl (C.sub.6), cyclohexadienyl (C.sub.6), and the like. Exemplary C.sub.3-8 carbocyclyl groups include the aforementioned C.sub.3-6 carbocyclyl groups as well as cycloheptyl (C.sub.7), cycloheptenyl (C.sub.7), cycloheptadienyl (C.sub.7), cycloheptatrienyl (C.sub.7), cyclooctyl (C.sub.8), cyclooctenyl (C.sub.8), bicyclo[2.2.1]heptanyl (C.sub.7), bicyclo[2.2.2]octanyl (C.sub.8), and the like. Exemplary C.sub.3-10 carbocyclyl groups include the aforementioned C.sub.3-8 carbocyclyl groups as well as cyclononyl (C.sub.9), cyclononenyl (C.sub.9), cyclodecyl (C.sub.10), cyclodecenyl (C.sub.10), octahydro-1H-indenyl (C.sub.9), decahydronaphthalenyl (C.sub.10), spiro[4.5]decanyl (C.sub.10), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic (monocyclic carbocyclyl) or polycyclic (e.g., containing a fused, bridged or spiro ring system such as a bicyclic system (bicyclic carbocyclyl) or tricyclic system (tricyclic carbocyclyl)) and can be saturated or can contain one or more carbon-carbon double or triple bonds. Carbocyclyl also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is independently unsubstituted (an unsubstituted carbocyclyl) or substituted (a substituted carbocyclyl) with one or more substituents. In certain embodiments, the carbocyclyl group is an unsubstituted C.sub.3-14 carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C.sub.3-14 carbocyclyl.
(38) In some embodiments, carbocyclyl is a monocyclic, saturated carbocyclyl group having from 3 to 14 ring carbon atoms (C.sub.3-14 cycloalkyl). In some embodiments, a cycloalkyl group has 3 to 10 ring carbon atoms (C.sub.3-10 cycloalkyl). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (C.sub.3-8 cycloalkyl). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (C.sub.3-6 cycloalkyl). In some embodiments, a cycloalkyl group has 4 to 6 ring carbon atoms (C.sub.4-6 cycloalkyl). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (C.sub.5-6 cycloalkyl). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (C.sub.5-10 cycloalkyl). Examples of C.sub.5-6 cycloalkyl groups include cyclopentyl (C.sub.5) and cyclohexyl (C.sub.5). Examples of C.sub.3-6 cycloalkyl groups include the aforementioned C.sub.5-6 cycloalkyl groups as well as cyclopropyl (C.sub.3) and cyclobutyl (C.sub.4). Examples of C.sub.3-8 cycloalkyl groups include the aforementioned C.sub.3-6 cycloalkyl groups as well as cycloheptyl (C.sub.7) and cyclooctyl (C.sub.8). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an unsubstituted cycloalkyl) or substituted (a substituted cycloalkyl) with one or more substituents. In certain embodiments, the cycloalkyl group is an unsubstituted C.sub.3-14 cycloalkyl. In certain embodiments, the cycloalkyl group is a substituted C.sub.3-14 cycloalkyl. In certain embodiments, the carbocyclyl includes 0, 1, or 2 CC double bonds in the carbocyclic ring system, as valency permits.
(39) The term heterocyclyl or heterocyclic refers to a radical of a 3- to 14-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (3-14 membered heterocyclyl). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (monocyclic heterocyclyl) or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system (bicyclic heterocyclyl) or tricyclic system (tricyclic heterocyclyl)), and can be saturated or can contain one or more carbon-carbon double or triple bonds. Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings. Heterocyclyl also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more cathocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless otherwise specified, each instance of heterocyclyl is independently unsubstituted (an unsubstituted heterocyclyl) or substituted (a substituted heterocyclyl) with one or more substituents. In certain embodiments, the heterocyclyl group is an unsubstituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl group is a substituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl is substituted or unsubstituted, 3- to 7-membered, monocyclic heterocyclyl, wherein 1,2, or 3 atoms in the heterocyclic ring system are independently oxygen, nitrogen, or sulfur, as valency permits.
