[3.2.0] Heterocyclic compounds and methods of using the same

1. A compound having the structure of Formula I, and pharmaceutically acceptable salts and pro-drug esters thereof:

wherein the dashed line indicates that the designated bond is either a single bond or a double bond, and wherein R 1 is separately selected from the group consisting of a hydrogen, a mono-substituted or poly-substituted saturated C 1 -C 24 alkyl, mono-substituted, poly-substituted or unsubstituted variants of the following residues: C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl,

wherein the mono-substituted or poly-substituted saturated C 1 -C 24 alkyl in R 1 is substituted with one or more substituents selected from the group consisting of alkoxy, substituted alkoxy, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl, acylamino, amino, substituted amino, aminoacyl, aminoacyloxy, oxyacylamino, cyano, halogen, carboxyl, carboxylalkyl, keto, thioketo, thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl, heteroaryloxy, heterocyclic, heterocyclooxy, hydroxyamino, alkoxyamino, nitro, —SO-alkyl, —SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO 2 -alkyl, —SO 2 -substituted alkyl, —SO 2 -aryl and —SO 2 -heteroaryl;

wherein the halogenated alkyl in R 1 is a C 1-24 -alkyl poly-halogenated with fluorine, bromine, chlorine or iodine; or

the halogenated alkyl is methyl or C 3-24 -alkyl mono-or poly-halogenated with fluorine, bromine, or iodine;

where n is equal to 1 or 2, and if n is equal to 2, then R 1 can be the same or different, and at least one R 1 is not hydrogen;

wherein R 2 is selected from the group consisting of hydrogen, a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarboyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein R 3 is selected from the group consisting of a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarboyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate esters, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein each of E 1 and E 3 is a substituted or unsubstituted heteroatom selected from the group consisting of O and S, E 2 is a substituted or unsubstituted N, and E 4 is a substituted or unsubstituted heteroatom selected from the group consisting of O, S, and N; and

with the proviso that Formula I is not Compound II-16,

wherein Compound II-16 has the structure:

2. A compound having the structure of Formula II, and pharmaceutically acceptable salts and pro-drug esters thereof:

wherein the dashed lines indicates that the designated bond is either a single bond or a double bond, and wherein R 1 is separately selected from the group consisting of a hydrogen, a mono-substituted or poly-substituted saturated C 1 -C 24 alkyl, mono-substituted, poly-substituted or unsubstituted variants of the following residues: C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl,

wherein the mono-substituted or poly-substituted saturated C 1 -C 24 alkyl in R 1 is substituted with one or more substituents selected from the group consisting of alkoxy, substituted alkoxy, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl, acylamino, amino, substituted amino, aminoacyl, aminoacyloxy, oxyacylamino, cyano, halogen, carboxyl, carboxylalkyl, keto, thioketo, thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl, heteroaryloxy, heterocyclic, heterocyclooxy, hydroxyamino, alkoxyamino, nitro, —SO-alkyl, —SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO 2 -alkyl, —SO 2 -substituted alkyl, —SO 2 -aryl and —SO 2 -heteroaryl;

wherein the halogenated alkyl in R 1 is a C 1-24 -alkyl poly-halogenated with fluorine, bromine, chlorine or iodine; or

the halogenated alkyl is methyl or C 3-24 -alkyl mono-or poly-halogenated with fluorine, bromine, or iodine;

where n is equal to 1 or 2, and if n is equal to 2, then R 1 can be the same or different, and at least one R 1 is not hydrogen;

wherein R 3 is selected from the group consisting of a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarboyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein R 4 is separately selected from the group consisting of a hydrogen, a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarboyloxy, nitro, azido, phenyl, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl, and m is equal to 1 or 2, and if m is equal to 2, then R 4 can be the same or different;

wherein each of E 1 and E 3 is a substituted or unsubstituted heteroatom selected from the group consisting of O and S, E 2 is a substituted or unsubstituted N, and each E 4 and E 5 are a substituted or unsubstituted heteroatom selected from the group consisting of O, S, and N; and

with the proviso that Formula II is not Compound II-16,

wherein Compound II-16 has the structure:

3. The compound of claim 2 , wherein E 5 is selected from the group consisting of OH, O, S, N, NH, NH 2 , NOH, NHOH, OR 10 , SR 11 , NR 12 , and NHOR 13 , wherein R 10 , R 11 , R 12 , and R 13 each is separately selected from the group consisting of hydrogen, and a substituted or unsubstituted alkyl, acyl, aryl, and heteroaryl.

