# Patent

## Title
Antimicrobial compounds and methods of making and using the same

## Abstract

The present invention relates generally to the field of antimicrobial compounds and to methods of making and using them. These compounds are useful for treating, preventing, and reducing the risk of microbial infections in humans and animals.

## Background
RELATED APPLICATIONS
The present application is a national stage application, filed under 35 U.S.C. §371, of International Application No. PCT/US2012/032994, filed on Apr. 11, 2012, which claims priority to and the benefit of U.S. provisional application No. 61/476,138, filed Apr. 15, 2011, U.S. provisional application No. 61/535,118, filed Sep. 15, 2011, and U.S. provisional application No. 61/610,363, filed Mar. 13, 2012. The contents the aforementioned applications are hereby incorporated by reference in their entirety.


FIELD OF THE INVENTION
The present invention relates generally to the field of antimicrobial compounds and to methods of making and using them. These compounds are useful for treating, preventing, and reducing the risk of microbial infections in humans and animals.
BACKGROUND
Since the discovery of penicillin in the 1920s and streptomycin in the 1940s, many new compounds have been discovered or specifically designed for use as antibiotic agents. It was once thought that infectious diseases could be completely controlled or eradicated with the use of such therapeutic agents. However, such views have been challenged because strains of cells or microorganisms resistant to currently effective therapeutic agents continue to evolve. Almost every antibiotic agent developed for clinical use has ultimately encountered problems with the emergence of resistant bacteria. For example, resistant strains of Gram-positive bacteria such as methicillin-resistant staphylococci, penicillin-resistant streptococci, and vancomycin-resistant enterococci have developed. Resistant bacteria can cause serious and even fatal results for infected patients. See, e.g., Lowry, F. D. “Antimicrobial Resistance: The Example of Staphylococcus aureus,” J. Clin. Invest., vol. 111, no. 9, pp. 1265-1273 (2003); and Gold, H. S. and Moellering, R. C., Jr., “Antimicrobial-Drug Resistance,” N. Engl. J. Med., vol. 335, pp. 1445-53 (1996).
The discovery and development of new antibacterial agents have been for decades a major focus in many pharmaceutical companies. Nonetheless, in more recent years there has been an exodus of pharmaceutical companies from this area of research and drug development. As a consequence of this exodus, there have been very few new antibiotics entering the market. This lack of new antibiotics is particularly disturbing, especially at a time when bacterial resistance to current therapies is increasing both in the hospital and community settings.
In the search for new antibiotic agents, researchers have tried combining or linking various portions of antibiotic molecules to create multifunctional or hybrid compounds Other researchers have tried making derivatives of known classes of antibiotics, e.g., telithromycin, which is sold under the trade name Ketek®, is a derivative of erythromycin. However, these approaches have met with limited success.
An approach to developing new antimicrobial compounds is to design modulators, for example, inhibitors, of bacterial ribosome function. By modulating or inhibiting bacterial ribosome function such antimicrobial compounds could interfere with essential processes such as RNA translation and protein synthesis, thereby providing an antimicrobial effect. In fact, some antibiotic compounds such as erythromycin, clindamycin, and linezolid are known to bind to the ribosome.
The present invention utilizes a structure based drug design approach for discovering and developing new antimicrobial agents. This approach starts with the high resolution X-ray crystal of the ribosome to design new classes of antimicrobial compounds having specific chemical structures, ribosome binding characteristics, and antimicrobial activity. This structure based drug discovery approach is described in the following publication: Franceschi, F. and Duffy, E. M., “Structure-based drug design meets the ribosome”, Biochemical Pharmacology, vol. 71, pp. 1016-1025 (2006).
Based on this structure based drug design approach, the present invention describes new chemical classes of antimicrobial compounds useful for treating bacterial infections in humans and animals. Without being limited by theories, these compounds are believed to inhibit bacterial ribosome function by binding to the ribosome. By taking advantage of these ribosome binding sites, the antimicrobial compounds of the present invention can provide better activity, especially against resistant strains of bacteria, than current antibiotic compounds.
The present invention therefore fills an important ongoing need for providing new antimicrobial agents, particularly for antimicrobial agents, having activity against resistant pathogenic bacterial organisms.
SUMMARY OF THE INVENTION
The present invention relates generally to the field of antimicrobial compounds and to methods of making and using them. These compounds and tautomers thereof are useful for treating, preventing, and reducing the risk of microbial infections in humans and animals. The present invention also provides pharmaceutically acceptable salts, esters, and prodrugs of these compounds and tautomers.
In one aspect, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein
X1 is CR1 or N; X2 is CR2 or N; X3 is CR3 or N; X4 is CR4 or N; X5 is CR5 or N; with the proviso that X1, X2, X3, X4, and X5 are not all N;
Y6 is CR6 or N; Y7 is CR7 or N; Y8 is CR8 or N; Y9 is CR9 or N; Y10 is CR10 or N; with the proviso that Y6, Y7, Y8, Y9, and Y10 are not all N; wherein
R1, R2, R4, R5, R6, R7, R8 and R10 are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) Br, (e) I, (f) —CF3, (g) —CF2H, (h) —CFH2, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —CN, (n) —N3, (o) —NO2, (p) —NR11C(O)R11, (r) —C(O)NR11R11, (s) —OR11, (t) —COH, (u) —CO(C1-C8 alkyl), (v) —COR11, (w) —NR11 (CNR11)NR11R11, (x) —S(O)pR11, (y) —NR11S(O)pR11, (z) —SR11, (aa) —SCF3, (bb) —C(CF3)H—NH—CHR11R11, (cc) —COOR11, (dd) —(OCH2CH2)tR11, (ee) —(OCH2CH2)tOR11, (ff) —C1-C8 alkyl, (gg) —C2-C8 alkenyl, (hh) —C2-C8 alkynyl, (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (jj) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (kk) -haloalkyl, (ll) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (mm) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (nn) —CHR11—NH-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one of more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur);
wherein each (ff) through (nn) is optionally substituted with one or more R12; alternatively, wherein two substituents selected from R6, R7, and R8 are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur; wherein each (a) through (b) is optionally substituted with one or more R12;
each R11 is independently selected from (a) hydrogen, (b) halogen, (c) —OH, (d) —SH, (e) —(C1-C8 alkyl)OH, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —OR12, (k) —COR12, (l) —CN, (m) —NO2, (n) —CONH2, (o) —CONR12R12, (p) —COCH3, (q) —S(O)pCH3, (r) —S(O)pNR12R12, —SR12, (t) —C(O)OH, (u) —C(O)OR12, (v) —N3, (w) —NH2, (x) —NR12C(O)R12, (y) —NH(C1-C8 alkyl), (z) —N(C1-C8 alkyl)2, (aa) —C1-C8 alkyl, (bb) —C2-C8 alkenyl, (cc) —C2-C8 alkynyl, (dd) -haloalkyl, (ee) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ff) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (gg) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (hh) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (ii) —(C═NH)NR12R12;
wherein each (y) through (hh) is optionally substituted with one or more R12;
alternatively two R11 substituents are taken together to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, wherein each (a) through (b) is optionally substituted with one or more R12;
R3 is selected from:




wherein R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l are each independently selected from (a) hydrogen, (b) halogen, (c) —CN, (d) —N3, (e) —NO2, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —OR11, (k) —C(O)R11, (l) —C(O)NR11R11, (m) —NH2, (n) —NR11R11, (o) —NR11C(O)R11, (p) —S(O)pR11, (q) —C(O)OH, (r) —C(O)OR11, (s) —C1-C8 alkyl, (t) —C2-C8 alkenyl, (u) —C2-C8 alkynyl, (v) haloalkyl, (w) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (x) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (s) through (x) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R3a and R3b, R3c and R3d, R3e and R3f, R3g and R3h, R3i and R3j, and R3k and R3l are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or wherein four substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
U is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p—, —NR11S(O)pNR11—, and —NR11C(O)NR11—;
T is selected from —NR11R11, —NR11(C═O)OR11, —NR11(C═NR11)NR11R11, and OR11;
alternatively, one R11 and one substituent selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R9 is selected from:




wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CN, (d) —N3, (e) —NO2, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —OR11, (k) —NH2, (l) —NR11R11, (m) —C(O)R11, (n) —C(O)OR11, (o) —C(O)NR11R11, (p) —NR11C(O)R11, (q) —S(O)pR11, (r) —C1-C8 alkyl, (s) —C2-C8 alkenyl, (t) —C1-C8 alkynyl, (u) haloalkyl, (v) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (w) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (r) through (w) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) 3-7 membered saturated or unsaturated carbocyclic, (b) 3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (c) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or four substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
Z is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p—, —NR11S(O)pNR11—, and —NR11C(O)NR11—;
W is selected from —NR11R11, —NR11(CO)OR11, —NR11(C═NR11)NR11R11, and —OR11;
alternatively, one R11 and one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R12 is independently selected from (a) hydrogen, (b) halogen, (c) —OH, (d) —SH, (e) —(C1-C8 alkyl)OH, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —O(C1-C8 alkyl), (k) —CN, (l) —NO2, (m) —CONH2, (n) C(O)NH(C1-C8 alkyl), (o) C(O)N(C1-C8 alkyl)2, (p) —COH, (q) —COCH3, (r) —S(O)pCH3, (s) —S(O)pN(C1-C8 alkyl)2, (t) —S(C1-C8 alkyl), (u) —C(O)OH, (v) —C(O)O(C1-C8 alkyl), (w) —N3, (x) —NHC(O)(C1-C8 alkyl), (y) —N(C1-C8 alkyl)C(O)(C1-C8 alkyl), (z) —NH2, (aa) —NH(C1-C8 alkyl), (bb) —N(C1-C8 alkyl)2, (cc) —C1-C8 alkyl, (dd) —C2-C8 alkenyl, (ee) —C2-C8 alkynyl, (ff) -haloalkyl, (gg) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (ii) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (jj) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (kk) —(C═NH)NH2, (ll) —C(═NH)NH2, (mm) —C(O)R13, (nn) ═O, and (oo) ═NR13;
wherein each (aa) through (jj) is optionally substituted with one or more R13;
R13 is independently selected from (a) hydrogen, (b) halogen, (c) —C1-C8 alkyl, (d) —C2-C8 alkenyl, (e) —C2-C8 alkynyl, (f) -haloalkyl, (g) —OH, (h) —OC1-C8 alkyl, (i) —OC2-C8 alkenyl, (j) —OC2-C8 alkynyl, (k) —OCF3, (l) —OCH3, (m) —OCF2H, (n) —OCFH2, (O)—NH2, (p) —CN, (q) —N3, (r) —S(O)pC1-C8 alkyl, (s) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (t) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
p is 0, 1, or 2; and
t is 0, 1, or 2.
In one aspect, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein

X1 is CR1 or N; X2 is CR2 or N; X3 is CR3 or N; X4 is CR4 or N; X5 is CR5 or N; with the proviso that X1, X2, X3, X4, and X5 are not all N;
Y6 is CR6 or N; Y7 is CR7 or N; Y8 is CR8 or N; Y9 is CR9 or N; Y10 is CR10 or N; with the proviso that Y6, Y7, Y8, Y9, and Y10 are not all N; wherein
R1, R2, R4, R5, R6, R7, R8 and R10 are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) Br, (e) I, (f) —CF3, (g) —CF2H, (h) —CFH2, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —CN, (n) —N3, (o) —NO2, (p) NR11R11, (q) NR11(CO)R11, (r) —(CO)NR11R11, (s) —OR11, (t) —COH, (u) —CO(C1-C8 alkyl), (v) —COR11, (w) —NR11(CNR11)NR11R11, (x) —S(O)pR11, (y) —NR11S(O)pR11, (z) —SR11, (aa) —SCF3, (bb) —C(CF3)H—NH—CHR11R11, (cc) —COOR11, (dd) —(OCH2CH2)tR11, (ee) —(OCH2CH2)tOR11, (ff) —C1-C8 alkyl, (gg) —C2-C8 alkenyl, (hh) —C2-C8 alkynyl, (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (jj) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (kk) -haloalkyl, (ll) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (mm) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (nn) —CHR1—NH-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one of more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur);
wherein each (ff) through (nn) is optionally substituted with one or more R12;
each R11 is independently selected from (a) hydrogen, (b) halogen, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OH, (g) —SH, (h) —(C1-C8 alkyl)OH, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —OR12, (n) —COR12, (o) —CN, (p) —NO2, (q) —CONH2, (r) —CONR12R12, (s) —C(O)CH3, (t) —S(O)pCH3, (u) —S(O)pNR12R12, (v) —SR12, (w) —C(O)OH, (x) —C(O)OR12, (y) —N3, (z) —NH2, (aa) —NR12C(O)R12, (bb) —NH(C1-C8 alkyl), (cc) —N(C1-C8 alkyl)2, (dd) —C1-C8 alkyl, (ee) —C2-C8 alkenyl, (ff) —C2-C8 alkynyl, (gg) -haloalkyl, (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (jj) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (kk) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (ll) —(C═NH)NR12R12;
wherein each (bb) through (kk) is optionally substituted with one or more R12;
alternatively two R11 substituents are taken together to form (a) 3-7 membered saturated or unsaturated carbocyclic or (b) 3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, wherein each (a) through (b) is optionally substituted with one or more R12;
R3 is selected from:




wherein R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j are each independently selected from (a) hydrogen, (b) halogen, (c) —CH3, (d) —CF3, (e) —CF2H, (f) —CFH2, (g) —OCF3, (h) —OCF2H, (i) —OCFH2, (j) —OCH3, (k) —OR11, (l) —C1-C8 alkyl, (m) haloalkyl, (n) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (o) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (l) through (o) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R3a and R3b, R3c and R3d, R3e and R3f, R3g and R3h, and R3i and R3j are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or wherein four substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
U is selected from —O—, —S(O)p—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p— and —NR11S(O)pNR11—;
T is selected from —NR11R11, —NR11(C═P)OR11, —N11(C═NR11)NR11R11, and OR11;
alternatively, one R11 and one substituent selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R9 is selected from:




wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CH3, (d) —CF3, (e) —CF2H, (f) —CFH2, (g) —OCF3, (h) —OCH3, (i) —OCF2H, (j) —OCFH2, (k) —OR11, (l) —C1-C8 alkyl, (m) haloalkyl, (n) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (o) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (l) through (o) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, and (e) thiocarbonyl group;
wherein each (a) through (c) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or four substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
Z is selected from —O—, —S(O)p—, —NR11, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11, —NR11S(O)p— and —NR11S(O)pNR11—;
W is selected from —NR11R11, —NR11(CO)OR11, —NR11(C═NR11)NR11R11, and —OR11;
alternatively, one R11 and one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R12 is independently selected from (a) hydrogen, (b) halogen, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OH, (g) —SH, (h) —(C1-C8 alkyl)OH, (i) —OCF3, (j) —OCH3, (k) —OCF2H, (l) —OCFH2, (m) —O(C1-C8 alkyl), (n) —CN, (o) —NO2, (p) —CONH2, (q) —C(O)H, (r) —C(O)CH3, (s) —S(O)pCH3, (t) —S(O)pN(C1-C8 alkyl)2, (u) —S(C1-C8 alkyl), (v) —C(O)OH, (w) —C(O)O(C1-C8 alkyl), (x) —N3, (y) —NHC(O)(C1-C8 alkyl), (z) —N(C1-C8 alkyl)C(O)(C1-C8 alkyl), (aa) —NH2, (bb) —NH(C1-C8 alkyl), (cc) —N(C1-C8 alkyl)2, (dd) —C1-C8 alkyl, (ee) —C2-C8 alkenyl, (ff) —C2-C8 alkynyl, (gg) -haloalkyl, (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (jj) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (kk) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (ll) —(C═NH)NH2, (mm) —C(O)NH(C1-C8 alkyl), (nn) —C(O)N(C1-C8 alkyl)2, and (oo) —C(═NH)NH2;
p is 0, 1, or 2; and
t is 0, 1, or 2.
In addition, the invention provides methods of synthesizing the foregoing compounds and tautomers thereof, and pharmaceutically acceptable salts, esters and prodrugs of said compounds and tautomers. Following synthesis, an effective amount of one or more of the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers can be formulated with a pharmaceutically acceptable carrier for administration to a human or animal for use as antimicrobial agents, particularly as antibacterial agents. In certain embodiments, the compounds of the present invention are useful for treating, preventing, or reducing the risk of microbial infections or for the manufacture of a medicament for treating, preventing, or reducing the risk of microbial infections. Accordingly, the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers or their formulations can be administered, for example, via oral, parenteral, intravenous, otic, ophthalmic, nasal, or topical routes, to provide an effective amount of the compound or tautomer thereof, or pharmaceutically acceptable salt, ester or prodrug of said compound or tautomer to the human or animal.
The foregoing and other aspects and embodiments of the invention can be more fully understood by reference to the following detailed description and claims.


DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a family of compounds or tautomers thereof that can be used as antimicrobial agents, more particularly as antibacterial agents.
The present invention also includes pharmaceutically acceptable salts, esters, and prodrugs of said compounds and tautomers.
The compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers described herein can have asymmetric centers. Compounds or tautomers thereof or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the present invention containing an asymmetrically substituted atom can be isolated in optically active or racemic forms. It is well known in the art how to prepare optically active forms, such as by resolution of racemic forms or by synthesis from optically active starting materials. Many geometric isomers of olefins, C═N double bonds, and the like can also be present in the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers described herein, and all such stable isomers are contemplated in the present invention. Cis and trans geometric isomers of the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the present invention are described and can be isolated as a mixture of isomers or as separate isomeric forms. All chiral, diastereomeric, racemic, and geometric isomeric forms of a structure are intended, unless specific stereochemistry or isomeric form is specifically indicated. All processes used to prepare compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the present invention and intermediates made therein are considered to be part of the present invention. All tautomers of shown or described compounds are also considered to be part of the present invention. Furthermore, the invention also includes metabolites of the compounds described herein.
The invention also comprehends isotopically-labeled compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers, which are identical to those recited in formulae of the invention and following, but for the fact that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number most commonly found in nature. Examples of isotopes that can be incorporated into compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the invention include isotopes of hydrogen, carbon, nitrogen, fluorine, such as 3H, 11C, 14C and 18F.
Compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the present invention that contain the aforementioned isotopes and/or other isotopes of other atoms are within the scope of the present invention. Isotopically-labeled compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the present invention, for example those into which radioactive isotopes such as 3H, 14C are incorporated, are useful in drug and/or substrate tissue distribution assays. Tritiated, i.e., 3H, and carbon-14, i.e., 14C, isotopes are particularly preferred for their ease of preparation and detectability. 11C and 8F isotopes are particularly useful in PET (positron emission tomography). PET is useful in brain imaging. Further, substitution with heavier isotopes such as deuterium, i.e., 2H, can afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements and, hence, may be preferred in some circumstances, isotopically labeled compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers having a formula of the invention can generally be prepared by carrying out the procedures disclosed in the Schemes and/or in the Examples below, by substituting a readily available isotopically labeled reagent for a non-isotopically labeled reagent. In one embodiment, the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the invention are not isotopically labelled.
When any variable (e.g., R12) occurs more than one time in any constituent or formulae of the invention, its definition at each occurrence is independent of its definition at every other occurrence. Thus, for example, if a group is shown to be substituted with one or more R12 moieties, then R12 at each occurrence is selected independently from the definition of R12. Also, combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds within a designated atom's normal valency.
A chemical structure showing a dotted line representation for a chemical bond indicates that the bond is optionally present. For example, a dotted line drawn next to a solid single bond indicates that the bond can be either a single bond or a double bond.
When a bond to a substituent is shown to cross a bond connecting two atoms in a ring, then such substituent can be bonded to any atom on the ring. When a substituent is listed without indicating the atom via which such substituent is bonded to the rest of the compound of a given formula, then such substituent can be bonded via any atom in such substituent. Combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds.
In cases wherein there are nitrogen atoms in the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers of the present invention, these, where appropriate, can be converted to N-oxides by treatment with an oxidizing agent (e.g., MCPBA and/or hydrogen peroxides). Thus, shown and claimed nitrogen atoms are considered to cover both the shown nitrogen and its N-oxide (N→O) derivative, as appropriate. In some embodiments, the present invention relates to N-oxides of the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers disclosed herein.
One approach to developing improved anti-proliferative and anti-infective agents is to provide modulators (for example, inhibitors) of ribosome function.
Ribosomes are ribonucleoproteins, which are present in both prokaryotes and eukaryotes. Ribosomes are the cellular organelles responsible for protein synthesis. During gene expression, ribosomes translate the genetic information encoded in a messenger RNA into protein (Garrett et al. (2000) “The Ribosome: Structure, Function, Antibiotics and Cellular Interactions,” American Society for Microbiology, Washington, D.C.).
Ribosomes comprise two nonequivalent ribonucleoprotein subunits. The larger subunit (also known as the “large ribosomal subunit”) is about twice the size of the smaller subunit (also known as the “small ribosomal subunit”). The small ribosomal subunit binds messenger RNA (mRNA) and mediates the interactions between mRNA and transfer RNA (tRNA) anticodons on which the fidelity of translation depends. The large ribosomal subunit catalyzes peptide bond formation, i.e. the peptidyl-transferase reaction of protein synthesis, and includes, at least, three different tRNA binding sites known as the aminoacyl, peptidyl, and exit sites. The aminoacyl site or A-site accommodates the incoming aminoacyl-tRNA that is to contribute its amino acid to the growing peptide chain. Also, the A space of the A-site is important. The peptidyl site or P-site accommodates the peptidyl-tRNA complex, i.e., the tRNA with its amino acid that is part of the growing peptide chain. The exit or E-site accommodates the deacylated tRNA after it has donated its amino acid to the growing polypeptide chain.
1. DEFINITIONS
“Isomerism” means compounds that have identical molecular formulae but that differ in the nature or the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers”. Stereoisomers that are not mirror images of one another are termed “diastereoisomers”, and stereoisomers that are non-superimposable mirror images are termed “enantiomers”, or sometimes optical isomers. A carbon atom bonded to four nonidentical substituents is termed a “chiral center”.
“Chiral isomer” means a compound with at least one chiral center. A compound with one chiral center has two enantiomeric forms of opposite chirality and may exist either as an individual enantiomer or as a mixture of enantiomers. A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a “racemic mixture”. A compound that has more than one chiral center has 2n-1 enantiomeric pairs, where n is the number of chiral centers. Compounds with more than one chiral center may exist as either an individual diastereomer or as a mixture of diastereomers, termed a “diastereomeric mixture”. When one chiral center is present, a stereoisomer may be characterized by the absolute configuration (R or S) of that chiral center. Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. The substituents attached to the chiral center under consideration are ranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog. (Cahn et al, Angew. Chem. Inter. Edit. 1966, 5, 385; errata 511; Cahn et al., Angew. Chem. 1966, 78, 413; Cahn and Ingold, J. Chem. Soc. 1951 (London), 612; Cahn et al., Experientia 1956, 12, 81; Cahn, J., Chem. Educ. 1964, 41, 116).
“Geometric Isomers” means the diastereomers that owe their existence to hindered rotation about double bonds. These configurations are differentiated in their names by the prefixes cis and trans, or Z and E, which indicate that the groups are on the same or opposite side of the double bond in the molecule according to the Cahn-Ingold-Prelog rules.
Further, the compounds discussed in this application include all atropic isomers thereof. “Atropic isomers” are a type of stereoisomer in which the atoms of two isomers are arranged differently in space. Atropic isomers owe their existence to a restricted rotation caused by hindrance of rotation of large groups about a central bond. Such atropic isomers typically exist as a mixture, however as a result of recent advances in chromatography techniques, it has been possible to separate mixtures of two atropic isomers in select cases.
“Tautomers” refers to compounds whose structures differ markedly in arrangement of atoms, but which exist in easy and rapid equilibrium. It is to be understood that compounds of present invention may be depicted as different tautomers. It should also be understood that when compounds have tautomeric forms, all tautomeric forms are intended to be within the scope of the invention, and the naming of the compounds does not exclude any tautomer form.
Some compounds of the present invention can exist in a tautomeric form which is also intended to be encompassed within the scope of the present invention.
The compounds, pharmaceutically acceptable salts, esters and prodrugs of the present invention can exist in several tautomeric forms, including the enol and imine form, and the keto and enamine form and geometric isomers and mixtures thereof. All such tautomeric forms are included within the scope of the present invention. Tautomers exist as mixtures of a tautomeric set in solution. In solid form, usually one tautomer predominates. Even though one tautomer may be described, the present invention includes all tautomers of the present compounds.
A tautomer is one of two or more structural isomers that exist in equilibrium and are readily converted from one isomeric form to another. This reaction results in the formal migration of a hydrogen atom accompanied by a switch of adjacent conjugated double bonds. In solutions where tautomerization is possible, a chemical equilibrium of the tautomers can be reached. The exact ratio of the tautomers depends on several factors, including temperature, solvent, and pH. The concept of tautomers that are interconvertable by tautomerizations is called tautomerism.
Of the various types of tautomerism that are possible, two are commonly observed. In keto-enol tautomerism a simultaneous shift of electrons and a hydrogen atom occurs. Ring-chain tautomerism, is exhibited by glucose. It arises as a result of the aldehyde group (—CHO) in a sugar chain molecule reacting with one of the hydroxy groups (—OH) in the same molecule to give it a cyclic (ring-shaped) form.
Tautomerizations are catalyzed by: Base: 1. deprotonation; 2. formation of a delocalized anion (e.g. an enolate); 3. protonation at a different position of the anion; Acid: 1. protonation; 2. formation of a delocalized cation; 3. deprotonation at a different position adjacent to the cation.
Common tautomeric pairs are: ketone-enol, amide-nitrile, lactam-lactim, amide-imidic acid tautomerism in heterocyclic rings (e.g. in the nucleobases guanine, thymine, and cytosine), amine-enamine and enamine-enamine. An example below is included for illustrative purposes, and the present invention is not limited to this example:




The terms “crystal polymorphs” or “polymorphs” or “crystal forms” means crystal structures in which a compound (or salt or solvate thereof) can crystallize in different crystal packing arrangements, all of which have the same elemental composition. Different crystal forms usually have different X-ray diffraction patterns, infrared spectral, melting points, density hardness, crystal shape, optical and electrical properties, stability and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Crystal polymorphs of the compounds can be prepared by crystallization under different conditions.
The term “substituted,” as used herein, means that any one or more hydrogens on the designated atom, usually a carbon, oxygen, or nitrogen atom, is replaced with a selection from the indicated group, provided that the designated atom's normal valency is not exceeded, and that the substitution results in a stable compound. When a substituent is keto (i.e., ═O), then 2 hydrogens on the atom are replaced. Ring double bonds, as used herein, are double bonds that are formed between two adjacent ring atoms (e.g., C═C, C═N, N═N, etc.).
As used herein, the term “anomeric carbon” means the acetal carbon of a glycoside.
As used herein, the term “glycoside” is a cyclic acetal.
As used herein, “alkyl” is intended to include both branched and straight-chain saturated aliphatic hydrocarbon groups having the specified number of carbon atoms. For example C1-4 is intended to include C1, C2, C3, and C4 C1-6 alkyl is intended to include C1, C2, C3, C4, C5, and C6 alkyl groups and C1-8 is intended to include C1, C2, C3, C4, C5, C6, C7, and C8. Some examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl, n-hexyl, n-heptyl, and n-octyl.
As used herein, “alkenyl” is intended to include hydrocarbon chains of either straight or branched configuration and one or more unsaturated carbon-carbon bonds that can occur in any stable point along the chain, such as ethenyl and propenyl. For example C2-6 alkenyl is intended to include C2, C3, C4, C5, and C6 alkenyl groups and C2-8 alkenyl is intended to include C2, C3, C4, C5, C6, C7, and C8.
As used herein, “alkynyl” is intended to include hydrocarbon chains of either straight or branched configuration and one or more triple carbon-carbon bonds that can occur in any stable point along the chain, such as ethynyl and propynyl. For example, C2-6 alkynyl is intended to include C2, C3, C4, C5, and C6 alkynyl groups and C2-8 alkynyl is intended to include C2, C3, C4, C5, C6, C7, and C8.
Furthermore, “alkyl”, “alkenyl”, and “alkynyl” are intended to include moieties which are diradicals, i.e., having two points of attachment. A nonlimiting example of such an alkyl moiety that is a diradical is —CH2CH2—, i.e., a C2 alkyl group that is covalently bonded via each terminal carbon atom to the remainder of the molecule. The alkyl diradicals are also known as “alkylenyl” radicals. The alkenyl diradicals are also known as “alkenylenyl” radicals. The alkynyl diradicals are also known as “alkynylenyl” radicals.
As used herein, “cycloalkyl” is intended to include saturated ring groups, such as cyclopropyl, cyclobutyl, or cyclopentyl. C3-8 cycloalkyl is intended to include C3, C4, C5, C6, C7, and C8 cycloalkyl groups.
As used herein “counterion” is used to mean a positively or negatively charged species present in conjunction with an ion of opposite charge. A nonlimiting example of a counterion is an ion or ions present to counterbalance the charge or charges on an organic compound. Nonlimiting examples of counterions include chloride, bromide, hydroxide, acetate, sulfate, and ammonium.
As used herein, “halo” or “halogen” refers to fluoro, chloro, bromo, and iodo substituents.
As used herein, “haloalkyl” is intended to include both branched and straight-chain saturated aliphatic hydrocarbon groups having the specified number of carbon atoms, substituted with 1 or more halogen (for example —CVFW wherein v=1 to 3 and w=1 to (2v+1)). Examples of haloalkyl include, but are not limited to, trifluoromethyl, trichloromethyl, pentafluoroethyl, and pentachloroethyl.
As used herein, “alkoxy” refers to an alkyl group as defined above with the indicated number of carbon atoms attached through an oxygen bridge. C1-6 alkoxy, is intended to include C1, C2, C3, C4, C5, and C6 alkoxy groups. C1-8 alkoxy, is intended to include C1, C2, C3, C4, C5, C6, C7, and C8 alkoxy groups. Examples of alkoxy include, but are not limited to, methoxy, ethoxy, n-propoxy, i-propoxy, n-butoxy, s-butoxy, t-butoxy, n-pentoxy, s-pentoxy, n-heptoxy, and n-octoxy.
As used herein, “alkylthio” refers to an alkyl group as defined above with the indicated number of carbon atoms attached through a sulfur bridge. C1-6 alkylthio, is intended to include C1, C2, C3, C4, C5, and C6 alkylthio groups. C1-8 alkylthio, is intended to include C1, C2, C3, C4, C5, C6, C7, and C8 alkylthio groups.
As used herein, “carbocycle” or “carbocyclic ring” is intended to mean, unless otherwise specified, any stable 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12-membered monocyclic, bicyclic or tricyclic ring, any of which can be saturated, unsaturated (including partially and fully unsaturated), or aromatic and said ring consists of carbon atoms in its core ring structure. Examples of such carbocycles or carbocyclic rings include, but are not limited to, cyclopropyl, cyclobutyl, cyclobutenyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, cycloheptenyl, adamantyl, cyclooctyl, cyclooctenyl, cyclooctadienyl, [3.3.0]bicyclooctane, [4.3.0]bicyclononane, [4.4.0]bicyclodecane, [2.2.2]bicyclooctane, fluorenyl, phenyl, naphthyl, indanyl, adamantyl, and tetrahydronaphthyl. As shown above, bridged rings are also included in the definition of carbocycle (e.g., [2.2.2]bicyclooctane). A bridged ring occurs when one or more carbon atoms link two non-adjacent carbon atoms. Preferred bridges are one or two carbon atoms. It is noted that a bridge always converts a monocyclic ring into a tricyclic ring. When a ring is bridged, the substituents recited for the ring can also be present on the bridge. Fused (e.g., naphthyl and tetrahydronaphthyl) and spiro rings are also included.
As used herein, the term “heterocycle” or “heterocyclic” ring means, unless otherwise stated, a stable 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12-membered monocyclic, bicyclic or tricyclic ring which is saturated, unsaturated (including partially and fully unsaturated), or aromatic, and said ring consists of carbon atoms and one or more heteroatoms in its core ring structure, e.g., 1 or 1-2 or 1-3 or 1-4 or 1-5 or 1-6 heteroatoms, independently selected from nitrogen, oxygen, and sulfur, and including any bicyclic or tricyclic group in which any of the above-defined heterocyclic rings is fused or attached to a second ring (e.g., a benzene ring). The nitrogen and sulfur heteroatoms can optionally be oxidized (i.e., N→O and S(O)p, wherein p=1 or 2). When a nitrogen atom is included in the ring it is either N or NH, depending on whether or not it is attached to a double bond in the ring (i.e., a hydrogen is present if needed to maintain the tri-valency of the nitrogen atom). The nitrogen atom can be substituted or unsubstituted (i.e., N or NR wherein R is H or another substituent, as defined). The heterocycle or heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure. The heterocycle or heterocyclic rings described herein can be substituted on carbon or on a nitrogen atom if the resulting compound is stable. A nitrogen in the heterocycle or heterocyclic ring can optionally be quaternized. Bridged rings are also included in the definition of heterocycle or heterocyclic ring. A bridged ring occurs when one or more atoms (i.e., C, O, N, or S) link two non-adjacent carbon or nitrogen atoms. Preferred bridges include, but are not limited to, one carbon atom, two carbon atoms, one nitrogen atom, two nitrogen atoms, and a carbon-nitrogen group. When a ring is bridged, the substituents recited for the ring can also be present on the bridge. Spiro and fused rings are also included.
As used herein, the term “aromatic heterocycle”, “aromatic heterocylic” or “heteroaryl” ring is intended to mean a stable 5, 6, 7, 8, 9, 10, 11, or 12-membered monocyclic or bicyclic aromatic ring which consists of carbon atoms and one or more heteroatoms, e.g., 1 or 1-2 or 1-3 or 1-4 or 1-5 or 1-6 heteroatoms, independently selected from nitrogen, oxygen, and sulfur. In the case of bicyclic aromatic heterocyclic or heterocycle or heteroaryl rings, only one of the two rings needs to be aromatic (e.g., 2,3-dihydroindole), though both can be (e.g., quinoline). The second ring can also be fused or bridged as defined above for heterocycles. The nitrogen atom can be substituted or unsubstituted (i.e., N or NR wherein R is H or another substituent, as defined). The nitrogen and sulfur heteroatoms can optionally be oxidized (i.e., N→O and S(O)p, wherein p=1 or 2). In certain compounds, the total number of S and O atoms in the aromatic heterocycle is not more than 1.
Examples of aromatic heterocycles, aromatic heterocyclics or heteroaryls include, but are not limited to, acridinyl, azabicyclooctanonyl, azepanyl, azetidinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzothiophenyl, benzoxazolyl, benzoxazolinyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazolinyl, benzodioxoly, benzooxadiazoly, carbazolyl, 4aH-carbazolyl, carbolinyl, chromanyl, chromenyl, cinnolinyl, cycloheptyl, decahydroquinolinyl, dihydrobenzodioxinyl, 2H,6H-1,5,2-dithiazinyl, dihydrofuro[2,3-b]tetrahydrofuran, furanyl, furazanyl, imidazolidinyl, imidazolidinylimine, imidazolinyl, imidazolyl, imidazolonyl, 1H-indazolyl, indolenyl, indolinyl, indolizinyl, indolyl, 3H-indolyl, isatinoyl, isobenzofuranyl, isochromanyl, isoindazolyl, isoindolinyl, isoindolyl, isoquinolinyl, isothiazolyl, isoxazolyl, methylenedioxyphenyl, methylbenztriazolyl, methylfuranyl, methylimidazolyl, methylthiazolyl, morpholinyl, naphthyridinyl, octahydroisoquinolinyl, oxadiazolyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl, oxazolidinyl, oxazolidinonyl, oxazolyl, oxindolyl, phenanthridinyl, phenanthrolinyl, phenazinyl, phenothiazinyl, phenoxathinyl, phenoxazinyl, phthalazinyl, piperazinyl, piperazinonyl, piperidinyl, piperidenyl, piperidonyl, 4-piperidonyl, piperonyl, pteridinyl, purinyl, pyranyl, pyrazinyl, pyrazolidinyl, pyrazolinyl, pyrazolyl, pyridazinyl, pyridooxazolyl, pyridoimidazolyl, pyridothiazolyl, pyridinyl, pyridinonyl, pyridyl, pyrimidinyl, pyrroldionyl, pyrrolidinyl, pyrrolidinonyl, pyrrolinyl, 2H-pyrrolyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, quinuclidinyl, tetrahydrofuranyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, tetrazolyl, 6H-1,2,5-thiadiazinyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thianthrenyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, thiophenyl, thiomorpholinyldioxidyl, triazinyl, triazolopyrimidinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, 1,3,4-triazolyl, and xanthenyl.
As used herein, the phrase “pharmaceutically acceptable” refers to those compounds or tautomers thereof, or salts, esters, or prodrugs thereof, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
As used herein, “pharmaceutically acceptable salts” refer to derivatives of the disclosed compounds or tautomers thereof, wherein the parent compound or a tautomer thereof, is modified by making acid or base salts thereof. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent compound or a tautomer thereof formed, for example, from non-toxic inorganic or organic acids. For example, such conventional non-toxic salts include, but are not limited to, those derived from inorganic and organic acids selected from 2-acetoxybenzoic, 2-hydroxyethane sulfonic, acetic, ascorbic, benzene sulfonic, benzoic, bicarbonic, carbonic, citric, edetic, ethane disulfonic, ethane sulfonic, fumaric, glucoheptonic, gluconic, glutamic, glycolic, glycollyarsanilic, hexylresorcinic, hydrabamic, hydrobromic, hydrochloric, hydroiodide, hydroxymaleic, hydroxynaphthoic, isethionic, lactic, lactobionic, lauryl sulfonic, maleic, malic, mandelic, methane sulfonic, napsylic, nitric, oxalic, pamoic, pantothenic, phenylacetic, phosphoric, polygalacturonic, propionic, salicylic, stearic, subacetic, succinic, sulfamic, sulfanilic, sulfuric, tannic, tartaric, and toluene sulfonic.
The pharmaceutically acceptable salts of the present invention can be synthesized from the parent compound or a tautomer thereof that contains a basic or acidic moiety by conventional chemical methods. Generally, such pharmaceutically acceptable salts can be prepared by reacting the free acid or base forms of these compounds or tautomers thereof with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, non-aqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are preferred. Lists of suitable salts are found in Remington's Pharmaceutical Sciences, 18th ed., Mack Publishing Company, Easton, Pa., USA, p. 1445 (1990).
Since prodrugs are known to enhance numerous desirable qualities of pharmaceuticals (e.g., solubility, bioavailability, manufacturing, etc.) the compounds or tautomers thereof of the present invention can be delivered in prodrug form. Thus, the present invention is intended to cover prodrugs of the presently claimed compounds or tautomers thereof, methods of delivering the same and compositions containing the same. “Prodrugs” are intended to include any covalently bonded carriers that release an active parent drug of the present invention in vivo when such prodrug is administered to a mammalian subject. Prodrugs of the present invention are prepared by modifying functional groups present in the compound or a tautomer thereof in such a way that the modifications are cleaved, either in routine manipulation or in vivo, to the parent compound or a tautomer thereof. Prodrugs include compounds or tautomers thereof of the present invention wherein a hydroxy, amino, or sulfhydryl group is bonded to any group that, when the prodrug of the present invention is administered to a mammalian subject, it cleaves to form a free hydroxyl, free amino, or free sulfhydryl group, respectively. Examples of prodrugs include, but are not limited to, acetate, formate, and benzoate derivatives of alcohol and amine functional groups in the compounds of the present invention.
As used herein, “stable compound” and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
As used herein, the term “patient”, as used herein, means the human or animal (in the case of an animal, more typically a mammal) subject that would be subjected to a surgical or invasive medical procedure. Such patient or subject could be considered to be in need of the methods of treating, reducing the risk of or preventing the infection due to a surgical procedure or an invasive medical procedure. Such patient or subject can also be considered to be in need of peri-operative prophylaxis.
As used herein, the term “treating” means to provide a therapeutic intervention to cure or ameliorate an infection.
As used herein, the term “preventing”, as used herein means, to completely or almost completely stop an infection from occurring, for example when the patient or subject is predisposed to an infection or at risk of contracting an infection. Preventing can also include inhibiting, i.e. arresting the development, of an infection.
As used herein, the term “reducing the risk of”, as used herein, means to lower the likelihood or probability of an infection occurring, for example when the patient or subject is predisposed to an infection or at risk of contracting an infection.
As used herein, “unsaturated” refers to compounds having at least one degree of unsaturation (e.g., at least one multiple bond) and includes partially and fully unsaturated compounds.
As used herein, the term “effective amount” refers to an amount of a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, (including combinations of compounds and/or tautomers thereof, and/or pharmaceutically acceptable salts, esters, or prodrugs of said compound or tautomer), of the present invention that is effective when administered alone or in combination as an antimicrobial agent. For example, an effective amount refers to an amount of the compound or tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug said compound or tautomer that is present in a composition, a formulation or on a medical device given to a recipient patient or subject sufficient to elicit biological activity, for example, anti-infective activity, such as e.g., anti-microbial activity, anti-bacterial activity, anti-fungal activity, anti-viral activity, or anti-parasitic activity.
The term “prophylactically effective amount” means an amount of a compound or a tautomer of said compound or tautomer, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer (including combinations of compounds and/or tautomers thereof, and/or pharmaceutically acceptable salts, esters, or prodrugs thereof), of the present invention that is effective prophylactically when administered alone or in combination as an antimicrobial agent. For example, a prophylactically effective amount refers to an amount of the compound or tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer that is present in a composition, a formulation, or on a medical device given to a recipient patient or subject sufficient to prevent or reduce the risk of an infection due to a surgical procedure or an invasive medical procedure.
It is to be further understood that the representations for “Hydrogen Bond Acceptor—Hydrogen Bond Acceptor—Hydrogen Bond Donor” and “Hydrogen Bond Acceptor—Hydrogen Bond Acceptor—Hydrogen Bond Acceptor” are meant to indicate the relative orientation of the hydrogen bond acceptors and donor and not meant to limit that such groups are directly connected together as it is contemplated that additional atoms or groups of atoms can be included between such groups.
In the specification, the singular forms also include the plural, unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In the case of conflict, the present specification will control. As used herein, “mammal” refers to human and non-human patients.
As used herein, the term “therapeutically effective amount” refers to an amount of a compound or a tautomer thereof or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, (also including combinations of compounds and/or tautomers thereof, and/or pharmaceutically acceptable salts, esters, or prodrugs or said compounds or tautomers), of the present invention that is effective when administered alone or in combination as an antimicrobial agent. For example, a therapeutically effective amount refers to an amount of the compound or tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer that is present in a composition, a formulation, or on a medical device given to a recipient patient or subject in an amount sufficient to elicit biological activity, for example, anti-microbial activity, anti-fungal activity, anti-viral activity, anti-parasitic activity, anti-diarrheal activity, and/or anti-proliferative activity. In one aspect, the combination of compounds and/or tautomers thereof, and/or pharmaceutically acceptable salts, esters, or prodrugs or said compounds or tautomers is a synergistic combination. Synergy, as described, for example, by Chou and Talalay, Adv. Enzyme Regul. vol. 22, pp. 27-55 (1984), occurs when the effect of the compounds or tautomers thereof or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers when administered in combination is greater than the additive effect of the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers when administered alone as a single agent. In general, a synergistic effect is most clearly demonstrated at sub-optimal concentrations of the compounds or tautomers thereof, or pharmaceutically acceptable salts, esters, or prodrugs of said compounds or tautomers. Synergy can be in terms of lower cytotoxicity, increased anti-proliferative and/or anti-infective effect, or some other beneficial effect of the combination compared with the individual components.
As used herein, the term “RNA microhelix binding site” refers to the ribofunctional locus of the large ribosomal subunit occupied by the RNA microhelix of Formula III. The RNA microhelix binding site defines at least a portion of or overlaps with the E-site.
As used herein, the term “A-site” refers to the ribofunctional locus occupied by an aminoacyl-tRNA molecule immediately prior to its participation in the peptide-bond forming reaction.
As used herein, the term “B-site” refers to the ribofunctional locus occupied by a deacylated tRNA molecule following its participation in the peptide-bond forming reaction.
As used herein, the term “P-site” refers to the ribofunctional locus occupied by a peptidyl-tRNA at the time it participates in the peptide-bond forming reaction.
As used herein, the term “A-space” refers to the portion of the A-site within the peptidyl transferase center in which the amino acid portion of the aminoacylated t-RNA binds, or alternatively the portion of the A-site in which the oxazolidinone ring of linezolid binds.
As used herein and in reference to a ribosome or ribosomal subunit, the terms “a portion of” or “a portion of the three-dimensional structure of” are understood to mean a portion of the three-dimensional structure of a ribosome or ribosomal subunit, including charge distribution and hydrophilicity/hydrophobicity characteristics, formed by at least three, more preferably at least three to ten, and most preferably at least ten amino acid residues and/or nucleotide residues of the ribosome or ribosomal subunit. The residues forming such a portion can be, for example, (i) contiguous residues based upon, for example, a primary sequence of a ribosomal RNA or ribosomal protein, (ii) residues which form a contiguous portion of the three-dimensional structure of the ribosome or ribosomal subunit, or (c) a combination thereof. As used herein and in reference to the RNA microhelix, the terms “a portion of” or “a portion of the three-dimensional structure of” are understood to mean a portion of the three-dimensional structure of RNA microhelix, including charge distribution and hydrophilicity/hydrophobicity characteristics, formed by at least three, more preferably at least three to ten atoms of one or more core residues of Formula III. The atoms forming such a portion can be, for example, (i) solvent inaccessible atoms buried within the core of the RNA microhelix, (ii) solvent accessible atoms of the RNA microhelix, or (iii) a combination thereof.
As used herein, the term ESBL is extended spectrum beta-lactamase. The term KPC is Klebsiella pneumonia carbapenemase.
As used herein, the term acute bacterial skin and skin structure infection (ABSSSI) encompasses complicated skin and skin structure infections (cSSSI) and complication skin and soft tissue infections (cSSTI), which have been used interchangeably. The terms uncomplicated skin and skin structure infections (uCSSSI) and uncomplicated skin and soft tissue infections (uCSSTI) have been used interchangeably.
As used herein, the term “spp.” is the abbreviation for species.
As used herein, the term “formulae of the invention” includes one or more of the formulae:
IA, I, II, III, IV, V, VI, VII, VIII, IX, X, XI, XII, XIII, XIV, XV, XVI, XVII, XVIII, Va, VIIa, VIIa, VIIIa, IXa, Xa, XIa, XIIa, XIIIa, XIVa, XVa, XVIa, XVIIa, XVIIIa, XXa, XXa1, XXb, XXb1,
A1, A2, A3, A4, A5, A6, A7, B1, B2, B3, B4, B5, B6, B7, C1, C2, C3, C4, C5, C6, C7, D1, D2, D3, D4, D5, D6, D7, E1, E2, E3, E4, E5, E6, E7,
A1a, A2a, A3a, A4a, A5a, A6a, A7a, A8a, A9a, B1a, B2a, B3a, B4a, B5a, B6a, B7a, B8a, B9a, C1a, C2a, C3a, C4a, C5a, C6a, C7a, C8a, C9a,
D1a, D2a, D3a, D4a, D5a, D6a, D7a, D8a, D9a, E1a, E2a, E3a, E4a, E5a, E6a, E1a, E8a, F1, F2, G1, G2, G3, G4,
H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12,
I1, I2, I3, I4, I5, I6, I7, I8, I9, I10, I11, and I12.
As used herein, the term “compound of the invention” includes one or more compounds of the formulae of the invention or a compound explicitly disclosed herein.
All percentages and ratios used herein, unless otherwise indicated, are by weight.
Throughout the description, where compositions are described as having, including, or comprising specific components, or where processes are described as having, including, or comprising specific process steps, it is contemplated that compositions of the present invention also consist essentially of, or consist of, the recited components, and that the processes of the present invention also consist essentially of, or consist of, the recited processing steps. Further, it should be understood that the order of steps or order for performing certain actions are immaterial so long as the invention remains operable. Moreover, two or more steps or actions can be conducted simultaneously.
2. COMPOUNDS OF THE INVENTION
In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein

X1 is CR1 or N; X2 is CR2 or N; X3 is CR3 or N; X4 is CR4 or N; X5 is CR5 or N; with the proviso that X1, X2, X3, X4, and X5 are not all N;
Y6 is CR6 or N; Y7 is CR7 or N; Y8 is CR8 or N; Y9 is CR9 or N; Y10 is CR10 or N; with the proviso that Y6, Y7, Y8, Y9, and Y10 are not all N; wherein
R1, R2, R4, R5, R6, R7, R8 and R10 are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) Br, (e) I, (f) —CF3, (g) —CF2H, (h) —CFH2, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —CN, (n) —N3, (o) —NO2, (p) —NR11R11, (q) —NR11C(O)R11, (r) —C(O)NR11R11, (s) —OR11, (t) —COH, (u) —CO(C1-C8 alkyl), (v) —COR11, (w) —NR11(CNR11)NR11R11, (x) —S(O)pR11, (y) —NR11S(O)pR11, (z) —SR11, (aa) —SCF3, (bb) —C(CF3)H—NH—CHR11R11, (cc) —COOR11, (dd) —(OCH2CH2)tR11, (ee) —(OCH2CH2)tOR11, (ff) —C1-C8 alkyl, (gg) —C2-C8 alkenyl, (hh) —C2-C8 alkynyl, (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (jj) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (kk) -haloalkyl, (ll) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (mm) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (nn) —CHR11—NH-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one of more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur);
wherein each (ff) through (nn) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R6, R7, and R8 are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur; wherein each (a) through (b) is optionally substituted with one or more R12;
each R11 is independently selected from (a) hydrogen, (b) halogen, (c) —OH, (d) —SH, (e) —(C1-C8 alkyl)OH, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —OR12, (k) —COR12, (l) —CN, (m) —NO2, (n) —CONH2, (o) —CONR12R12, (p) —COCH3, (q) —S(O)pCH3, (r) —S(O)pNR12R12, (s) —SR12, (t) —C(O)OH, (u) —C(O)OR12, (v) —N3, (w) —NH2, (x) —NR12C(O)R12, (y) —NH(C1-C8 alkyl), (z) —N(C1-C8 alkyl)2, (aa) —C1-C8 alkyl, (bb) —C2-C8 alkenyl, (cc) —C2-C8 alkynyl, (dd) -haloalkyl, (ee) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ff) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (gg) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (hh) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (ii) —(C═NH)NR12R12;
wherein each (y) through (hh) is optionally substituted with one or more R12;
alternatively two R11 substituents are taken together to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, wherein each (a) through (b) is optionally substituted with one or more R12;
R3 is selected from:




wherein R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l are each independently selected from (a) hydrogen, (b) halogen, (c) —CN, (d) —N3, (e) —NO2, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —OR11, (k) —C(O)R11, (l) —C(O)NR11R11, (m) —NH2, (n) —NR11R11, (o) —NR11C(O)R11, (p) —S(O)pR11, (q) —C(O)OH, (r) —C(O)OR11, (s) —C1-C8 alkyl, (t) —C2-C8 alkenyl, (u) —C2-C8 alkynyl, (v) haloalkyl, (w) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (x) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (s) through (x) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R3a and R3b, R3c and R3d, R3e and R3f, R3g and R3h, R3i and R3j, and R3k and R3l are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or wherein four substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
U is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, S(O)pNR11—, —NR11S(O)p—, —NR11S(O)pNR11—, and —NR11C(O)NR11—;
T is selected from —NR11R11, —NR11(C═O)OR11, —NR11(C═NR11)NR11R11, and OR11;
alternatively, one R11 and one substituent selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R9 is selected from:




wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CN, (d) —N3, (e) —NO2, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —OR11, (k) —NH2, (l) —NR11R11, (m) —C(O)R11, (n) —C(O)OR11, (o) —C(O)NR11R11, (p) —NR11C(O)R11, (q) —S(O)pR11, (r) —C1-C8 alkyl, (s) —C2-C8 alkenyl, (t) —C1-C8 alkynyl, (u) haloalkyl, (v) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (w) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (r) through (w) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) 3-7 membered saturated or unsaturated carbocyclic, (b) 3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (c) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or four substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
Z is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p—, —NR11S(O)pNR11—, and —NR11C(O)NR11—;
W is selected from —NR11R11, —NR11(CO)OR11, —NR11(C═NR11)NR11R11, and —OR11;
alternatively, one R11 and one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R12 is independently selected from (a) hydrogen, (b) halogen, (c) —OH, (d) —SH, (e) —(C1-C8 alkyl)OH, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —O(C1-C8 alkyl), (k) —CN, (l) —NO2, (m) —CONH2, (n) C(O)NH(C1-C8 alkyl), (o) C(O)N(C1-C8 alkyl)2, (p) —COH, (q) —COCH3, (r) —S(O)pCH3, (s) —S(O)pN(C1-C8 alkyl)2, (t) —S(C1-C8 alkyl), (u) —C(O)OH, (v) —C(O)O(C1-C8 alkyl), (w) —N3, (x) —NHC(O)(C1-C8 alkyl), (y) —N(C1-C8 alkyl)C(O)(C1-C8 alkyl), (z) —NH2, (aa) —NH(C1-C8 alkyl), (bb) —N(C1-C8 alkyl)2, (cc) —C1-C8 alkyl, (dd) —C2-C8 alkenyl, (ee) —C2-C8 alkynyl, (ff) -haloalkyl, (gg) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (ii) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (jj) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (kk) —(C═NH)NH2, (ll) —C(═NH)NH2, (mm) —C(O)R13, (nn) ═O, and (oo) ═NR13;
wherein each (aa) through (jj) is optionally substituted with one or more R13;
R13 is independently selected from (a) hydrogen, (b) halogen, (c) —C1-C8 alkyl, (d) —C2-C8 alkenyl, (e) —C2-C8 alkynyl, (f) -haloalkyl, (g) —OH, (h) —OC1-C8 alkyl, (i) —OC2-C8 alkenyl, (j) —OC2-C8 alkynyl, (k) —OCF3, (l) —OCH3, (m) —OCF2H, (n) —OCFH2, (o) —NH2, (p) —CN, (q) —N3, (r) —S(O)pC1-C8 alkyl, (s) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (t) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
p is 0, 1, or 2; and
t is 0, 1, or 2.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein

X1 is CR1 or N; X2 is CR2 or N; X3 is CR3 or N; X4 is CR4 or N; X5 is CR5 or N; with the proviso that X1, X2, X3, X4, and X5 are not all N;
Y6 is CR6 or N; Y7 is CR7 or N; Y8 is CR8 or N; Y9 is CR9 or N; Y10 is CR10 or N; with the proviso that Y6, Y7, Y8, Y9, and Y10 are not all N; wherein
R1, R2, R4, R5, R6, R7, R8 and R10 are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) Br, (e) I, (f) —CF3, (g) —CF2H, (h) —CFH2, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —CN, (n) —N3, (o) —NO2, (p) —NR11R11, (q) —NR11(CO)R11, (r) —(CO)NR11R11, (s) —OR11, (t) —COH, (u) —CO(C1-C8 alkyl), (v) —COR11, (w) —NR11(CNR11)NR11R11, (x) —S(O)pR11, (y) —NR11S(O)pR11, (z) —SR11, (aa) —SCF3, (bb) —C(CF3)H—NH—CHR11R11, (cc) —COOR11, (dd) —(OCH2CH2)tR11, (ee) —(OCH2CH2)tOR11, (ff) —C1-C8 alkyl, (gg) —C2-C8 alkenyl, (hh) —C2-C8 alkynyl, (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (jj) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (kk) -haloalkyl, (ll) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (mm) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (nn) —CHR11—NH-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one of more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur);
wherein each (ff) through (nn) is optionally substituted with one or more R12;
each R11 is independently selected from (a) hydrogen, (b) halogen, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OH, (g) —SH, (h) —(C1-C8 alkyl)OH, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —OR12, (n) —COR12, (o) —CN, (p) —NO2, (q) —CONH2, (r) —CONR12R12, (s) —C(O)CH3, (t) —S(O)pCH3, (u) —S(O)pNR12R12, (v) —SR12, (w) —C(O)OH, (x) —C(O)OR12, (y) —N3, (z) —NH2, (aa) —NR12C(O)R12, (bb) —NH(C1-C8 alkyl), (cc) —N(C1-C8 alkyl)2, (dd) —C1-C8 alkyl, (ee) —C2-C8 alkenyl, (ff) —C2-C8 alkynyl, (gg) -haloalkyl, (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (jj) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (kk) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (ll) —(C═NH)NR12R12;
wherein each (bb) through (kk) is optionally substituted with one or more R12;
alternatively two R11 substituents are taken together to form (a) 3-7 membered saturated or unsaturated carbocyclic or (b) 3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, wherein each (a) through (b) is optionally substituted with one or more R12;
R3 is selected from:




wherein R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j are each independently selected from (a) hydrogen, (b) halogen, (c) —CH3, (d) —CF3, (e) —CF2H, (f) —CFH2, (g) —OCF3, (h) —OCF2H, (i) —OCFH2, (j) —OCH3, (k) —OR11, (l) —C1-C8 alkyl, (m) haloalkyl, (n) —3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (o) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (l) through (o) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R3a and R3b, R3c and R3d, R3e and R3f, R3g and R3h, and R3i and R3j are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or wherein four substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
U is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p— and —NR11S(O)pNR11—;
T is selected from —NR11R11, —NR11(C═O)OR11, —NR11(C═NR11)NR11R11, and OR11;
alternatively, one R11 and one substituent selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, and R3j are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R9 is selected from:




wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CH3, (d) —CF3, (e) —CF2H, (f) —CFH2, (g) —OCF3, (h) —OCH3, (i) —OCF2H, (j) —OCFH2, (k) —OR11, (l) —C1-C8 alkyl, (m) haloalkyl, (n) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (o) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (l) through (o) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, and (e) thiocarbonyl group;
wherein each (a) through (c) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or four substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
Z is selected from —O—, —S(O)p—, —NR11—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p— and —NR11S(O)pNR11—;
W is selected from —NR11R11, —NR11(CO)OR11, —NR11(C═NR11)NR11R11, and —OR11;
alternatively, one R11 and one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R12 is independently selected from (a) hydrogen, (b) halogen, (c) —CF3, (d) —CF2H, (e) —CFH2, (O—OH, (g) —SH, (h) —(C1-C8 alkyl)OH, (i) —OCF3, (j) —OCH3, (k) —OCF2H, (l) —OCFH2, (m) —O(C1-C8 alkyl), (n) —CN, (o) —NO2, (p) —CONH2, (q) —C(O)H, (r) —C(O)CH3, (s) —S(O)pCH3, (t) —S(O)pN(C1-C8 alkyl)2, (u) —S(C1-C8 alkyl), (v) —C(O)OH, (w) —C(O)O(C1-C8 alkyl), (x) —N3, (y) —NHC(O)(C1-C8 alkyl), (z) —N(C1-C8 alkyl)C(O)(C1-C8 alkyl), (aa) (bb) —NH(C1-C8 alkyl), (cc) —N(C1-C8 alkyl)2, (dd) —C1-C8 alkyl, (ee) —C2-C8 alkenyl, (ff) —C2-C8 alkynyl, (gg) -haloalkyl, (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (jj) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (kk) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (ll) —(C═NH)NH2, (mm) —C(O)NH(C1-C8 alkyl), (nn) —C(O)N(C1-C8 alkyl)2, and (oo) —C(═NH)NH2;
p is 0, 1, or 2; and
t is 0, 1, or 2.
In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein X1, X2, X4, X5, Y6, Y7, Y8, Y10, R3 and R9 are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3, R4, R5, R6, R7, R8, R9, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R8, R9, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R8, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R8, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R8, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R8, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R9k, R9l, R9m, R9n, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R9k, R9l, R9m, R9n, R9o, and R9 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R8, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R8, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R8, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R8, R9k, R9l, R9m, R9n, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R7, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R6, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R7, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R1, R2, R3a, R3b, R4, R5, R8, R9k, R9l, R9m, R9n, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to any formulae of the invention, wherein at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to any formulae of the invention, wherein at least two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are not hydrogen.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to any formulae of the invention, wherein R1, R2, R4 and R5 are each independently selected from hydrogen and F. In some embodiments, R1, R2, R4, and R5 are each hydrogen.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to any formulae of the invention, wherein R3a and R3b are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) —CH3, (e) —CF3, (f) —CF2H, (g) —CFH2, (h) —OCF3, (i) —OCF2H, (j) —OCFH2, (k) —OCH3, and (l) —OH. In some embodiments, R3a and R3b are each hydrogen. In some embodiments, R3a and R3b are each hydrogen. In some embodiments, the stereochemistry of R3a and R3b is




and R3a is methyl and R3b is hydrogen. In some embodiments, the stereochemistry of R3a and R3b is





and R3a is methyl and R3b is hydrogen. In some embodiments, the stereochemistry of R3a and R3b is





and R3a is hydrogen and R3b is methyl. In some embodiments, the stereochemistry of R3a and R3b is





and R3a is hydrogen and R3b is methyl.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9k, R9l, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9m, R9n, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9o, R9p, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6 and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7 and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8 and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9k, R9l and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9k and R9l are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9m, R9n and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9m and R9n are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o, R9p and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9q, R9r, and R10 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9q and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, and R8 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6 and R7 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6 and R8 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7 and R8 are as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6 is as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R7 is as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R8 is as defined herein.

In some embodiments, the present invention relates to a compound having formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R10 is as defined herein.

In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R10 is selected from hydrogen, F and Cl.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, and R8 are each independently selected from (a) F, (b) Cl, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —CN, (k) —OR11, (l) —S(O)pR11, (m) —SCF3, (n) —C1-C8 alkyl, (o) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (p) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (q) —CHCHCN and (r) —CHCH—C(O)NH-t-butyl.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, and R8 are each independently selected from (a) F, (b) Cl, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —CN, (k) —OR11, (l) —S(O)pR11, (m) —SCF3, (n) —C1-C8 alkyl, (o) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (p) -3-14 membered saturated, unsaturated, or aromatic carbocycle.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, and R8 are each independently selected from are each independently selected from (a) F; (b) Cl; (c) —CF3; (d) —CF2H; (e) —CFH2; (f) —OCF3; (g) —OCF2H; (h) —OCFH2; (i) —OCH3; (j) —O(C1-C4 alkyl); (k) —S(O)CH3; (l) —S(O)CF3; (m) —S(O)2CH3; (n) —S(O)2CF3; (o) —SCF3;
(p) —C1-C4 alkyl selected from methyl, ethyl, isopropyl, and t-butyl;
(q) -3-7 membered saturated, unsaturated, or aromatic heterocycle selected from oxetanyl, azepanyl, pyridyl, dihydropyridyl, furanyl, tetrahydrofuranyl, tetrahydropyridyl, azetidinyl, pyrrolidinyl, piperidinyl, and piperidenyl; and
(r) -3-7 membered saturated, unsaturated, or aromatic carbocycle selected from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, phenyl, cyclohexenyl, and cyclohexadienyl.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R6, R7, and R8 are each independently selected from are each independently selected from (a) F, (b) Cl, (c) —CF3, (d) —OCF3, (e) —OCH3, (f) methyl, (g) ethyl, (h) isopropyl, (i) t-butyl, (j) azepanyl, (k) cyclopropyl, (l) cyclobutyl, (m) cyclohexyl, (n) phenyl, (o) pyridyl, (p) azetidinyl, (q) pyrrolidinyl, (r) piperidinyl, and (s) piperidenyl.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —OR11, (k) —C1-C8 alkyl, (l) haloalkyl, (m) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (n) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
alternatively, one or more of pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) 3-7 membered saturated or unsaturated carbocyclic or (b) 3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur; and
at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen; (b) halogen; (c) —CF3; (d) —CF2H; (e) —CFH2; (f) —OCF3; (g) —OCH3; (h) —OCF2H; (i) —OCFH2; (j) —OH; (k) —O(C1-C4 alkyl);
(l) —C1-C4 alkyl selected from methyl, ethyl, isopropyl, and t-butyl;
(m) -3-7 membered saturated, unsaturated, or aromatic heterocycle selected from oxetanyl, azepanyl, pyridyl, dihydropyridyl, furanyl, tetrahydrofuranyl, tetrahydropyridyl, azetidinyl, pyrrolidinyl, piperidinyl, and piperidenyl; and
(n) -3-7 membered saturated, unsaturated, or aromatic carbocycle selected from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, phenyl, cyclohexenyl, and cyclohexadienyl;
alternatively, one or more of pairs of substituents are selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached form cyclopropyl, cyclobutyl, or oxetanyl; and
at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen;
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (d) —CF3, (e) —CF2H, (f) —CFH2, (g) —OCF3, (h) —OCH3, (i) —OCF2H, (j) —OCFH2, (k) —OH, (l) —OCH3, (l) methyl, (m) ethyl, (n) isopropyl, and (o) t-butyl; and
at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein




is selected from:



































or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

In some embodiments,




is selected from




















In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3 is selected from:
















In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R3b, R6, R7, R8, Z, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R3b, R6, R7, R8, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound of formula F1 or F2, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein
Z is selected from —O—, —S(O)p—, —NR11, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p—, and —NR11S(O)pNR11—;
R3a is selected from halogen and —C1-C6 alkyl;
R3b is selected from hydrogen, halogen, —OCF3, —OCF2H, —OCFH2, —OCH3, —OR11, —C1-C6 alkyl, and haloalkyl;
R6, R7, and R8 are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) Br, (e) I, (f) —CF3, (g) —CF2H, (h) —CFH2, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —CN, (n) —N3, (o) —NO2, (p) —NR11R11, (q) —NR11(CO)R11, (r) —(CO)NR11R11, (s) —OR11, (t) —COH, (u) —CO(C1-C8 alkyl), (v) —COR11, (w) —NR11(CNR11)NR11R11, (x) —S(O)pR11, (y) —NR11S(O)pR11, (z) —SR11, (aa) —SCF3, (bb) —C(CF3)H—NH—CHR11R11, (cc) —COOR11, (dd) —(OCH2CH2)tR11, (ee) —(OCH2CH2)tOR11, (ff) —C1-C8 alkyl, (gg) —C2-C8 alkenyl, and (hh) —C2-C8 alkynyl;
R9o, R9p, R9q, and R9r are each independently selected from (a) hydrogen, (b) halogen, (c) —OCF3, (d) —OCH3, (e) —OCF2H, (f) —OCFH2, (g) —OR11, (h) —C1-C8 alkyl, and (i) haloalkyl;
R11 is selected from hydrogen, —C1-C6 alkyl, —C2-C6 alkenyl, —C2-C6 alkynyl, and haloalkyl;
p is 0, 1, or 2; and
t is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formula F1, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein Z is O;
R9o, R9p, R9q, and R9r are each independently selected from C1-C6 alkyl and hydrogen;
R6 and R8 are each independently selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)pC1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3; and
R3a is selected from halogen and —C1-C6 alkyl;
R3b is selected from hydrogen, halogen, —CF3, —CF2H, —CFH2, —C1-C6 alkyl, and haloalkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formula F2, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o, R9p, R9q, and R9r are each independently selected from —C1-C6 alkyl and hydrogen;
R6 and R8 are each independently selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3; and
R3a is selected from halogen and —C1-C6 alkyl;
R3b is selected from hydrogen, halogen, —CF3, —CF2H, —CFH2, —C1-C6 alkyl, and haloalkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, R9p, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound of formulae G1, G2, G3, or G4, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o, R9p, R9q, and R9r are each independently selected from —C1-C6 alkyl and hydrogen;
R6 and R8 are each independently selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3; and
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae G1, G2, G3, or G4, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o, R9p, R9q, and R9r are each independently selected from —C1-C6 alkyl and hydrogen;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)pC1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9q, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




wherein R3a, R6, R7, R8, and R9r are as defined herein,

or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9r are as defined herein.

In some embodiments, the present invention relates to a compound of formulae H1, H2, H3, or H4, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9q and R9r are each independently selected from —C1-C6 alkyl and hydrogen;
R6 and R8 are each independently selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3; and
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae H1, H2, H3, or H4, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9q and R9r are each independently selected from —C1-C6 alkyl and hydrogen;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae H5, H6, H7, H8, H9, H10, H11, or H12, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9r is —C1-C6 alkyl;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae H5, H6, H7, H8, H9, H10, H11, or H12, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9r is —CH3;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is —CH3; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, R9o, and R9p are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R3a, R6, R7, R8, and R9o are as defined herein.