(40) In some embodiments, a heterocyclyl group is a 5-10 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-10 membered heterocyclyl). In some embodiments, a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 rings heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-8 membered heterocyclyl). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-6 membered heterocyclyl). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
(41) Exemplary 3-membered heterocyclyl groups containing 1 heteroatom include azirdinyl, oxiranyl, and thiiranyl. Exemplary 4-membered heterocyclyl groups containing 1 heteroatom include azetidinyl, oxetanyl, and thietanyl. Exemplary 5-membered heterocyclyl groups containing 1 heteroatom include tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolindinyl, dihydropyrrolyl, and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groups containing 2 heteroatoms include dioxolanyl, oxathiolanyl and dithiolanyl. Exemplary 5-membered heterocyclyl groups containing 3 heteroatoms include triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing 1 heteroatom include piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocyclyl groups containing 2 heteroatoms include piperazinyl, morpholinyl, dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groups containing 3 heteroatoms include triazinyl. Exemplary 7-membered heterocyclyl groups containing 1 heteroatom include azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing 1 heteroatom include azocanyl, oxecanyl and thiocanyl. Exemplary bicyclic heterocyclyl groups include indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyl, decahydronaphthyridinyl, decahydro-1,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyl, 1H-benzo[e][1,4]diazepinyl, 1,4,5,7-tetrahydropyrano[3,4-b]pyrrolyl, 5,6-dihydro-4H-furo[3,2-b]pyrrolyl, 6,7-dihydro-5H-furo[3,2-b]pyranyl, 5,7-dihydro-4H-thieno[2,3-c]pyranyl, 2,3-dihydro-1H-pyrrolo[2,3-b]pyridinyl, 2,3-dihydrofuro[2,3-b]pyridinyl, 4,5,6,7-tetrahydro-1H-pyrrolo[2,3-b]pyridinyl, 4,5,6,7-tetrahydrofuro[3,2-c]pyridinyl, 4,5,6,7-tetrahydrothieno[3,2-b]pyridinyl, 1,2,3,4-tetrahydro-1,6-naphthyridinyl, and the like.
(42) The term aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (C.sub.6-14 aryl). In some embodiments, an aryl group has 6 ring carbon atoms (C.sub.6 aryl; e.g., phenyl). In some embodiments, an aryl group has 10 ring carbon atoms (C.sub.10 aryl; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms (C.sub.14 aryl; e.g., anthracyl). Aryl also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently unsubstituted (an unsubstituted aryl) or substituted (a substituted aryl) with one or more substituents. In certain embodiments, the aryl group is an unsubstituted C.sub.6-14 aryl. In certain embodiments, the aryl group is a substituted C.sub.6-14 aryl.
(43) The term heteroaryl refers to a radical of a 5-14 membered monocyclic or polycyclic (e.g., bicyclic, tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-14 membered heteroaryl). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl polycyclic ring systems can include one or more heteroatoms in one or both rings. Heteroaryl includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. Heteroaryl also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring system. Polycyclic heteroaryl groups wherein one ring does not contain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2indolyl) or the rims that does not contain a heteroatom (e.g., 5-indolyl). In certain embodiments, the heteroaryl is substituted or unsubstituted, 5- or 6-membered, monocyclic heteroaryl, wherein 1, 2, 3, or 4 atoms in the heteroaryl ring system are independently oxygen, nitrogen, or sulfur. In certain embodiments, the heteroaryl is substituted or unsubstituted, 9- or 10-membered, bicyclic heteroaryl, wherein 1, 2, 3, or 4 atoms in the heteroaryl ring system are independently oxygen, nitrogen, or sulfur.
(44) In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-10 membered heteroaryl). In some embodiments, a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-8 membered heteroaryl). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (5-6 membered heteroaryl). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently unsubstituted (an unsubstituted heteroaryl) or substituted (a substituted heteroaryl) with one or more substituents. In certain embodiments, the heteroaryl group is an unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is a substituted 5-14 membered heteroaryl.
(45) Exemplary 5-membered heteroaryl groups containing 1 heteroatom include pyrrolyl, furanyl, and thiophenyl. Exemplary 5-membered heteroaryl groups containing 2 heteroatoms include imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroaryl groups containing 3 heteroatoms include triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-membered heteroaryl groups containing 4 heteroatoms include tetrazolyl. Exemplary 6-membered heteroaryl groups containing 1 heteroatom include pyridinyl. Exemplary 6-membered heteroaryl groups containing 2 heteroatoms include pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups containing 3 or 4 heteroatoms include triazinyl and tetrazinyl, respectively. Exemplary 7-membered heteroaryl groups containing 1 heteroatom include azepinyl, oxepinyl, and thiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6-bicyclic heteroaryl groups include naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplary tricyclic heteroaryl groups include phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.
(46) Affixing the suffix -ene to a group indicates the group is a divalent moiety, e.g., alkylene is the divalent moiety of alkyl, alkenylene is the divalent moiety of alkenyl, alkynylene is the divalent moiety of alkynyl, heteroalkylene is the divalent moiety of heteroalkyl, heteroalkenylene is the divalent moiety of heteroalkenyl, heteroalkynylene is the divalent moiety of heteroalkynyl, carbocyclylene is the divalent moiety of carbocyclyl, heterocyclylene is the divalent moiety of heterocyclyl, arylene is the divalent moiety of aryl, and heteroarylene is the divalent moiety of heteroaryl.
(47) A group is optionally substituted unless expressly provided otherwise. The term optionally substituted refers to being substituted or unsubstituted. In certain embodiments, alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups are optionally substituted. Optionally substituted refers to a group which may be substituted or unsubstituted (e.g., substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heteroalkenyl, substituted or unsubstituted heteroalkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl group). In general, the term substituted means that at least one hydrogen present on a group is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a substituted group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term substituted is contemplated to include substitution with all permissible substituents of organic compounds, and includes any of the substituents described herein that results in the formation of a stable compound. The present invention contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety. The invention is not intended to be limited in any manner by the exemplary substituents described herein.