4. The compound of claim 2 , wherein E 5 is OH.

5. The compound of claim 2 , wherein each of E 1 , E 3 and E 4 is O and E 2 is NH.

6. The compound of claim 2 , wherein R 3 is methyl.

7. The compound of claim 2 , wherein R 4 is an unsubstituted or substituted cycloalkyl.

8. The compound of claim 2 , wherein at least one R 4 is an unsubstituted or substituted cycloalkyl and E 5 is an oxygen.

9. The compound of claim 2 , wherein at least one R 4 is a di-substituted cyclohexane.

10. The compound of claim 2 , wherein at least one R 4 is a substituted or an unsubstituted branched C 4 -C 24 alkyl.

11. The compound of claim 2 , wherein:

at least one R 4 is

wherein R 5 is separately selected from the group consisting of a hydrogen, a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, oxy, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl, and

m′ is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 and if m′ is more than 1, then R 5 can be the same or different; and where the substituents R 5 can form a ring.

12. The compound of claim 11 , wherein R 3 is methyl.

13. A compound having the structure of Formula I, and pharmaceutically acceptable salts and pro-drug esters thereof:

wherein the dashed line indicates that the designated bond is either a single bond or a double bond, and wherein R 1 is separately selected from the group consisting of a hydrogen, a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl,

where n is equal to 1 or 2, and if n is equal to 2, then R 1 can be the same or different, and at least one R 1 is not hydrogen;

wherein R 2 is selected from the group consisting of a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein R 3 is selected from the group consisting of a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein each of E 1 , and E 3 is a substituted or unsubstituted heteroatom selected from the group consisting of O and S, E 2 is a substituted or unsubstituted N, and E 4 is a substituted or unsubstituted heteroatom selected from the group consisting of O, S, and N; and

with the proviso that Formula II is not Compound II-16,

wherein Compound II-16 has the structure:

14. A compound having the structure of Formula II, and pharmaceutically acceptable salts and pro-drug esters thereof:

wherein the dashed lines indicates that the designated bond is either a single bond or a double bond, and wherein R 1 is separately selected from the group consisting of a hydrogen, a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl,

where n is equal to 1 or 2, and if n is equal to 2, then R 1 can be the same or different, and at least one R 1 is not hydrogen;

wherein R 3 is selected from the group consisting of a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein R 4 is separately selected from the group consisting of a hydrogen, a halogen, a mono-substituted or poly-substituted variant of the following residues: C 1 -C 24 saturated alkyl, cycloalkyl, cycloalkenyl and aryl, a mono-substituted, poly-substituted or unsubstituted variants of the following residues: unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, alkoxy, cycloalkoxy, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl, and m is equal to 1 or 2, and if m is equal to 2, then R 4 can be the same or different;

wherein the mono-substituted or poly-substituted saturated C 1 -C 24 alkyl, cycloalkyl, cycloalkenyl or aryl in R 4 is substituted with one or more substituents selected from the group consisting of alkoxy, substituted alkoxy, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aminoacyloxy, oxyacylamino, cyano, halogen, carboxyl, carboxylalkyl, keto, thioketo, thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl, heteroaryloxy, heterocyclic, heterocyclooxy, hydroxyamino, alkoxyamino, nitro, —SO-alkyl, —SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO 2 -alkyl, —SO 2 -substituted alkyl, —SO 2 -aryl and —SO 2 -heteroaryl;

wherein each of E 1 and E 3 is a substituted or unsubstituted heteroatom selected from the group consisting of O and S, E 2 is a substituted or unsubstituted N, and each E 4 and E 5 are a substituted or unsubstituted heteroatom selected from the group consisting of O, S, and N; and

with the proviso that Formula II is not Compound II-16,

wherein Compound II-16 has the structure:

15. The compound of claim 14 , wherein each of E 1 , E 3 and E 4 is O and E 2 is NH.

16. The compound of claim 14 , wherein R 3 is methyl.

17. The compound of claim 14 , wherein n is equal to 1 or 2, and where n is equal to 2, at least one R 1 is CH 2 CH 2 X, wherein X is selected from the group consisting of H, F, Cl, Br, and I.