In some embodiments, the present invention relates to a compound of formulae I1, I2, I3, or I4, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o and R9p are each independently selected from —C1-C6 alkyl and hydrogen;
R6 and R8 are each independently selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, OCHF2, —OCF3, S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3; and
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae I1, I2, I3, or I4, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o and R9p are each independently selected from —C1-C6 alkyl and hydrogen;
R6 is selected from hydrogen, F, Cl, Br, I, C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae I5, I6, I7, I8, I9, I10, I11, or I12, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o is —C1-C6 alkyl;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)pCH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae I5, I6, I7, I8, I9, I10, I11, or I12, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein R9o is —CH3;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)pCH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is —CH3; and
p is 0, 1, or 2.
In some embodiments, the present invention relates to a compound of formulae IV, V, VI, VII, VIII, IX, X, XI, XXa, XXa1, Va, VIIa, VIIa, VIIIa, IXa, Xa, XIa, XII, XIII, XIV, XV, XVI, XVII, XVIII, XXb, XXb1, XIIa, XIIIa, XIVa, XVa, XVIa, XVIIa, XVIIIa, F1, or F2, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein the moiety




and R3b is H, is selected from:























In some embodiments, the present invention relates to a compound of formulae F1 (R3b is H), F2 (R3b is H), G2, G4, H2, H4, H6, H8, H10, H12, I2, I4, I6, I8, I10, or I12, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein the moiety




is selected from:














In some embodiments, the present invention relates to a compound of formulae F1 (R3b is H), F2 (R3b is H), G1, G3, H1, H3, H5, H7, H9, H11, I1, I3, I5, I7, I9, or I11, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein the moiety




is selected from:











In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to any one the compounds in Table 1, Table 2, Table 2a, and Table 2aa.
In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer that binds the ribosome. In some embodiments, the ribosome is a bacterial ribosome.
In some embodiments, the present invention relates to a pharmaceutical composition comprising a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, and a pharmaceutically acceptable carrier. In some embodiments, the present invention relates to a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer of the invention and a means for delivery.
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a disease state in a human or animal comprising administering to the human or animal in need thereof an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.
In some embodiments, the present invention relates to a method of treating, preventing, or reducing a microbial infection in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.
In some embodiments, the present invention relates to use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing, or reducing a microbial infection in a human or animal.
In some embodiments, the present invention relates to a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, for use in treating, preventing, or reducing a microbial infection in a human or animal.
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a microbial infection in a human or animal comprising administering to the human or animal an effective amount of a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein said microbial infection is caused by one or more of the following microorganisms: Acinetobacter spp. (Acinetobacter baumanni), Bacteroides distasonis, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Citrobacter freundii, Citrobacter koser, Clostridium clostridioforme, Clostridium perfringens, Enterobacter aerogenes, Enterobacter cloacae, Enterococcus faecalis, Enterococcus spp. (vancomycin susceptible and resistant isolates), Escherichia coli (including ESBL and KPC producing isolates), Eubacterium lentum, Fusobacterium spp., Haemophilus influenzae (including beta-lactamase positive isolates), Haemophilus parainfluenzae, Klebsiella pneumoniae (including ESBL and KPC producing isolates), Klebsiella oxytoca (including ESBL and KPC producing isolates), Legionella pneumophilia Moraxella catarrhalis, Morganella morganii, Mycoplasma spp., Peptostreptococcus spp., Porphyromonas asaccharolytica, Prevotella bivia, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Serratia marcescens, Streptococcus anginosus, Staphylococcus aureus (methicillin susceptible and resistant isolates), Staphylococcus epidermidis (methicillin susceptible and resistant isolates), Stenotrophomonas maltophilia, Streptococcus agalactiae, Streptococcus constellatus, Streptococcus pneumoniae (penicillin susceptible and resistant isolates), Streptococcus pyogenes, or Streptococcus pyogenes. 
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a microbial infection in a human or animal comprising administering to the human or animal an effective amount of a compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein said infection is caused by or involves one or more microorganisms selected from: Acinetobacter spp. (Acinetobacter baumanni), Bacteroides distasonis, Bacteroides fragilis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Citrobacter freundii, Citrobacter koser, Clostridium clostridioforme, Clostridium perfringens, Enterobacter aerogenes, Enterobacter cloacae, Enterococcus faecalis, Enterococcus spp., Escherichia coli, Eubacterium lentum, Fusobacterium spp., Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella pneumoniae, Klebsiella oxytoca, Legionella pneumophilia, Moraxella catarrhalis, Morganella morganii, Mycoplasma spp., Peptostreptococcus spp., Porphyromonas asaccharolytica, Prevotella bivia, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, Pseudomonas aeruginosa, Serratia marcescens, Streptococcus anginosus, Staphylococcus aureus, Staphylococcus epidermidis, Stenotrophomonas maltophilia, Streptococcus agalactiae, Streptococcus constellatus, Streptococcus pneumoniae, Streptococcus pyogenes, and Streptococcus pyogenes. 
In some embodiments, the present invention relates to a method wherein said infection is caused by or involves one or more of aerobic and facultative gram-positive microorganism selected from: Staphylococcus aureus, Streptococcus pneumoniae, Enterococcus spp., Streptococcus agalactiae, Streptococcus pyogenes, and Staphylococcus epidermidis. 
In some embodiments, the present invention relates to a method wherein said infection is caused by or involves one or more of aerobic and facultative gram-negative microorganism selected from: Escherichia coli, Haemophilus influenzae, Klebsiella pneumoniae, Citrobacter freundii, Enterobacter aerogenes, Enterobacter cloacae, Morganella morganii, Serratia marcescens, Pseudomonas aeruginosa, Acinetobacter baumanni, Moraxella catarrhalis, Proteus mirabilis, Citrobacter koseri, Haemophilus parainfluenzae, Klebsiella oxytoca, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. 
In some embodiments, the present invention relates to a method wherein, said infection is caused by or involves one or more of anaerobic microorganism: Bacteroides fragilis, Bacteroides distasonis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Clostridium clostridioforme, Eubacterium lentum, Peptostreptococcus spp., Porphyromonas asaccharolytica, Prevotella bivia, Bacteroides vulgatus, Clostridium perfringens, and Fusobacterium spp.
In some embodiments, the present invention relates to a method, wherein the microorganism Enterococcus spp. is selected from vancomycin susceptible isolate and vancomycin resistant isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Escherichia coli is selected from extended spectrum beta-lactamase (ESBL) producing isolate and Klebsiella pneumoniae carbapenemase (KPC) producing isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Haemophilus influenzae is a beta-lactamase positive isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Klebsiella pneumoniae is selected from extended spectrum beta-lactamase (ESBL) producing isolate and Klebsiella pneumoniae carbapenemase (KPC) producing isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Klebsiella oxytoca selected from extended spectrum beta-lactamase (ESBL) producing isolate and Klebsiella pneumoniae carbapenemase (KPC) producing isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Staphylococcus aureus is selected from methicillin susceptible isolate and methicillin resistant isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Staphylococcus epidermidis is selected from methicillin susceptible isolate and methicillin resistant isolate.
In some embodiments, the present invention relates to a method wherein, the microorganism Streptococcus pneumoniae is selected from penicillin susceptible isolate and penicillin resistant isolate.
In some embodiments, the present invention relates to a method of treating, preventing or reducing the risk of a microbial infection in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing, or reducing the risk of a microbial infection in a human or animal,

    
    
        wherein the microbial infection is selected from the group consisting of a skin infection, a Gram positive infection, a Gram negative infection, nosocomial pneumonia, community acquired pneumonia, post-viral pneumonia, hospital acquired pneumonia/ventilator associated pneumonia, a respiratory tract infection such as chronic respiratory tract infection (CRTI), acute pelvic infection, a complicated skin and skin structure infection, a skin and soft tissue infection (SSTI) including uncomplicated skin and soft tissue infections (uSSTI)s and complicated skin and soft tissue infections, an abdominal infection, a complicated intra-abdominal infection, a urinary tract infection, bacteremia, septicemia, endocarditis, an atrio-ventricular shunt infection, a vascular access infection, meningitis, surgical prophylaxis, a peritoneal infection, a bone infection, a joint infection, a methicillin-resistant Staphylococcus aureus infection, a vancomycin-resistant Enterococci infection, a linezolid-resistant organism infection, a Bacillus anthracis infection, a Francisella tularensis infection, a Yersinia pestis infection, and tuberculosis.
    
    


The compounds of the present invention can be used, for example for the treatment of patients with moderate to severe infections, which may be caused by susceptible isolates of the indicated microorganisms:
In some embodiments, the present invention relates to a method of treating, preventing or reducing the risk of a complicated intra-abdominal infection in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a complicated intra-abdominal infection in a human or animal,
In some embodiments, the complicated intra-abdominal infection is selected from polymicrobial infections such as abscess due to Escherichia coli, Clostridium clostridioforme, Eubacterium lentum, Peptostreptococcus spp., Bacteroides fragilis, Bacteroides distasonis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Streptococcus anginosus, Streptococcus constellatus, Enterococcus faecalis, Proteus mirabilis, or Clostridium perfringens. 
In some embodiments, the present invention relates to a method of treating, preventing or reducing the risk of a complicated skin and skin structure infection (cSSSI, also known as acute bacterial skin and skin structure infections or ABSSSI) in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a complicated skin and skin structure infection,
In some embodiments, the complicated skin and skin structure infection is selected from diabetic foot infections without osteomyelitis due to Staphylococcus aureus (methicillin susceptible and resistant isolates), Streptococcus agalactiae, Streptococcus pyogenes, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Bacteroides fragilis, Peptostreptococcus species, Porphyromonas asaccharolytica, or Prevotella bivia. 
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a community acquired pneumonia (CAP) in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of community acquired pneumonia,
In some embodiment, the community acquired pneumonia is due to Streptococcus pneumoniae (penicillin susceptible and resistant isolates) including cases with concurrent bacteremia, Haemophilus influenzae (including beta-lactamase positive isolates), Moraxella catarrhalis, or atypical bacteria like Mycoplasma spp.
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a complicated urinary tract infection (cUTI) in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a complicated urinary tract infection,
In some embodiment, the complicated urinary tract infection is selected from pyelonephritis due to Escherichia coli, concurrent bacteremia, or Klebsiella pneumoniae. 
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of an acute pelvic infection in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of an cute pelvic infection,
In some embodiments, the acute pelvic infection is selected from postpartum endomyometritis, septic abortion and post surgical gynecologic infections and the infection is due to a microorganism selected from Streptococcus agalactiae, Escherichia coli, Bacteroides fragilis, Porphyromonas asaccharolytica, Peptostreptococcus spp., and Prevotella bivia. 
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a hospital acquired pneumonia (HAP)/ventilator associated pneumonia (VAP) in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of hospital acquired pneumonia/ventilator associated pneumonia,
In some embodiments, the hospital acquired pneumonia/ventilator associated pneumonia is due to a microorganism selected from Streptococcus pneumoniae (penicillin susceptible and resistant isolates), Staphylococcus aureus (methicillin susceptible and resistant isolates), Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., Stenotrophomonas maltophilia, Haemophilus influenzae (including beta-lactamase positive isolates), and Legionella pneumophilia. 
The compounds or tautomers or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers of the present invention may also be useful for the prevention, prophylaxis, or reduction of surgical site infections. In some embodiments, the compounds or tautomers or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers of the present invention are useful following elective colorectal surgery.
Appropriate specimens for bacteriological examination should be obtained in order to isolate and identify the causative organisms and to determine their susceptibility to the compounds of the present invention. Therapy with the compounds or tautomers or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers of the present invention may be initiated empirically before results of these tests are known; once results become available, antimicrobial therapy should be adjusted accordingly.
To reduce the development of drug-resistant bacteria and maintain the effectiveness of the compounds or tautomers or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers of the present invention and other antibacterial drugs, the compounds or tautomers or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers should be used only to treat or prevent infections that are proven or strongly suspected to be caused by susceptible bacteria. When culture and susceptibility information are available, they should be considered in selecting or modifying antibacterial therapy. In the absence of such data, local epidemiology and susceptibility patterns may contribute to the empiric selection of therapy.
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a microbial infection due to an aerobic or facultative gram-positive microorganism in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a microbial infection due to an aerobic or facultative gram-positive microorganism.
In some embodiments, the aerobic or facultative gram-positive microorganism is selected from:
Staphylococcus aureus (methicillin susceptible and resistant isolates), Streptococcus pneumoniae (penicillin susceptible and resistant isolates), Enterococcus spp. (vancomycin susceptible and resistant isolates), Streptococcus agalactiae, Streptococcus pyogenes, and Staphylococcus epidermidis (methicillin susceptible and resistant isolates).
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a microbial infection due to an aerobic and facultative gram-negative microorganism in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a microbial infection due to an aerobic or facultative gram-positive microorganism.
In some embodiments, the aerobic and facultative gram-negative microorganism is selected from: Escherichia coli [including extended spectrum beta-lactamase (ESBL) and Klebsiella pneumonia (KPC) producing isolates), Haemophilus influenzae (including Beta-lactamase positive isolates), Klebsiella pneumoniae (including ESBL and KPC producing isolates), Citrobacter freundii, Enterobacter aerogenes, Enterobacter cloacae, Morganella morganii, Serratia marcescens, Pseudomonas aeruginosa, Acinetobacter baumanni, Moraxella catarrhalis, Proteus mirabilis, Citrobacter koseri, Haemophilus parainfluenzae, Klebsiella oxytoca (including ESBL and KPC producing isolates), Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. 
In some embodiments, the present invention relates to a method of treating, preventing, or reducing the risk of a microbial infection due to an anaerobic microorganism in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a microbial infection due to an anaerobic microorganism.
In some embodiments, the anaerobic microorganism is selected from: Bacteroides fragilis, Bacteroides distasonis, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Clostridium clostridioforme, Eubacterium lentum, Peptostreptococcus species, Porphyromonas asaccharolytica, Prevotella bivia, Bacteroides vulgates, Clostridium perfringens, and Fusobacterium spp.
In some embodiments, the present invention relates to a method of treating or reducing the risk of a microbial infection in a human or animal comprising administering to the human or animal an effective amount of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, or to the use of a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, in the manufacture of a medicament for treating, preventing or reducing the risk of a microbial infection.
In some embodiments, the microorganism is Legionella pneumophilia. 
In some embodiments, the microorganism Enterococcus spp. is selected from vancomycin susceptible isolate and vancomycin resistant isolate. In some embodiments, the microorganism Escherichia coli is selected from extended spectrum beta-lactamase (ESBL) producing isolate and Klebsiella pneumoniae carbapenemase (KPC) producing isolate. In some embodiments, the microorganism Haemophilus influenzae is a beta-lactamase positive isolate. In some embodiments, the microorganism Klebsiella pneumoniae is selected from extended spectrum beta-lactamase (ESBL) producing isolate and Klebsiella pneumoniae carbapenemase (KPC) producing isolate. In some embodiments, the microorganism Klebsiella oxytoca selected from extended spectrum beta-lactamase (ESBL) producing isolate and Klebsiella pneumoniae carbapenemase (KPC) producing isolate. In some embodiments, the microorganism Staphylococcus aureus is selected from methicillin susceptible isolate and methicillin resistant isolate. In some embodiments, the microorganism Staphylococcus epidermidis is selected from methicillin susceptible isolate and methicillin resistant isolate. In some embodiments, the microorganism Streptococcus pneumoniae is selected from penicillin susceptible isolate and penicillin resistant isolate.
In some embodiments, the present invention relates to a method, use, or compound of the invention, wherein the amount of compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer comprises from 0.1 mg to 1500 mg.
In some embodiments, the present invention relates to a method, use, or compound of the invention wherein the amount of compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer comprises about 25 mg, or about 50 mg, or about 75 mg, or about 100 mg, or about 125 mg, or about 150 mg, or about 175 mg, or about 200 mg, or about 225 mg, or about 250 mg, or about 275 mg, or about 300 mg, or about 325, or about 350 mg, or about 375 mg, or about 400 mg, or about 425 mg, or about 450 mg, or about 475 mg, or about 500 mg, or about 525 mg, or about 550 mg, or about 575 mg, or about 600 mg, or about 625 mg, or about 650 mg, or about 675 mg, or about 700 mg, or about 725 mg, or about 750 mg, or about 775 mg, or about 800 mg, or about 825 mg, or about 850 mg, or about 875 mg, or about 900 mg, or about 925 mg, or about 950 mg, or about 975 mg, or about 1000 mg, or about 1025 mg, or about 1050, mg, or about 1075 mg, or about 1100 mg, or about 1125 mg, or about 1150 mg, or about 1175 mg, or about 1200 mg, or about 1225 mg, or about 1250 mg, or about 1275 mg, or about 1300 mg, or about 1325 mg, or about 1350 mg, or about 1375 mg, or about 1400 mg, or about 1425 mg, or about 1450 mg, or about 1475 mg, or about 1500 mg.
In some embodiments, the present invention relates to a method, use, or compound of the invention wherein the compound, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, is administered otically, ophthalmically, nasally, orally, parenterally, topically, or intravenously.
In some embodiments, the present invention relates to a method of synthesizing a compound of the invention, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.
In some embodiments, the present invention relates to a medical device containing a compound of the invention or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer. In some embodiments, the device is a stent.
3. SYNTHESIS OF THE COMPOUNDS OF THE INVENTION
Compounds of the invention can be prepared according to methods known in the art. More specifically, compounds of the invention can be prepared according to the procedures and examples described herein. In one aspect, a compound of the invention can be synthesized by coupling two fragments A and B:




In one aspect, a compound of the invention can be synthesized as outlined Scheme 1.