(48) Exemplary carbon atom substituents include halogen, CN, NO.sub.2, N.sub.3, SO.sub.2H, SO.sub.3H, OH, OR.sup.aa, ON(R.sup.bb).sub.2, N(R.sup.bb).sub.2, N(R.sup.bb).sub.3.sup.+X.sup., N(OR.sup.cc)R.sup.bb, SH, SR.sup.aa, C(O)R.sup.aa, CO.sub.2H, CHO, C(OR.sup.cc).sub.2, CO.sub.2R.sup.aa, OC(O)R.sup.aa, OCO.sub.2R.sup.aa, C(O)N(R.sup.bb).sub.2, OC(O)N(R.sup.bb).sub.2, NR.sup.bbC(O)R.sup.aa, NR.sup.bbCO.sub.2R.sup.aa, NR.sup.bbC(O)N(R.sup.bb).sub.2, C(NR.sup.bb)R.sup.aa, C(NR.sup.bb)OR.sup.aa, OC(NR.sup.bb)R.sup.aa, OC(NR.sup.bb)OR.sup.aa, C(NR.sup.bb)N(R.sup.bb).sub.2, OC(NR.sup.bb)N(R.sup.bb).sub.2, NR.sup.bbC(NR.sup.bb)N(R.sup.bb).sub.2, C(O)NR.sup.bbSO.sub.2R.sup.aa, NR.sup.bbSO.sub.2R.sup.aa, SO.sub.2N(R.sup.bb).sub.2, SO.sub.2R.sup.aa, SO.sub.2OR.sup.aa, OSO.sub.2R.sup.aa, S(O)R.sup.aa, OS(O)R.sup.aa, Si(R.sup.aa).sub.3, OSi(R.sup.aa).sub.3C(S)N(R.sup.bb).sub.2, C(O)SR.sup.aa, C(S)SR.sup.aa, SC(S)SR.sup.aa, SC(O)SR.sup.aa, OC(O)SR.sup.aa, SC(O)OR.sup.aa, SC(O)R.sup.aa, P(O).sub.2R.sup.aa, OP(O).sub.2R.sup.aa, P(O)R.sup.aa).sub.2, OP(O)(R.sup.aa).sub.2, OP(O)(OR.sup.cc).sub.2, P(O).sub.2N(R.sup.bb).sub.2, OP(O).sub.2N(R.sup.bb).sub.2, P(O)(NR.sup.bb).sub.2, OP(O)(NR.sup.bb).sub.2, NR.sup.bbP(O)(OR.sup.cc).sub.2, NR.sup.bbP(O)(NR.sup.bb).sub.2, P(R.sup.cc).sub.2, P(R.sup.cc).sub.3, OP(R.sup.cc).sub.2, B(R.sup.aa).sub.2, B(OR.sup.cc).sub.2, BR.sup.aa(OR.sup.cc), C.sub.1-10 alkyl, C.sub.1-10 perhaloalkyl, C.sub.2-10 alkenyl, C.sub.2-10 alkynyl, heteroC.sub.1-10 alkyl, heteroC.sub.2-10 alkenyl, heteroC.sub.2-10 alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd groups; or two geminal hydrogens on a carbon atom are replaced with the group O, S, NN(R.sup.bb).sub.2, NNR.sup.bbC(O)R.sup.aa, NNR.sup.bbC(O)OR.sup.aa, NNR.sup.bbS(O).sub.2R.sup.aa, NR.sup.bb, or NOR.sup.cc; each instance of R.sup.aa is, independently, selected from C.sub.1-10 alkyl, C.sub.1-.sub.10 perhaloalkyl, C.sub.2-10 alkenyl, C.sub.2-10 alkynyl, heteroC.sub.1-10 alkyl, heteroC.sub.2-10alkenyl, heteroC.sub.2-10alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, or two R.sup.aa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd groups; each instance of R.sup.bb is, independently, selected from hydrogen, OH, OR.sup.aa, N(R.sup.cc).sub.2, CN, C(O)R.sup.aa, C(O)N(R.sup.cc).sub.2, CO.sub.2R.sup.aa, SO.sub.2R.sup.aa, C(NR.sup.cc)OR.sup.aa, C(NR.sup.cc)N(R.sup.cc).sub.2, SO.sub.2N(R.sup.cc).sub.2, SO.sub.2R.sup.cc, SO.sub.2OR.sup.cc, SOR.sup.aa, C(S)N(R.sup.cc).sub.2, C(O)SR.sup.cc, C(S)SR.sup.cc, P(O).sub.2R.sup.aa, P(O)(R.sup.aa).sub.2, P(O).sub.2N(R.sup.cc).sub.2, P(O)(NR.sup.cc).sub.2, C.sub.1-10 alkyl, C.sub.1-10 to perhaloalkyl, C.sub.2-10 alkenyl, C.sub.2-10 alkynyl, heteroC.sub.1-10alkyl, heteroC.sub.2-10alkenyl, heteroC.sub.2-10alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, or two R.sup.bb groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd groups; each instance of R.sup.cc is, independently, selected from hydrogen, C.sub.1-10 alkyl, C.sub.1-10 perhaloalkyl, C.sub.2-10 alkenyl, C.sub.2-10 alkynyl, heteroC.sub.1-10 alkyl, heteroC.sub.2-10 alkenyl, heteroC.sub.2-10 alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, or two R.sup.cc groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd groups; each instance of R.sup.dd is, independently, selected from halogen, CN, NO.sub.2, N.sub.3, SO.sub.2H, SO.sub.3H, OH, OR.sup.ee, ON(R.sup.ff).sub.2, N(R.sup.ff).sub.2, N(R.sup.ff).sub.3.sup.