18. The compound of claim 14 , wherein:

n is equal to 2;

at least one of the R 1 substituents is hydrogen and the other R 1 substituent is CH 2 CH 2 X, wherein X is selected from the group consisting of H, F, Cl Br, and I;

R 3 is methyl;

at least one R 4 is a substituted cyclohexane;

each of E 1 , E 3 and E 4 is O and E 2 is NH; and

E 5 is OH.

19. The compound of claim 14 , wherein R 1 is a substituted C 1 to C 5 alkyl.

20. The compound of claim 14 , wherein E 5 is OH.

21. A pharmaceutical composition comprising at least one compound of claim 14 .

22. A compound having the structure of Formula II, and pharmaceutically acceptable salts and pro-drug esters thereof:

wherein the dashed lines indicates that the designated bond is either a single bond or a double bond, and wherein R 1 is separately selected from the group consisting of a hydrogen; a halogen; azidoethyl; thiocyanatoethyl; boronic acid(C 0-6 alkyl); boronic ester(C 0-6 alkyl); hydroxyethyl; an unsubstituted saturated C 2-3 alkyl; a mono-substituted or poly-substituted C 1-24 alkyl substituted with one or more substituents selected from the group consisting of alkoxy, substituted alkoxy, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyloxy, oxyacylamino, cyano, carboxyl, carboxylalkyl, keto, thioketo, thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl, heteroaryloxy, heterocyclic, heterocyclooxy, hydroxyamino, alkoxyamino, nitro, sulfonate ester, —SO-alkyl, —SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO 2 -alkyl, —SO 2 -substituted alkyl, —SO 2 -aryl and —SO 2 -heteroaryl; and mono-substituted, poly-substituted or unsubstituted variants of the following residues: unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarboyloxy, nitro, azido, phenyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

where n is equal to 1 or 2, and if n is equal to 2, then R 1 can be the same or different, and at least one R 1 is not hydrogen;

wherein R 3 is selected from the group consisting of a halogen, mono-substituted, poly-substituted or unsubstituted variants of the following residues: saturated C 1 -C 24 alkyl, unsaturated C 2 -C 24 alkenyl, C 2 -C 24 alkynyl, acyl, acyloxy, alkyloxycarbonyloxy, aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, alkoxy, cycloalkoxy, aryl, heteroaryl, arylalkoxy carbonyl, alkoxy carbonylacyl, amino, aminocarbonyl, aminocarbonyloxy, nitro, azido, phenyl, cycloalkylacyl, hydroxy, alkylthio, arylthio, oxysulfonyl, carboxy, cyano, thio, sulfoxide, sulfone, sulfonate ester, thiocyano, boronic acid, boronic ester, and halogenated alkyl including polyhalogenated alkyl;

wherein R 4 is separately selected from the group consisting of a hydrogen, and an unsubstituted, a mono-substituted or poly-substituted cycloalkyl, cycloalkenyl, and aryl, and m is equal to 1 or 2, and if m is equal to 2, then R 4 can be the same or different;

wherein each of E 1 and E 3 is a substituted or unsubstituted heteroatom selected from the group consisting of O and S, E 2 is a substituted or unsubstituted N, and each E 4 and E 5 are a substituted or unsubstituted heteroatom selected from the group consisting of O, S, and N; and

with the proviso that Formula II is not Compound II-16,

wherein Compound II-16 has the structure:

23. The compound of claim 22 , wherein the compound of Formula II is selected from the group consisting of:

and, wherein R 8 is selected from the group consisting of H, F, Cl, Br and I.

24. The compound of claim 22 , wherein the compound of Formula II is selected from the group consisting of:

wherein when the compound of Formula II is the compound II-3 9 or the compound II-40, then R is selected from the group consisting of H, unsubstituted alkyl, substituted alkyl, unsubstituted aryl and substituted aryl;

wherein: when the compound of Formula II is the compound II-42, then n is 0, 1, 2, 3, 4, 5 or 6, and each R is independently selected from the group consisting of H and alkyl.

25. A compound having the following structure, and pharmaceutically acceptable salts and pro-drug esters thereof:

wherein R 8 is selected from the group consisting of fluorine, chlorine, bromine and iodine.

26. The compound of claim 25 , where R 8 is chlorine.