In one aspect, a compound of the invention can be synthesized as outlined in Scheme 2. The scheme depicts the preparation of a compound of formula I having certain values where X3 is CR3 and Y9 is CR9. It is understood that one skilled in the art would be able to readily apply this scheme for the synthesis of compounds having other R3 and R9 groups as described herein.




In one aspect, the transformation of step 1 of the synthesis described above is based on a coupling reaction of Fragments A and B to form the core pyrrolocytosine ring. See e.g., Wojciechowski, F., Hudson, R. H. E. “Peptide Nucleic Acid Containing a Meta-Substituted Phenylpyrrolocytosine Exhibits a Fluorescence Response and Increased Binding Affinity toward RNA.” Org. Lett. 2009, 11(21), 4878-4881 and Wojciechowski, F., Hudson, R. H. E. “Fluorescence and Hybridization Properties of Peptide Nucleic Acid Containing a Substituted Phenylpyrrolocytosine Designed to Engage Guanine with an Additional H-Bond” J. Am. Chem. Soc., 2008, 130(38), 12574-12575. In one aspect, X in Fragment A is I or Br and R3a, R3b, R3e, R3f, R3g, R3h, R3i, R3j, R6, R7, R8, R9k, R9l, R9o, R9p, R9q, R9p, R9q, R9r, and Z are as described herein.
Fragments A and B can be coupled using a variety of methods known in the art. Step 2 of the synthesis involves the installation of a guanidine functional group using methods known in the art. In one aspect, the protected terminal amine on the left-hand side of the molecule can be deprotected to afford the primary amine. Guanidine can then be installed by selective addition to the primary amine on the basis of steric factors and the diminished reactivity of the benzylic nitrogen. Global deprotection then produces the final compound in the form of a polyamine salt.
In one aspect, a compound of the invention can be synthesized as shown in the Scheme 3. The scheme depicts the preparation of a compound having certain values defined, however one skilled in the art would understand that the methodology outlined below could be readily applied for the preparation of other compounds of the invention described herein.




Although Scheme 3 shown above is depicted with certain values for R3a, R9o, R9r, and Z, it is understood that one skilled in the art would be able to readily apply this scheme for the synthesis of compounds having other R3a, R9o, R9r, and Z groups. Furthermore, it is understood that Scheme 3 above is applicable for the variety of aryl groups described herein e.g.,




Preparation of Fragment A

Fragment A intermediates can be prepared according to methods known in the art. The schemes below outline strategies that can be applied for the synthesis of Fragment A intermediates and used to prepare compounds of the invention. Procedures for the preparation of Fragment A intermediates are also found in the examples provided herein. In one aspect, Fragment A can be synthesized using a 4 step process as outlined below.
Step 1 uses a reductive amination strategy to form a benzyl amine intermediate. The amine and aldehyde groups can be on either one of the compounds involved in the reductive amination reaction. Reductive amination is a well known procedure in the chemical arts and thus, the skilled person would be able to optimize Step 1 for the preparation of a compound of the invention.




Following formation of the benzyl amine intermediate, Step 2 is a coupling reaction to form a pinacol borane compound, which is then coupled in Step 3 with an iodocytosine moiety. Step 4 involves acylation of the amine group of the pyrimidinone to form a Fragment A intermediate.





Scheme 6 and Scheme 7 below show a 4-step for the synthesis of the Fragment A intermediate:




Although the schemes depict the preparation of compounds having certain values defined, one skilled in the art would understand that the methodology outlined below could be readily applied for the preparation of other compounds of the invention described herein. The scheme below shows two alternative procedures for Step 1 in the synthesis of the Fragment A intermediate above. In the first procedure, the resulting benzyl amine intermediate does not have a substituent at the benzylic position (i.e., R3a═H). In the second procedure, the resulting benzyl amine intermediate has at least one substituent (R3a is not H) in the benzylic position. It is understood that the second procedure can be used to prepare a variety of different benzyl amine intermediates e.g., intermediates with R3a selected from ethyl, propyl, alkenyl, cyclopropyl, CO2H, CO2Me, alkyl substituted with CO2Me, CO2H, etc.





Steps 2-4 are shown below for the preparation of Fragment A. The steps are the same for compounds having R3a as H or CH3. Although the steps are depicted with compounds having R3a defined as H or CH3, one skilled in the art could readily apply the procedures described herein and in the examples for the preparation of a different Fragment A e.g., a Fragment A with R3a selected from ethyl, propyl, alkenyl, cyclopropyl, CO2H, CO2Me, alkyl substituted with CO2Me, CO2H, etc.





Preparation of Fragment B

Fragment B intermediates can be prepared according to methods known in the art. The schemes below outline strategies that can be applied for the synthesis of Fragment B intermediates and used to prepare compounds of the invention. Procedures for the preparation of Fragment B intermediates are also found in the examples provided herein. Scheme 8 below is a retro-synthetic analysis which shows the strategy for attaching a R9 group to the aryl moiety. The strategy involves the coupling of an aryl halide with an aminoalkene moiety. This strategy is applicable for the synthesis of Fragment B intermediates where the R9 group is an all carbon chain (i.e., Z is CH2). Although the Scheme 8 illustrates a transformation to form a Fragment B intermediate with a certain R9 group, it is understood that the strategy can be applied to prepare different Fragment B intermediates with a different R9 group as described herein, where Z is CH2.




An example of the preparation of the aminoalkene compound is shown below. Further details regarding the preparation of this aminoalkene compound are found in the examples herein.




Alternatively, Scheme 9 below depicts a retro-synthetic strategy for the synthesis of Fragment B intermediates that have an oxygen atom in the R9 chain. In one aspect, the synthesis of the Fragment B intermediate begins with a dibromide or dihalide (Br and I) aryl compound (labeled A and B below). The synthesis involves conversion of an aryl bromide or iodide to an aldehyde group, reduction of the aldehyde to a primary alcohol, which is next converted to a leaving group (LG). The R9 chain is then elaborated by the displacement of the OLG group with a primary alcohol. The primary alcohol has functionality that can be unmasked and elaborated to a nitrogen group using chemistry known in the art.




Alternatively, the R9 chain can be installed to produce a Fragment B intermediate starting with an aldehyde aryl compound (labeled C in Scheme 9). The synthesis can involve a Wittig olefination reaction to install the R9 chain as shown in Scheme 10, which depicts the retro-synthesis of fragment B.




It is understood that the synthetic procedures described above and in the examples can be used to prepare compounds of the invention having a variety of different aryl groups. Some representative aryl groups include e.g.,




It is understood that the synthetic procedures described above and in the examples can be used to prepare compounds of the invention having a variety of different R9 chains. Some representative R9 chains include e.g.,




In the last R9 chain, there is no CH2 group between the aryl group and cyclic group.

Precursors for the preparation of the R9 chain include e.g.,




The three schemes (Schemes 11-13) below illustrate several general strategies for preparing Fragment B intermediates. Scheme 11 illustrates how the dihalide aryl compound (labelled compound 8) is a key intermediate which can be coupled with a variety of different R9 chains to synthesize a Fragment B intermediate and used to prepare many of the compounds of the invention. Synthetic procedures for the preparation of dihalide aryl intermediates used to prepare compounds of the invention are found in the examples herein.




Scheme 12 shows a key transformation of the dihalide aryl intermediate compound 8 to compound 21, which can be elaborated to many different Fragment B intermediates.







Scheme 13 emphasizes the utility of the aniline moiety for the regioselective installation of either iodide or bromide either in a stepwise manner (eg. 2→6→7) or in one pot (2→3). The diversity of aniline compounds, either commercially available or prepared from other starting materials (eg. 1→2), allows access to a variety of substitution patterns.




Scheme 14 below shows the preparation of a Fragment B intermediate having a ring in the R9 chain. In one aspect, the process of attaching the R9 group to the aryl moiety includes coupling of a dihalide aryl intermediate compound 8 with an aminoalkene moiety having a ring structure e.g.,




Scheme 14 illustrates a strategy for preparing R9 chains having any size ring incorporated into the chain e.g., a 3-, 4-, 5-, 6-, etc. membered ring. In one aspect, the amino group can be installed via either a Curtius rearrangement (2→3) or a nitrile reduction (1→7). In one aspect, the aminoalkene moiety can be attached to the aryl moiety via the Suzuki-coupling reaction. For example, the aminoalkene can first be converted to a alkylborane by treatment with 9-BBN and then reacted with compound 8, replacing the more reactive iodide first. The terminal alkyne can be installed by a variety of methods know in the art. Reagents such as trimethylsilyl acetylene can be employed to generate fragment B.




4. CHARACTERIZATION OF COMPOUNDS OF THE INVENTION
Compounds designed, selected and/or optimized by methods described above, once produced, can be characterized using a variety of assays known to those skilled in the art to determine whether the compounds have biological activity. For example, the molecules can be characterized by conventional assays, including but not limited to those assays described below, to determine whether they have a predicted activity, binding activity and/or binding specificity.
Furthermore, high-throughput screening can be used to speed up analysis using such assays. As a result, it can be possible to rapidly screen the molecules described herein for activity, for example, as anti-cancer, anti-bacterial, anti-fungal, anti-parasitic or anti-viral agents. Also, it can be possible to assay how the compounds interact with a ribosome or ribosomal subunit and/or are effective as modulators (for example, inhibitors) of protein synthesis using techniques known in the art. General methodologies for performing high-throughput screening are described, for example, in Devlin (1998) High Throughput Screening, Marcel Dekker; and U.S. Pat. No. 5,763,263. High-throughput assays can use one or more different assay techniques including, but not limited to, those described below.
(1) Surface Binding Studies.
A variety of binding assays can be useful in screening new molecules for their binding activity. One approach includes surface plasmon resonance (SPR) that can be used to evaluate the binding properties of molecules of interest with respect to a ribosome, ribosomal subunit or a fragment thereof.
SPR methodologies measure the interaction between two or more macromolecules in real-time through the generation of a quantum-mechanical surface plasmon. One device, (BIAcore Biosensor® from Pharmacia Biosensor, Piscataway, N.J.) provides a focused beam of polychromatic light to the interface between a gold film (provided as a disposable biosensor “chip”) and a buffer compartment that can be regulated by the user. A 100 nm thick “hydrogel” composed of carboxylated dextran that provides a matrix for the covalent immobilization of analytes of interest is attached to the gold film. When the focused light interacts with the free electron cloud of the gold film, plasmon resonance is enhanced. The resulting reflected light is spectrally depleted in wavelengths that optimally evolved the resonance. By separating the reflected polychromatic light into its component wavelengths (by means of a prism), and determining the frequencies that are depleted, the BIAcore establishes an optical interface which accurately reports the behavior of the generated surface plasmon resonance. When designed as above, the plasmon resonance (and thus the depletion spectrum) is sensitive to mass in the evanescent field (which corresponds roughly to the thickness of the hydrogel). If one component of an interacting pair is immobilized to the hydrogel, and the interacting partner is provided through the buffer compartment, the interaction between the two components can be measured in real time based on the accumulation of mass in the evanescent field and its corresponding effects of the plasmon resonance as measured by the depletion spectrum. This system permits rapid and sensitive real-time measurement of the molecular interactions without the need to label either component.
(2) Fluorescence Polarization.
Fluorescence polarization (FP) is a measurement technique that can readily be applied to protein-protein, protein-ligand, or RNA-ligand interactions in order to derive IC50s and Kds of the association reaction between two molecules. In this technique one of the molecules of interest is conjugated with a fluorophore. This is generally the smaller molecule in the system (in this case, the compound of interest). The sample mixture, containing both the ligand-probe conjugate and the ribosome, ribosomal subunit or fragment thereof, is excited with vertically polarized light. Light is absorbed by the probe fluorophores, and re-emitted a short time later. The degree of polarization of the emitted light is measured. Polarization of the emitted light is dependent on several factors, but most importantly on viscosity of the solution and on the apparent molecular weight of the fluorophore. With proper controls, changes in the degree of polarization of the emitted light depends only on changes in the apparent molecular weight of the fluorophore, which in-turn depends on whether the probe-ligand conjugate is free in solution, or is bound to a receptor. Binding assays based on FP have a number of important advantages, including the measurement of IC50s and Kds under true homogenous equilibrium conditions, speed of analysis and amenity to automation, and ability to screen in cloudy suspensions and colored solutions.
(3) Protein Synthesis.
It is contemplated that, in addition to characterization by the foregoing biochemical assays, the compound of interest can also be characterized as a modulator (for example, an inhibitor of protein synthesis) of the functional activity of the ribosome or ribosomal subunit.
Furthermore, more specific protein synthesis inhibition assays can be performed by administering the compound to a whole organism, tissue, organ, organelle, cell, a cellular or subcellular extract, or a purified ribosome preparation and observing its pharmacological and inhibitory properties by determining, for example, its inhibition constant (IC50) for inhibiting protein synthesis. Incorporation of 3H leucine or 35S methionine, or similar experiments can be performed to investigate protein synthesis activity. A change in the amount or the rate of protein synthesis in the cell in the presence of a molecule of interest indicates that the molecule is a modulator of protein synthesis. A decrease in the rate or the amount of protein synthesis indicates that the molecule is a inhibitor of protein synthesis.
(4) Antimicrobial Assays and Other Evaluation.
Furthermore, the compounds can be assayed for anti-proliferative or anti-infective properties on a cellular level. For example, where the target organism is a microorganism, the activity of compounds of interest can be assayed by growing the microorganisms of interest in media either containing or lacking the compound. Growth inhibition can be indicative that the molecule can be acting as a protein synthesis inhibitor. More specifically, the activity of the compounds of interest against bacterial pathogens can be demonstrated by the ability of the compound to inhibit growth of defined strains of human pathogens. For this purpose, a panel of bacterial strains can be assembled to include a variety of target pathogenic species, some containing resistance mechanisms that have been characterized. Use of such a panel of organisms permits the determination of structure-activity relationships not only in regards to potency and spectrum, but also with a view to obviating resistance mechanisms.
The in vitro activity of the compounds of the present invention can be determined. Antimicrobial testing is typically performed to determine the minimum inhibitory concentration (MIC). Minimum inhibitory concentrations (MICs) are determined by the microdilution method in a final volume of 100 μl according to protocols outlined by The Clinical and Laboratory Standards Institute (CLSI). Performance standards for reference strains are assessed within the same experimental design to maintain quality control. See, for example, Clinical Laboratory Standards Institute: Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically M7-A8. Approved Standard-Eighth Edition. Wayne, Pa.: CLSI; December 2008; and Clinical Laboratory Standards Institute: Performance Standards for Antimicrobial Susceptibility Testing M100-S20; Approved Standard-Twentieth Edition. Wayne, Pa.: CLSI; June 2010.
The antimicrobial and other drug properties of the compounds can further be evaluated in various in vivo mammalian assays, such as a mouse or rat peritonitis infectious models, skin and soft tissue models (often referred to as the thigh model), or a mouse pneumonia model. There are septicemia or organ infection models known to those skilled in the art. These efficacy models can be used as part of the evaluation process and can be used as a guide of potential efficacy in humans. Endpoints can vary from reduction in bacterial burden to lethality. For the latter endpoint, results are often expressed as a PD50 value, or the dose of drug that protects 50% of the animals from mortality.
To further assess a compound's drug-like properties, measurements of inhibition of cytochrome P450 enzymes and phase II metabolizing enzyme activity can also be measured either using recombinant human enzyme systems or more complex systems like human liver microsomes. Further, compounds can be assessed as substrates of these metabolic enzyme activities as well. These activities are useful in determining the potential of a compound to cause drug-drug interactions or generate metabolites that retain or have no useful antimicrobial activity.
To get an estimate of the potential of the compound to be orally bioavailable, one can also perform solubility and Caco-2 assays. The latter is a cell line from human epithelium that allows measurement of drug uptake and passage through a Caco-2 cell monolayer often growing within wells of a 24-well microtiter plate equipped with a 1 micron membrane. Free drug concentrations can be measured on the basolateral side of the monolayer, assessing the amount of drug that can pass through the intestinal monolayer. Appropriate controls to ensure monolayer integrity and tightness of gap junctions are needed. Using this same system one can get an estimate of P-glycoprotein mediated efflux. P-glycoprotein is a pump that localizes to the apical membrane of cells, forming polarized monolayers. This pump can abrogate the active or passive uptake across the Caco-2 cell membrane, resulting in less drug passing through the intestinal epithelial layer. These results are often done in conjunction with solubility measurements and both of these factors are known to contribute to oral bioavailability in mammals. Measurements of oral bioavailability in animals and ultimately in man using traditional pharmacokinetic experiments will determine the absolute oral bioavailability.
Experimental results can also be used to build models that help predict physical-chemical parameters that contribute to drug-like properties. When such a model is verified, experimental methodology can be reduced, with increased reliance on the model predictability.
(5) Animal Pharmacology and Toxicology.
The compounds of the present invention can be evaluated for efficacy in well-known animal models. The following table provides representative animal models for various infection indications.