+X.sup., N(OR.sup.ee)R.sup.ff, SH, SR.sup.ee, SSR.sup.ee, C(O)R.sup.ee, CO.sub.2H, CO.sub.2R.sup.ee, OC(O)R.sup.ee, OCO.sub.2R.sup.ee, C(O)N(R.sup.ff).sub.2, OC(O)N(R.sup.ff).sub.2, NR.sup.ffC(O)R.sup.ee, NR.sup.ffCO.sub.2R.sup.ee, NR.sup.ffC(O)N(R.sup.ff).sub.2, C(NR.sup.ff)OR.sup.ee, OC(NR.sup.ff)R.sup.ee, OC(NR.sup.ff)OR.sup.ee, C(NR.sup.ff)N(R.sup.ff).sub.2, OC(NR.sup.ff)N(R.sup.ff).sub.2, NR.sup.ffC(NR.sup.ff)N(R.sup.ff).sub.2, NR.sup.ffSO.sub.2R.sup.ee, SO.sub.2N(R.sup.ff).sub.2, SO.sub.2R.sup.ee, SO.sub.2OR.sup.ee, OSO.sub.2R.sup.ee, S(O)R.sup.ee, Si(R.sup.ee).sub.3, OSi(R.sup.ee).sub.3, C(S)N(R.sup.ff).sub.2, C(O)SR.sup.ee, C(S)SR.sup.ee, SC(S)SR.sup.ee, P(O).sub.2R.sup.ee, P(O)(R.sup.ee).sub.2, OP(O)(R.sup.ee).sub.2, OP(O)(OR.sup.ee).sub.2, C.sub.1-6 alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6 alkenyl, C.sub.2-6 alkynyl, heteroC.sub.1-6alkyl, heteroC.sub.2-6alkenyl, heteroC.sub.2-6alkynyl, C.sub.3-10 carbocyclyl, 3-10 membered heterocyclyl, C.sub.6-10 aryl, 5-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.gg groups, or two geminal R.sup.dd substituents can be joined to form O or S; each instance of R.sup.ee is, independently, selected from C.sub.1-6 alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6 alkenyl, C.sub.2-6 alkynyl, heteroC.sub.1-6 alkyl, heteroC.sub.2-6alkenyl, heteroC.sub.2-6 alkynyl, C.sub.3-10 carbocyclyl, C.sub.6-10 aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.gg groups; each instance of R.sup.ee is, independently, selected from hydrogen, C.sub.1-6 alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6 alkenyl, C.sub.2-6 alkynyl, heteroC.sub.1-6alkyl, heteroC.sub.2-6alkenyl, heteroC.sub.2-6alkynyl, C.sub.3-10 carbocyclyl, 3-10 membered heterocyclyl, C.sub.6-10 aryl and 5-10 membered heteroaryl, or two R.sup.ff groups are joined to form a 3-10 membered heterocyclyl or 5-10 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.gg groups; and each instance of R.sup.gg is, independently, halogen, CN, NO.sub.2, SO.sub.2H, SO.sub.3H, OH, OC.sub.1-6 alkyl, ON(C.sub.1-6 alkyl).sub.2, N(C.sub.1-6 alkyl).sub.2, N(C.sub.1-6 alkyl).sub.3.sup.+X.sup., NH(C.sub.1-6 alkyl).sub.2.sup.+X.sup., NH.sub.2(C.sub.1-6 alkyl).sup.+X.sup., NH.sub.3.sup.+X.sup., N(OC.sub.1-6 alkyl)(C.sub.1-6 alkyl), N(OH)(C.sub.1-6alkyl), NH(OH), SH, SC.sub.1-6 alkyl, SS(C.sub.1-6 alkyl), C(O)(C.sub.1-6 alkyl), CO.sub.2H, CO.sub.2(C.sub.1-6 alkyl), OC(O)(C.sub.1-6 alkyl), OCO.sub.2(C.sub.1-6 alkyl), C(O)NH.sub.2, C(O)N(C.sub.1-6 alkyl).sub.2, C(O)NH(C.sub.1-6 alkyl), NHC(O)(C.sub.1-6 alkyl), N(C.sub.1-6 alkyl)C(O)(C.sub.1-6 alkyl), NHCO.sub.2(C.sub.1-6 alkyl), NHC(O)N(C.sub.1-6 alkyl).sub.2, NHC(O)NH(C.sub.1-6 alkyl), NHC(O)NH.sub.2, C(NH)O(C.sub.1-6 alkyl), OC(NH)(C.sub.1-6 alkyl), OC(NH)OC.sub.1-6 alkyl, C(NH)N(C.sub.1-6 alkyl).sub.2, C(NH)NH(C.sub.1-6 alkyl), C(NH)NH.sub.2, OC(NH)N(C.sub.1-6 alkyl).sub.2, OC(NH)NH(C.sub.1-6 alkyl), OC(NH)NH.sub.2, NHC(NH)N(C.sub.1-6 alkyl).sub.2, NHC(NH)NH.sub.2, NHSO.sub.2(C.sub.1-6 alkyl), SO.sub.2N(C.sub.1-6 alkyl).sub.2, SO.sub.2NH(C.sub.1-6 alkyl), SO.sub.2NH.sub.2, SO.sub.2C.sub.1-6 alkyl, SO.sub.2C.sub.1-6 alkyl, OSO.sub.2C.sub.1-6 alkyl, SOC.sub.1-6 alkyl, Si(C.sub.1-6 alkyl).sub.3, OSi(C.sub.1-6 alkyl).sub.3C(S)N(C.sub.1-6 alkyl).sub.2, C(S)NH(C.sub.1-6 alkyl), C(S)NH.sub.2, C(O)S(C.sub.1-6 alkyl), C(S)SC.sub.1-6 alkyl, SC(S)SC.sub.1-6 alkyl, P(O).sub.2(C.sub.1-6 alkyl), P(O)(C.sub.1-6 alkyl).sub.2, PP(O)(C.sub.1-6 alkyl).sub.2, OP(O)(OC.sub.1-6 alkyl).sub.2, C.sub.1-6 alkyl, perhaloalkyl, C.sub.2-6 alkenyl, C.sub.2-6 alkynyl, heteroC.sub.1-6alkyl, heteroC.sub.2-6alkenyl, heteroC.sub.2-6alkynyl, C.sub.3-10 carbocyclyl, C.sub.6-10 aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or two geminal R.sup.gg substituents can be joined to form O or S; wherein X.sup. is a counterion.
(49) In certain embodiments, the carbon atom substituents are independently halogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, OR.sup.aa, SR.sup.aa, N(R.sup.bb).sub.2, CN, SCN, NO.sub.2, C(O)R.sub.aa, CO.sub.2R.sup.aa, C(O)N(R.sup.bb).sub.2, OC(O)R.sup.aa, OCO.sub.2R.sup.aa, OC(O)N(R.sup.bb).sub.2, NR.sup.bbC(O)R.sup.aa, NR.sup.bbCO.sub.2R.sup.aa, or NR.sup.bbC(O)N(R.sup.bb).sub.2. In certain embodiments, the carbon atom substituents are independently halogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, OR.sup.aa, SR.sup.aa, N(R.sup.bb).sub.2, CN, SCN, NO.sub.2, C(O)R.sup.aa, CO.sub.2R.sup.aa, C(O)N(R.sup.bb).sub.2, OC(O)R.sup.aa, OCO.sub.2R.sup.aa, OC(O)N(R.sup.bb).sub.2, NR.sup.bbC(O)R.sup.aa, NR.sup.bbCO.sub.2R.sup.aa, or NR.sup.bbC(O)N(R.sup.bb).sub.2, wherein R.sup.aa is hydrogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, an oxygen protecting group (e.g., silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl) when attached to an oxygen atom, or a sulfur protecting group (e.g., acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl) when attached to a sulfur atom; and each R.sup.bb is independently hydrogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, or a nitrogen protecting group (e.g., Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts). In certain embodiments, the carbon atom substituents are independently halogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, OR.sup.aa, N(R.sup.bb).sub.2, CN, SCN, or NO.sub.2. In certain embodiments, the carbon atom substituents are independently halogen, substituted (e.g., substituted with one or more halogen moieties) or unsubstituted C.sub.1-6 alkyl, OR.sup.aa, SR.sup.aa, N(R.sup.bb).sub.2, CN, SCN, or NO.sub.2, wherein R.sup.aa is hydrogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, an oxygen protecting group (e.g., silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl) when attached to an oxygen atom, or a sulfur protecting group (e.g., acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl) when attached to a sulfur atom; and each R.sup.bb is independently hydrogen, substituted (e.g., substituted with one or more halogen) or unsubstituted C.sub.1-6 alkyl, or a nitrogen protecting group (e.g., Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts).