Target



Infection


Indication
Animal Model of Efficacy







HAP/VAP
Efficacy in mouse and/or rat pneumoniae model vs.



respiratory tract infection pathogens of interest



(Streptococcus pneumoniae, including multi-drug resistant



Streptococcus pneumoniae, H. influenzae, methicillin



resistant Staphylococcus aureus (MRSA), and



Pseudomonas. aeruginosa)


cSSSI
Efficacy in mouse model against pathogens of interest



(MRSA, K. pneumoniae)


Sepsis
Efficacy in mouse peritonitis model vs. pathogens of



interest (E. coli, K. pneumoniae, E. faecalis, MRSA)


cUTI
Efficacy in mouse model against E. coli, K. pneumoniae



and/or MRSA)


Febrile
Efficacy in mouse peritonitis model against S. aureus,


neutropenia
S. epidermidis, S. pneumoniae, S. pyogenes, P. aeruginosa









Animal Model for Complicated Skin and Skin Structure Infections (cSSSI): Murine Skin and Soft Tissue Infection Model of Klebsiella pneumoniae 1705966 in Thighs of Neutropenic Female CD-1 Mice

This model is useful to assess the efficacy of compounds of the present invention in a Klebsiella pneumoniae 1705966 neutropenic mouse thigh infection model using female ICR (CD-1) mice.
Study Design:
Species: Female ICR (CD-1) Mice, 8 to 9 weeks old, weighting 25-29 g.
Inoculum: Klebsiella pneumoniae 17059663 was streaked from frozen stock onto Blood agar (Tryptic Soy Agar+5% Sheep Blood), BD, #221261) and incubated overnight at 35° C. After overnight incubation, enough bacteria (approx. 1 full loop) to measure OD625=0.990 was transferred from plate and diluted into 10 ml pre-warmed Mueller-Hinton broth. This culture was further diluted 1:1000 into pre-warmed MH broth and grown for approximately 2 hrs at 35° C. with shaking. Each mouse was given 0.1 mL of 1:1000 dilution culture injected into both caudal thigh muscles under isoflurane inhalation anesthesia.

















Final O.D.



Dilution
Initial O.D.
(after ~2 hr. incubation)









1:10
0.135
0.424



1:100
0.014
0.215



1:1000
0.001
0.035










Neutropenia is induced by intraperitoneal (I.P.) administration of Cyclophosphamide monohydrateon Day −4 (150 mg/kg) and Day −1 (100 mg/kg).

    
    
        Vehicle: 0.9% sodium chloride
        Dosing: Each mouse in the treated groups was given the appropriate dose of the compound to be tested in a volume of 0.2 ml, 2 and 8 hrs. post bacterial inoculation.
        Time points:
        Controls: 0, 2, 6, and 24 hrs.
        Treated: 24 hrs.
    
    


Sampling: 2 or 3 mice/time point were euthanized via CO2, and their caudal thigh muscles excised and homogenized. The thigh muscles were placed in 5 ml sterile PBS in Stomacher Filter bag and homogenized with MicroBiomaster80 (Brinkmann) for 60 seconds, normal setting and 1:10 dilutions were made per standard protocol in a 96-well plate. Aliquots of 25 ul for each dilution, as well as the homogenate, were plated on blood agar plates and incubated at 35° C. to determine the CFU/mL over the time course. After overnight incubation, colonies were counted.
Animal Model for Sespsis:
Murine Peritonitis Model (E. Coli, K. Pneumoniae, E. Faecalis, MRSA)
This model is used to evaluate the effect of subcutaneous (SC) treatment with compounds of the present invention on growth of Escherichia coli ATCC 25922 in a mouse peritonitis model using female Swiss Webster mice.
Controls:


    
    
        Negative: Inoculum only
        Inoculum Vehicle Intraperitoneal
        Positive: Ciprofloxacin

Study Design:

    
    


Species: Female Swiss Webster Mice
Inoculation: Escherichia coli ATCC 25922 is made by adding 1 ml (Apr. 6, 2007) stock to 9 ml 0.25% Brewer's Yeast to make (1:10), then 1 ml of the (1:10) will be added to 9 ml 0.25% Brewer's Yeast to make (1:100), then 1 ml of the (1:100) will be added to 9 ml 0.25% Brewer's Yeast to make (1:1000), then 2.5 ml of the (1:1000) will be added to 122.5 ml 0.25% Brewer's Yeast to make (1:50,000), 1 ml/mouse will by inoculated intraperitoneally (IP).
Route of Administration: SC
Dosing: Vehicle for compounds of the present invention: Saline or 50 mM Sodium phosphate buffer in 10% Captisol in water, pH=7.2.
Dose Administration: Q3H×3 beginning at 30 min post bacterial inoculation
Study Duration: 24 hrs. 0.25% Brewer's Yeast Extract (BYE): Dilute 2% prepared on Nov. 12, 2009 (Lot. 2158K, MP Biomedicals) 25 ml 2%+175 ml 1×PBS.
Outcome Measures: Colony Forming Unit's from peritoneal wash and spleen homogenate and drug levels from wash, spleen homogenate, and plasma.
Blood is collected via cardiac puncture while mouse is under CO2 narcosis. The whole blood sample is placed in heparinized eppendorf tubes and kept on wet ice until centrifuged (4 min@14,000 rpm). Plasma is transferred to 96 deep-well block on dry ice and stored at −20° C. Immediately following blood collection, 2 ml of sterile PBS (phosphate buffered saline) was injected into the peritoneal cavity with a 25G needle. The abdomen was gently massaged, and a small incision was made to allow access to the peritoneal cavity. The peritoneal wash fluid was collected using sterile technique, serially diluted 1:10, plated on blood agar plates, and incubated overnight at 35° C.
Spleens were harvested and placed in 1 ml sterile PBS in Stomacher bag and homogenized with MicroBiomaster80 (Brinkmann) for 60 seconds, normal setting and 1:10 dilutions were made. 25 ul of each dilution, as well as the homogenate, was plated on blood agar plates and incubated at 35° C. to determine the CFU/mL over the time course. After overnight incubation, colonies were counted.
Other Animal Models
Similarly, other animal infection models can be used for hospital acquired pneumonia (HAP)/ventilator acquired pneumonia (VAP), complicated urinary tract infections (cUTI), and febrile neutropenia.
5. FORMULATION AND ADMINISTRATION
The compositions and methods of the present invention can be practiced by delivering the compounds of the present invention using a means for delivery e.g., any suitable carrier. The dose of active compound, mode of administration and use of suitable carrier will depend upon the intended patient or subject and the targeted microorganism, e.g., the target bacterial organism. The formulations, both for human medical use and veterinary use, of compounds according to the present invention typically include such compounds in association with a pharmaceutically acceptable carrier.
The carrier(s) should be “acceptable” in the sense of being compatible with compounds of the present invention and not deleterious to the recipient. Pharmaceutically acceptable carriers, in this regard, are intended to include any and all solvents, dispersion media, coatings, absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds (identified or designed according to the invention and/or known in the art) also can be incorporated into the compositions. The formulations can conveniently be presented in dosage unit form and can be prepared by any of the methods well known in the art of pharmacy/microbiology. In general, some formulations are prepared by bringing the compound into association with a liquid carrier or a finely divided solid carrier or both, and then, if necessary, shaping the product into the desired formulation.
A pharmaceutical composition of the invention should be formulated to be compatible with its intended route of administration. Solutions or suspensions can include the following components: a sterile diluent such as water, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
A wide variety of formulations and administration methods, including, e.g., intravenous formulations and administration methods can be found in S. K. Niazi, ed., Handbook of Pharmaceutical Formulations, Vols. 1-6 [Vol. 1 Compressed Solid Products, Vol. 2 Uncompressed Drug Products, Vol. 3 Liquid Products, Vol. 4 Semi-Solid Products, Vol. 5 Over the Counter Products, and Vol. 6 Sterile Products], CRC Press, Apr. 27, 2004.
Useful solutions for oral or parenteral administration can be prepared by any of the methods well known in the pharmaceutical art, described, for example, in Remington's Pharmaceutical Sciences, 18th ed. (Mack Publishing Company, 1990). Formulations for parenteral administration can also include glycocholate for buccal administration, methoxysalicylate for rectal administration, or citric acid for vaginal administration. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. Suppositories for rectal administration also can be prepared by mixing the drug with a non-irritating excipient such as cocoa butter, other glycerides, or other compositions which are solid at room temperature and liquid at body temperatures. Formulations also can include, for example, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, and hydrogenated naphthalenes. Formulations for direct administration can include glycerol and other compositions of high viscosity. Other potentially useful parenteral carriers for these drugs include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation administration can contain as excipients, for example, lactose, or can be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or oily solutions for administration in the form of nasal drops, or as a gel to be applied intranasally. Retention enemas also can be used for rectal delivery.
Formulations of the present invention suitable for oral administration can be in the form of: discrete units such as capsules, gelatin capsules, sachets, tablets, troches, or lozenges, each containing a predetermined amount of the drug; a powder or granular composition; a solution or a suspension in an aqueous liquid or non-aqueous liquid; or an oil-in-water emulsion or a water-in-oil emulsion. The drug can also be administered in the form of a bolus, electuary or paste. A tablet can be made by compressing or molding the drug optionally with one or more accessory ingredients. Compressed tablets can be prepared by compressing, in a suitable machine, the drug in a free-flowing form such as a powder or granules, optionally mixed by a binder, lubricant, inert diluent, surface active or dispersing agent. Molded tablets can be made by molding, in a suitable machine, a mixture of the powdered drug and suitable carrier moistened with an inert liquid diluent.
Oral compositions generally include an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients. Oral compositions prepared using a fluid carrier for use as a mouthwash include the compound in the fluid carrier and are applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose; a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). It should be stable under the conditions of manufacture and storage and should be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filter sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation include vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Formulations suitable for intra-articular administration can be in the form of a sterile aqueous preparation of the drug that can be in microcrystalline form, for example, in the form of an aqueous microcrystalline suspension. Liposomal formulations or biodegradable polymer systems can also be used to present the drug for both intra-articular and ophthalmic administration.
Formulations suitable for topical administration, including eye treatment, include liquid or semi-liquid preparations such as liniments, lotions, gels, applicants, oil-in-water or water-in-oil emulsions such as creams, ointments or pastes; or solutions or suspensions such as drops. Formulations for topical administration to the skin surface can be prepared by dispersing the drug with a dermatologically acceptable carrier such as a lotion, cream, ointment or soap. Useful are carriers capable of forming a film or layer over the skin to localize application and inhibit removal. For topical administration to internal tissue surfaces, the agent can be dispersed in a liquid tissue adhesive or other substance known to enhance adsorption to a tissue surface. For example, hydroxypropylcellulose or fibrinogen/thrombin solutions can be used to advantage. Alternatively, tissue-coating solutions, such as pectin-containing formulations can be used.
For inhalation treatments, inhalation of powder (self-propelling or spray formulations) dispensed with a spray can, a nebulizer, or an atomizer can be used. Such formulations can be in the form of a fine powder for pulmonary administration from a powder inhalation device or self-propelling powder-dispensing formulations. In the case of self-propelling solution and spray formulations, the effect can be achieved either by choice of a valve having the desired spray characteristics (i.e., being capable of producing a spray having the desired particle size) or by incorporating the active ingredient as a suspended powder in controlled particle size. For administration by inhalation, the compounds also can be delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
Systemic administration also can be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants generally are known in the art, and include, for example, for transmucosal administration, detergents and bile salts. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds typically are formulated into ointments, salves, gels, or creams as generally known in the art.
The active compounds can be prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. Liposomal suspensions can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.
Oral or parenteral compositions can be formulated in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals. Furthermore, administration can be by periodic injections of a bolus, or can be made more continuous by intravenous, intramuscular or intraperitoneal administration from an external reservoir (e.g., an intravenous bag).
Where adhesion to a tissue surface is desired the composition can include the drug dispersed in a fibrinogen-thrombin composition or other bioadhesive. The compound then can be painted, sprayed or otherwise applied to the desired tissue surface. Alternatively, the drugs can be formulated for parenteral or oral administration to humans or other mammals, for example, in effective amounts, e.g., amounts that provide appropriate concentrations of the drug to target tissue for a time sufficient to induce the desired effect.
Where the active compound is to be used as part of a transplant procedure, it can be provided to the living tissue or organ to be transplanted prior to removal of tissue or organ from the donor. The compound can be provided to the donor host. Alternatively or, in addition, once removed from the donor, the organ or living tissue can be placed in a preservation solution containing the active compound. In all cases, the active compound can be administered directly to the desired tissue, as by injection to the tissue, or it can be provided systemically, either by oral or parenteral administration, using any of the methods and formulations described herein and/or known in the art. Where the drug comprises part of a tissue or organ preservation solution, any commercially available preservation solution can be used to advantage. For example, useful solutions known in the art include Collins solution, Wisconsin solution, Belzer solution, Eurocollins solution and lactated Ringer's solution.
In conjunction with the methods of the present invention, pharmacogenomics (i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug) can be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug. Thus, a physician or clinician can consider applying knowledge obtained in relevant pharmacogenomics studies in determining whether to administer a drug as well as tailoring the dosage and/or therapeutic regimen of treatment with the drug.
Generally, an effective amount of dosage of active compound will be in the range of from about 0.1 to about 100 mg/kg of body weight/day, more preferably from about 1.0 to about 50 mg/kg of body weight/day. The amount administered will also likely depend on such variables as the type of surgery or invasive medical procedure, the overall health status of the patient, the relative biological efficacy of the compound delivered, the formulation of the drug, the presence and types of excipients in the formulation, and the route of administration. Also, it is to be understood that the initial dosage administered can be increased beyond the above upper level in order to rapidly achieve the desired blood-level or tissue level, or the initial dosage can be smaller than the optimum.
Nonlimiting doses of active compound comprise from about 0.1 to about 1500 mg per dose. Nonlimiting examples of doses, which can be formulated as a unit dose for convenient administration to a patient include: about 25 mg, about 50 mg, about 75 mg, about 100 mg, about 125 mg, about 150 mg, about 175 mg, about 200 mg, about 225 mg, about 250 mg, about 275 mg, about 300 mg, about 325, about 350 mg, about 375 mg, about 400 mg, about 425 mg, about 450 mg, about 475 mg, about 500 mg, about 525 mg, about 550 mg, about 575 mg, about 600 mg, about 625 mg, about 650 mg, about 675 mg about 700 mg, about 725 mg, about 750 mg, about 775 mg, about 800 mg, about 825 mg, about 850 mg, about 875 mg, about 900 mg, about 925 mg, about 950 mg, about 975 mg, about 1000 mg, about 1025 mg, about 1050, mg, about 1075 mg, about 1100 mg, about 1125 mg, about 1150 mg, about 1175 mg, about 1200 mg, about 1225 mg, about 1250 mg, about 1275 mg, about 1300 mg, about 1325 mg, about 1350 mg, about 1375 mg, about 1400 mg, about 1425 mg, about 1450 mg, about 1475 mg, and about 1500 mg. The foregoing doses are useful for administering the compounds of the present invention according to the methods of the present invention.
As is understood by one of ordinary skill in the art, generally, when dosages are described for a pharmaceutical active, the dosage is given on the basis of the parent or active moiety. Therefore, if a salt, hydrate, or another form of the parent or active moiety is used, a corresponding adjustment in the weight of the compound is made, although the dose is still referred to on the basis of the parent or active moiety delivered. As a nonlimiting example, if the parent or active moiety of interest is a monocarboxylic acid having a molecular weight of 250, and if the monosodium salt of the acid is desired to be delivered to be delivered at the same dosage, then an adjustment is made recognizing that the monosodium salt would have a molecular weight of approximately 272 (i.e. minus 1H or 1.008 atomic mass units and plus 1 Na or 22.99 atomic mass units). Therefore, a 250 mg dosage of the parent or active compound would correspond to about 272 mg of the monosodium salt, which would also deliver 250 mg of the parent or active compound. Said another way, about 272 mg of the monosodium salt would be equivalent to a 250 mg dosage of the parent or active compound.
Formulation Examples
I. Formulation for Intravenous Administration














Ingredients
Amount









Antimicrobial Compound
0.1-1500 total mg



of the present invention











Dextrose, USP
50
mg/ml



Sodium citrate, USP
1.60-1.75
mg/ml



Citric Acid, USP
0.80-0.90
mg/ml










Water, USP
q.s










This formulation for intravenous administration is formulated by heating water for injection to about 60° C. Next the sodium citrate, citric acid and dextrose are added and stirred until dissolved. A solution or aqueous slurry of the antimicrobial compound is added to the previous mixture and stirred until dissolved. The mixture is cooled to 25° C. with stirring. The pH is measured and adjusted if necessary. Lastly the mixture is brought to the desired volume, if necessary, with water for injection. The mixture is filtered, filled into the desired container (vial, syringe, infusion container, etc.), over wrapped and terminally moist heat sterilized.

This formulation is useful for intravenous administration, either bolus or infusion, to a patient for treating, preventing, or reducing the risk of infection.