(50) In certain embodiments, the molecular weight of a carbon atom substituent is lower than 250, lower than 200, lower than 150, lower than 100, or lower than 50 g/mol. In certain embodiments, a carbon atom substituent consists of carbon, hydrogen, fluorine, chlorine, bromine, iodine, oxygen, sulfur, nitrogen, and/or silicon atoms. In certain embodiments, a carbon atom substituent consists of carbon, hydrogen, fluorine, chlorine, bromine, iodine, oxygen, sulfur, and/or nitrogen atoms. In certain embodiments, a carbon atom substituent consists of carbon, hydrogen, fluorine, chlorine, bromine, and/or iodine atoms. In certain embodiments, a carbon atom substituent consists of carbon, hydrogen, fluorine, and/or chlorine atoms.
(51) The term halo or halogen refers to fluorine (fluoro, F), chlorine (chloro, Cl), bromine (bromo, Br), or iodine (iodo, I).
(52) The term oxo refers to the moiety O.
(53) A counterion or anionic counterion is a negatively charged group associated with a positively charged group in order to maintain electronic neutrality. An anionic counterion may be monovalent (i.e., including one formal negative charge). An anionic counterion may also be multivalent (i.e., including more than one formal negative charge), such as divalent or trivalent. Exemplary counterions include halide ions (e.g., F.sup., Cl.sup., Br.sup., I.sup.), NO.sub.3.sup., ClO.sub.4.sup., OH.sup., H.sub.2PO.sub.4.sup., HCO.sub.3.sup., HSO.sub.4.sup., sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic acid-2-sulfonate, and the like), carboxylate ions (e.g., acetate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, gluconate, and the like), BF.sub.4.sup., PF.sub.4.sup., PF.sub.6.sup., AsF.sub.6.sup., SbF.sub.6.sup., B[3,5-(CF.sub.3).sub.2C.sub.6H.sub.3].sub.4].sup., B(C.sub.6F.sub.5).sub.4.sup., BPh.sub.4.sup., Al(OC(CF.sub.3).sub.3).sub.4.sup., and carborane anions (e.g., CB.sub.11H.sub.12.sup. or (HCB.sub.11Me.sub.5Br.sub.6).sup.). Exemplary counterions which may be multivalent include CO.sub.3.sup.2, HPO.sub.4.sup.2, PO.sub.4.sup.3, B.sub.4O.sub.7.sup.2, SO.sub.4.sup.2, S.sub.2O.sub.3.sup.2, carboxylate anions (e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like), and carboranes.
EXAMPLES
Example 1
Sensing Intracellular Calcium Ions Using a Manganese-Based MRI Contrast Agent Building Block for Intracellular MRI Calcium Sensors
(54) To examine the potential of Mn-PDA contrast agents to function as building blocks for the sensor design of
(55) Mixtures of MnL1 and MnL3 with BAPTA both showed calcium-dependent MRI properties. The spectroscopic behavior of MnL1 and MnL3 in the presence of BAPTA over time was examined, and it was found that the MnL1-containing mixture displayed sharp changes indicative of degradation, while the MnL3 mixture remained unperturbed and apparently stable (
Synthesis and Characterization of ManICS1 and ManICS1-AM
(56) To form a first manganese-based intracellular calcium sensor (ManICS1) from MnL3 and BAPTA, ManICS1 and its AM ester derivative ManICS1-AM were synthesized using a series of multistep reactions starting from 5-methyl-2-nitrophenol (1) (
(57) The calcium responsiveness of ManICS 1 was measured in buffer by titrating the compound with calcium chloride over a concentration range relevant to intracellular signaling. Images indicated clear enhancement of T.sub.1-weighted MRI intensity as calcium ions were added. (
(58) To probe the mechanism of calcium sensing by ManICS1, a series of experiments were performed. The apparent calcium affinity of the probe was relatively low for the BAPTA derivative that was used, which in the context of fluorescent sensors generally confers calcium binding with submicromolar calcium K.sub.d values. To further evaluate calcium sensing, a manganese-free ManICS1 analog was formed and its calcium affinity was measured by titration with a spectroscopic readout. A separate calcium titration series was also performed with three different concentrations of ManICS1. Data from the three datasets produced K.sub.d estimates that did not differ significantly from one another.
(59) To demonstrate that the ester groups of ManICS1-AM are capable of undergoing cleavage in the cytosolic milieu, the compound was incubated in clarified cell lysate (10% by volume) and the high performance liquid chromatography (HPLC) time course was compared to that of ManICS1 and ManICS1-AM incubated in buffer alone. It was found that five hours of exposure to cell lysate was sufficient to result in complete conversion of the ManICS1-AM HPLC peak into a product that eluted at the same time as ManICS1 (
ManICS1-AM Labeled Cells and Enabled Intracellular Calcium-Sensitive MRI
(60) To validate the potential for ManICS1-AM to enable readouts of intracellular calcium by T.sub.1-weighted MRI, the ability of ManICS1-AM to label cells and subsequently be retained was first examined. Cultured HEK293 cells were incubated with ManICS1-AM or ManICS1 followed by washing and then MRI analysis. It was found that cells incubated with the two agents underwent a comparable increase in R, compared with control cells (
(61) To assess the potential for internalized ManICS1 to transduce cytosolic calcium concentrations into R.sub.1 changes detectable by MRI, cultured HEK293 cells were labeled again with ManICS1-AM and then challenged with stimuli known to elevate intracellular [Ca.sup.2+]. Cells treated with thapsigargin and carbachol did not show elevated R.sub.1, whereas addition of calcimycin or arachidonic acid produced substantial increases in mean R.sub.1. The same four stimulants were applied separately to cells prelabeled with the fluorescent calcium indicator derivative Fura-2-AM. Fluorescence ratio measurements from these cells closely paralleled the results obtained by MRI analysis of ManICS1-AM-labeled cells, indicating that the variable MRI results were indicative of actual intracellular calcium responses.
(62) As a further test of the calcium-dependent contrast properties conferred by ManICS1-AM, intracellular calcium levels were titrated and the profile of resulting R.sub.1 changes was examined. Intracellular calcium levels were regulated by controlling extracellular calcium using a standard buffering system in the presence of the ionophore calcimycin, which equilibrates calcium levels across the cell membrane. Results demonstrated progressive changes in R.sub.1 as [Ca.sup.2+] ranged from 1 micromolar (M) to 100 micromolar (M), establishing a midpoint (EC.sub.50) for intracellular calcium sensing by ManICS1 of about 5 micromolar (M) (
(63) These results showed MRI-based measurement of intracellular calcium using a manganese-based MRI contrast agent that parallelled properties of fluorescent probes for cytosolic Ca.sup.2+ imaging. In this work, ManICS1 was synthesized, which incorporated membrane-permeable building blocks and involved the AM ester-based approach for cell labeling and intracellular trapping of the probe. ManICS1 reported calcium levels analogously to the widely used optical calcium sensor Fura-2. The novel probe may be used for MRI-based spatiotemporal mapping of calcium signaling processes in contexts where optical imaging approaches have previously been successful.
Example 2
Methods and Materials
Magnetic Resonance Imaging
(64) Most MRI data were acquired on a 7 T Bruker Biospec0 system using a T.sub.1-weighted 2D gradient echo sequence (echo time, TE=5 ms, repetition time, TR=100 ms; flip angle, FA=65 degrees ()). Longitudinal relaxivity (r.sub.1) measurements were acquired using a 2D spin echo sequence (TE=11 ms, TR=125, 200, 400, 800, 1500, 3000, and 5000 ms), with in-plane resolution of 200200 microns squared ((m).sup.2) and 2 mm slice thickness. R.sub.1 maps and values were generated using an MRI Analysis Calculator Plugin for ImageJ (National Institutes of Health, Bethesda, Md.) or Matlab scripts (Mathworks, Natick, Mass.). Stimulus-dependent R.sub.1 changes in cells were calculated as R.sub.1/R.sub.1=[R.sub.1(incubated cells)R.sub.1(naive cells)]/R.sub.1(naive cells). Statistical comparisons between paired conditions were performed using Student's t-test, and all error bars denote the standard error of the mean from multiple measurements, unless otherwise noted.
In Vitro Characterization of ManICS1 and ManICS1-AM
(65) ManICS1, calcium, and magnesium stock solutions were all prepared in 25 mM 3-(N-morpholino)propanesulfonic acid (MOPS), pH 7.4, with 100 mM KCl. Titration series were prepared as separate triplicates for each data point in the presence of constant concentrations of ManICS1, confirmed subsequently by ICP-OES analysis. Samples were arrayed into microtiter plates and measured by MRI using a Bruker (Billerica, Mass.) Avance 7 T scanner. Unused wells were filled with buffer, and imaging was performed on a 2 mm slice through the sample. Calcium affinity of manganese-free ManICS1 was determined using optical spectroscopy.
Cell Labeling with ManICS1-AM
(66) HEK293 cells (Freestyle 293-F, Thermo Fischer Scientific, Waltham, Mass.) were cultured and prepared for relaxometry. To assess uptake, cells were exposed to contrast agents in media for 30 min, washed with Hank's buffered saline solution (HBSS), and then immediately pelleted by centrifugation at 750 g for imaging, incubated in media again for varying time intervals, or stimulated with pharmacological agents. Subcellular fractionation analysis of ManICS1-AM-labeled cells was conducted. Cells were incubated with agent for 30 min, washed in HBSS and permeablized on ice with saponin to collect cytosolic fractions for analysis with ICP-OES.
Measurement of Intracellular Calcium Responses
(67) For stimulation experiments, cells were incubated with 10 micromolar (M) ManICS1-AM for 2 h for labeling and AM ester cleavage. Pharmacological stimulation was conducted by adding 10 micromolar (M) thapsigargin, 5 micromolar (M) charbocol, 5 micromolar (M) calcimycin, or 10 micromolar (M) arachidonic acid (Sigma-Aldrich, St. Louis, Mo.). To test reversibility of the calcium response, cells were prepared with ManICS1-AM and 5 micromolar (M) calcimycin maintained for the duration of the experiment, washed in calcium free media, divided into two aliquots to be washed again or returned to 2 mM Ca.sup.2+. For the titration curve cells were maintained in 5 micromolar (M) calcimycin first in 100 volume calcium-free buffer, then while incubated in 100 volume media with 0-1 mM calcium for 1.5 min at 37 degrees Celsius ( C.).
(68) For comparison stimulation measurements performed with Fura-2, adherent HEK293 cells were seeded onto a 96 well plate at 5,000 cells/well and grown for two days until 90% confluent. Cells were then incubated for 45 min in 10 micromolar (M) Fura-2 and then washed with media. Stimulants (10 micromolar (M) thapsigargin, 5 micromolar charbocol, 5 micromolar (M) calcimycin, or 10 micromolar (M) arachidonic acid) were quickly added to multiple wells via multipipettor and fluorescence output was measured using a plate reader. Measurements were repeated every 5 minutes for 40 minutes to chart the time course of calcium concentration changes at room temperature.
Example 3
ManICS1-AM Labels Cells and Enables Intracellular Calcium-Sensitive MRI
(69) To test the ability of ManICS1-AM to enable readouts of intracellular calcium by T.sub.1-weighted MRI, its propensity was first examined to accumulate within cells. Cultured HEK293 cells were incubated with 10 M ManICS1-AM or ManICS1 for 30 minutes, followed by washing and MRI analysis (
(70) To assess the potential for internalized ManICS1 to report stimulus-induced cytosolic calcium concentrations as changes detectable by MRI, HEK293 cells were again labeled with ManICS1-AM; then the cells were challenged with pharmacological agents that elevate cytosolic calcium levels (
(71) To examine the reversibility and dynamics of ManICS1-based calcium sensing the optogenetic Ca.sup.2+ actuator BACCS2 was used to stimulate contrast agent-labeled cells while performing functional imaging with MRI. In preparation for these experiments, cells were embedded in a gel matrix that permitted effective Ca.sup.2+ exchange at high cell density. BACCS2-expressing cells loaded with ManICS1-AM showed dynamic light-dependent image changes averaging 0.80.2% in amplitude (
Example 4
ManICS1-AM Permits Detection of Deep Brain Activation in Rats
(72) To determine whether ManICS1-AM could enable detection of intracellular calcium signals in vivo, the probe was injected into the brains of adult rats and responses were examined to stimulation with potassium ions, which induce neural depolarization and calcium concentration changes in brain tissue. Intracranial infusion of ManICS1-AM into the striatum resulted in substantial T.sub.1-weighted MRI signal enhancement over a 4 mm diameter region around the injection site, as well as more remote tissue along the ventricles (
(73) Infusion of artificial cerebrospinal fluid (aCSF) formulated isotonically with 125 mM KCl elicited a robust signal change proximal to the infusion site in ManICS1-AM-infused brain areas (
(74) These experiments thus demonstrate a cell-permeable manganese-based MRI contrast agent that emulates properties of fluorescent probes for cytosolic Ca.sup.2+ imaging, and that can detect signaling events in deep tissue. The ManICS1 calcium sensor introduced here incorporates membrane-permeable building blocks and can exploit the AM ester-based approach for cell labeling and cytosolic trapping of the probe. Upon internalization, ManICS1-AM reports calcium levels consistent with readouts from optical calcium sensors and compatible with T.sub.1-weighted functional MRI in rat brain, suggesting that the new probe could be used for spatiotemporal mapping of calcium signaling processes previously accessible only to optical imaging approaches, but with the expanded depth and field of view afforded by MRI.
(75) While several embodiments of the present invention have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the functions and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the present invention. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the teachings of the present invention is/are used. 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. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, the invention may be practiced otherwise than as specifically described and claimed. The present invention is directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the scope of the present invention.
(76) The indefinite articles a and an, as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean at least one.
(77) The phrase and/or, as used herein in the specification and in the claims, should be understood to mean either or both of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Other elements may optionally be present other than the elements specifically identified by the and/or clause, whether related or unrelated to those elements specifically identified unless clearly indicated to the contrary. Thus, as a non-limiting example, a reference to A and/or B, when used in conjunction with open-ended language such as comprising can refer, in one embodiment, to A without B (optionally including elements other than B); in another embodiment, to B without A (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.
(78) As used herein in the specification and in the claims, or should be understood to have the same meaning as and/or as defined above. For example, when separating items in a list, or or and/or shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as only one of or exactly one of, or, when used in the claims, consisting of, will refer to the inclusion of exactly one element of a number or list of elements. In general, the term or as used herein shall only be interpreted as indicating exclusive alternatives (i.e. one or the other but not both) when preceded by terms of exclusivity, such as either, one of, only one of, or exactly one of. Consisting essentially of, when used in the claims, shall have its ordinary meaning as used in the field of patent law.
(79) As used herein in the specification and in the claims, the phrase at least one, in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase at least one refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, at least one of A and B (or, equivalently, at least one of A or B, or, equivalently at least one of A and/or B) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.
(80) In the claims, as well as in the specification above, all transitional phrases such as comprising, including, carrying, having, containing, involving, holding, and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases consisting of and consisting essentially of shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.