II. Lyophilisate for Reconstitution
Alternatively, the antimicrobial compound can be provided as a lyophilisate which can be reconstituted before intravenous or intramuscular administration.














Ingredient
mg per injection vial









Antimicrobial Compound
0.1-1500



of the present invention



Cyclodextin
1500










Reconstitution solution for a volume to be administered of 50 ml (infusion): 5% aqueous glucose solution.
Reconstitution solution for a volume to be administered of 15 ml (bolus): 3.3% aqueous glucose solution.
The foregoing lyophilisate is useful for reconstitution and intravenous administration, either bolus or infusion, to a patient for treating, preventing, or reducing the risk of infection.
III. Lyophilisate for Reconstitution














Ingredient
mg per injection vial









Antimicrobial Compound
0.1 -1500



of the present invention



soya lecithin
2250



Sodium cholate
1500










Reconstitution solution for a volume to be administered of 50 ml (infusion): 4% aqueous glucose solution.
Reconstitution solution for a volume to be administered of 15 ml (bolus): 2% aqueous glucose solution
The foregoing lyophilisate is useful for reconstitution and intravenous administration, either bolus or infusion, to a patient for treating, preventing, or reducing the risk of infection.
IV. Lyophilisate for Reconstitution














Ingredient
mg per injection vial









Antimicrobial Compound
0.1-1500



of the present invetnion



soya lecithin
900



Sodium glycocholate
540










Reconstitution solution for a volume to be administered of 15 ml (bolus): 3.3% aqueous glucose solution.
The foregoing lyophilisate is useful for reconstitution and intravenous administration, either bolus or infusion, to a patient for treating, preventing, or reducing the risk of infection.
V. Tablet for Oral Administration
















Ingredients

Per Tablet
Per 4000 Tablets






















Antimicrobial Compound
0.1-1500
mg
0.4-6000
g



of the present invention



Anhydrous Lactose, NF
110.45
mg
441.8
g



Microcrystalline
80.0
mg
320.0
g



Cellulose NF



Magnesium Stearate
1.00
mg
4.0
g



Impalpable Powder NF



Croscarmellose Sodium
2.00
mg
8.0
g



NF Type A










The antimicrobial compound (any of the compounds equivalent to the desired delivery strength, e.g., 50 to 1500 mg per tablet) is premixed with 1⁄3 of the microcrystalline cellulose NF and 1⁄2 of the anhydrous lactose NF in a ribbon blender for 5 minutes at 20 RPM. To the premix is added the remaining 2⁄3 of the microcrystalline cellulose NF and the remaining 1⁄2 of the anhydrous lactose NF. This is blended for 10 minutes at 20 RPM. Crosscarmellose sodium is added to the blended powders and mixed for 5 minutes at 20 RPM. Finally the magnesium stearate is added to the mixture by passing through a 90 mesh screen and blended for an additional 5 minutes at 20 RPM. The lubricated mixture is compressed to provide tablets of 500 mg active ingredient.

These tablets are useful for oral administration to a patient for treating, prevention, or reducing the risk of infection.
6. EXAMPLES
Nuclear magnetic resonance (NMR) spectra were obtained on a Bruker Avance 300 or Avance 500 spectrometer, or in some cases a GE-Nicolet 300 spectrometer. Common reaction solvents were either high performance liquid chromatography (HPLC) grade or American Chemical Society (ACS) grade, and anhydrous as obtained from the manufacturer unless otherwise noted. “Chromatography” or “purified by silica gel” refers to flash column chromatography using silica gel (EM Merck, Silica Gel 60, 230-400 mesh) unless otherwise noted.
The compounds or tautomers thereof, or pharmaceutically acceptable salts, esters or prodrugs of said compounds or tautomers of the present invention can be prepared using known chemical transformations adapted to the particular situation at hand.
Some of the abbreviations used in the following experimental details of the synthesis of the examples are defined below: h or hr=hour(s); min=minute(s); mol=mole(s); mmol=millimole(s); M=molar; μM=micromolar; g=gram(s); μg=microgram(s); rt=room temperature; L=liter(s); mL=milliliter(s); Et2O=diethyl ether; THF=tetrahydrofuran; DMSO=dimethyl sulfoxide; EtOAc=ethyl acetate; Et3N=triethylamine; i-Pr2NEt or DIPEA=diisopropylethylamine; CH2Cl2=methylene chloride; CHCl3=chloroform; CDCl3=deuterated chloroform; CCl4=carbon tetrachloride; MeOH=methanol; CD3OD=deuterated methanol; EtOH=ethanol; DMF=dimethylformamide; BOC=t-butoxycarbonyl; CBZ=benzyloxycarbonyl; TBS=t-butyldimethylsilyl; TBSCl=t-butyldimethylsilyl chloride; TFA=trifluoroacetic acid; DBU=diazabicycloundecene; TBDPSCl=t-butyldiphenylchlorosilane; Hunig's Base=N,N-diisopropylethylamine; DMAP=4-dimethylaminopyridine; CuI=copper (I) iodide; MsCl=methanesulfonyl chloride; NaN3=sodium azide; Na2SO4=sodium sulfate; NaHCO3=sodium bicarbonate; NaOH=sodium hydroxide; MgSO4=magnesium sulfate; K2CO3=potassium carbonate; KOH=potassium hydroxide; NH4OH=ammonium hydroxide; NH4Cl=ammonium chloride; SiO2=silica; Pd—C=palladium on carbon; Pd(dppf)Cl2=dichloro[1,1′-bis(diphenylphosphino)ferrocene] palladium (II).
Exemplary compounds synthesized in accordance with the invention are listed in Table 1, Table 2, Table 2a and Table 2aa. A bolded or dashed bond is shown to indicate a particular stereochemistry at a chiral center, whereas a wavy bond indicates that the substituent can be in either orientation or that the compound is a mixture thereof. It should also be known that in the interest of conserving space, the chemical structures of some compounds have been split into two parts with the two points of connection each being indicated by a bond crossed by a wavy line. See, e.g. compound 1, which was drawn in two parts as:




but corresponds to the complete chemical structure:





The compounds of the present invention can be prepared, formulated, and delivered as salts, esters, and prodrugs. For convenience, the compounds are generally shown without indicating a particular salt, ester, or prodrug form.
Compounds of the present invention are shown in Table 1, Table 2, Table 2a, and Table 2aa. LCMS (liquid chromatography mass spectral) data are provided, where available. When data is not available this is indicated by “NA”. The LCMS data are provided using the convention for m/z in the format, [M+H]+, except where otherwise indicated.









TABLE 1





Comp.




No.
Structure
LCMS

















1




543.1


 


2




563.1


 


3




531.1


 


4




542.1


 


5




505.2


 


6




541.1


 


7




523.1


 


8




589.1


 


9




501.1


 


10




555.1


 


11




561.1


 


12




589.1


 


13




628.2


 


14




517.1


 


15




555.1


 


16




621.1


 


17




569.1


 


18




527.2


 


19




585.1


 


20




627.2


 


21




586.1


 


22




593.1


 


23




539.1


 


24




507.1


 


25




585.1


 


26




558.3


 


27




569.2


 


28




628.1


 


29




571.2


 


30




607.1


 


31




599.1


 


32




549.1


 


33




565.1


 


34




585.1


 


35




585.1


 


36




573.0


 


37




539.0


 


38




581.1


 


39




589.0


 


40




541.1


 


41




544.4


 


42




587.1


 


43




666.9


 


44




601.1


 


45




659.0


 


46




529.1


 


47




631.1


 


48




580.0


 


49




545.0


 


50




571.1


 


51




537.0


 


52




607.1


 


53




541.1


 


54




523.1


 


55




554.1


 


56




596.1


 


57







 


58




589.0


 


59




553.0


 


60




558.1


 


61




564.3


 


62




555.1


 


63




535.0


 


64




589.0


 


65




605.0


 


66




474.1


 


67




553.1


 


68




605.3


 


69




601.0


 


70




587.1


 


71




557.0


 


72







 


73




519.1


 


74




561.1


 


75




587.0


 


76




587  


 


77




547.1


 


78




543.1


 


79




503.2


 


80




573.1


 


81




539.0


 


82




508.0


 


83




535.1


 


84




523.0


 


85




585.1


 


86




599.1


 


87




603.3


 


88




587.0


 


89




585.0


 


90




589.1


 


91




539.0


 


92




621.0


 


93




585.1


 


94




585.5


 


95




583.5


 


96




611.0


 


97




557.0


 


98




539.0


 


99




587.1


 


100




583.1


 


101




587.1


 


102




585.0


 


103




569.0


 


104




599.0


 


105




553.1


 


106




519.1


 


107




589.0


 


108




535.1


 


109




535.1


 


110




553.1


 


111




573.1


 


112




607.1


 


113




519.1


 


114




546.0


 


115




566.1


 


116




545.0


 


117




533.0


 


118




546.0


 


119




553.1


 


120




546.1


 


121




546.0


 


122




530.1


 


123




515.1


 


124







 


125




567.0


 


126




613.1


 


127




613.1


 


128




553.1


 


129




552.9


 


130




533.1


 


131




599.0


 


132




553.0


 


133




519.0


 


134




526.1


 


135




533.1


 


136




531.0


 


137




597.0


 


138




579.0


 


139




571.0


 


140




589.0


 


141




529.0


 


142




589.0


 


143




511.0


 


144




576.1


 


145







 


146




611.1


 


147




519.1


 


148




525.0


 


149




555.0


 


192







 


194







 


195







 


196







 


197







 


198







 


199







 


200







 


201







 


202







 


203







 


204







 


205







 


206







 


207







 


208







 


209







 


210







 


211







 


212




569.0


 


213




568.1


 


214




587.1


 


215




642.3


 


216




601.0


 


217




549.1


 


218




573.0


 


219




533.1


 


220




637.0


 


221




570.1


 


222




569.0


 


223




565.0


 


224




541.0


 


225




591.0


 


226




589.0 [M]


 


227




624.1


 


228




525.0


 


229




599.1


 


230




599.0


 


231







 


232




657.0


 


233




583.1


 


234




567.2


 


235




601.0


 


236




583.0


 


237




567.1


 


238




587.0


 


239




587.0


 


240




587.0


 


241




571.0


 


242




555.0


 


243




567.0


 


244




587.1


 


245




549.1


 


246




585.1


 


247




615.1


 


248




569.1


 


249




569.1


 


250




584.3


 


251




613.1


 


252




587.0


 


253







 


254







 


255







 


256







 


257







 


258







 


259







 


260







 


261




577.1


 


262




601.1


 


263




556.1


 


264




613.2


 


265




585.1


 


266




549.1


 


267




539.1


 


268




553.3


 


269




567.3


 


270







 


271







 


272







 


273







 


274




602.2


 


275




588.2


 


276




625.0 [M/2] + 1


 


277




314.4 [M + 1]/2


 


278







 


279







 


280







 


281




310.3 [M + 2H]/2


 


282




317.2 [M + 2H]/2


 


283




563.1


 


284




605.1


 


285




591.1


 


286




603.0


 


287




583.0


 


288




635.2


 


289




649.1


 


290




597.0


 


291




553.1


 


292




567.2


 


293




623.2


 


294




615.1


 


295




567.1


 


296




581.1


 


297




585.1


 


298




581.1


 


299




599.1


 


300




561.4


 


301




547.1


 


302




629.1


 


303




615.1


 


304




629.1


 


305




583.0


 


306




583.1


 


307




613.1 (m/e)


 


308




597.0


 


309




597.0


 


310




627.4 (m/e)


 


311




587.3 (m/e)


 


312




551.1 (m/e)


 


313




549.1


 


314




571.2


 


315




585.1


 


316




617.0


 


317




583.1


 


318




597.2


 


319




581.1


 


320




579.3


 


321




619.8


 


322




585.3


 


323




571.3


 


324




567.0


 


325




581.0


 


326




603.3


 


327




617.3


 


328




565.5


 


329




579.1


 


330




543.3


 


331




557.7


















TABLE 2





Comp.




No.
Structure
LCMS







150




689.0


 


151




543.0


 


152




587.0


 


153




597.0


 


154




598.0


 


155




626.0


 


156




601.0


 


157




693.0


 


158




603.0


 


159




619.0


 


160




585.0


 


161




590.0


 


162




652.0


 


163




522.0


 


164




613.0


 


165




522.0


 


166




522.0


 


167




538.0


 


168




633.0


 


169




615.0


 


170




526.0


 


171




526.0


 


172




542.0


 


173




526.0


 


174




576.0


 


175




542.0


 


176




550.0


 


177




576.0


 


178




538.0


 


179




538.0


 


180




537.0


 


181




548.0


 


182




550.0


 


183




592.0


 


184




548.0


 


185




538.0


 


186




550.0


 


187




542.0


 


188




558.0


 


189




548.0


 


190




538.0


 


332




580.3


















TABLE 2a





Comp.




No.
Structure
LCMS







333




552.0


 


334




566.0


 


335




516.0


 


336




619.1


 


337




632.9


 


338




569.3


 


339




583.4


 


340




597.1


 


341




567.2


 


342




569.2


 


343




566.9


 


344




603.1


 


345




617.1


 


346




621.4


 


347




695.5


 


348




581.0


 


349




581.0


 


350




595.0


 


351




536.1


 


352




550.1


 


353




428.0


 


354




496.3


 


355




486.3


 


356




500.2


 


357




514.1


 


358




528.1


 


359




565.0


 


360




579.0


 


361




541.4


 


362




595.4


 


363




555.2


 


364




609.1


 


365




569.0


 


366




552.0


 


367




584.0


 


368




621.2


 


369




516.1


 


370




502.1


 


371




530.2


 


372




468.2


 


373




482.2


 


374




581.2


 


375




555.0


 


376




569.0


 


377




647.5


 


378




554.6


 


379




568.1


 


380




615.1


 


381




629.5


 


382




567.1


 


383




622.3


 


384




579.1


 


385




571.0


 


386




553.1


 


387




530.2


 


388




544.1


 


389




570.1


 


390




584.1


 


391




583.1


 


392




581.3


 


393




555.2


 


394




598.1


 


395




581.0


 


396




581.1


 


397




587.6


 


398




601.7


 


399




550.1


 


400




597.2


 


401




627.1


 


402




627.1


 


403




627.1


 


404




544.4


 


405




500.1


 


406




468.1


 


407




629.1


 


408




561.4


 


409




550.0


 


410




569.1


 


411




553.1


 


412




641.0


 


413




593.1


 


414




579.1


 


415




595.1


 


416




643.3


 


417




569.2


 


418




601.0


 


419




615.1


 


420




627.3


 


421




579.2


 


422




599.0


 


423




613.0


 


424




631.2


 


425




581.1


 


426




595.1


 


427




611.2


 


428




550.1


 


429




595.1


 


430




609.1


 


431




575.0


 


432




589.0


 


433




595.2


 


434




571.2


 


435




599.0


 


436




613.1


 


437




599.1


 


438




613.1


 


439




557.1


 


440




641.0


 


441




557.0


 


442




543.1


 


443




557.1


 


444




543.1


 


445




583.1


 


446




557.1


 


447




575.1


 


448




579.2


 


449




593.0


 


450




579.0


 


451




593.0


 


452




571.0


 


453




585.0


 


454




585.1


 


455




599.1


 


456




585.2


 


457




553.1


 


458




603.0


 


459




615.0


 


460




629.0


 


461




569.1


 


462




551.1


 


463




537.0


 


464




551.1


 


465




537.1


 


466




603.1


 


467




529.1


 


468




543.1


















TABLE 2aa





Comp.




No.
Structure
LCMS







469




573.1


 


470




551.1


 


471




633.1


 


472




593.1


 


473




627.2


 


474




609.1


 


475




579.1


 


476




613.1


 


477




627.2


 


478




599.2


 


479




599.1


 


480




613.1


 


481




579.1


 


482




595.1


 


483




569.3


 


484




583.1


 


485




595.1


 


486




579.1


 


487




625.1


 


488




641.0


 


489




611.1


 


490




627.1


 


491




673.2


 


492




659.1


 


493




585.1


 


494




611.1


 


495




597.0


 


496




627.1


 


497




613.0


 


498




659.2


 


499




571.0


 


500




627.0


 


501




595.1


 


502




627.1


 


503




645.1


 


504




306.9 [M + 1]/2


 


505




613.1


 


506




597.1


 


507




645.3


 


508




707.1









In one embodiment, the invention is not the compound selected from:








TABLE AA










 



Z1


 





 



Z2


 





 



Z3


 





 



Z4


 





 



Z5


 





 



Z6


 





 



Z7


 





 



Z8


 





 



Z9


 





 



Z10


 





 



Z11


 





 



Z12


 





 



Z13


 





 



Z14


 





 



Z15


 





 



Z16


 





 



Z17


 





 



Z18


 





 



Z19


 





 



Z20


 






Z21


 





 



Z22


 





 



Z23


 






Z24


 






Z25


 





 



Z26


 





 



Z27









The compounds of the present invention can be made using synthetic chemical techniques well known to those of skill in the art.
EXAMPLES
Example 1
Synthesis of Alkyne Intermediate
The alkyne intermediate can generally be synthesized according to the scheme:




Example 2
Synthesis of Pyrrolocytosines Compound 37 (R1═Cl, R2═F) and Compound 91 (R1═F, R2═Cl)




Compounds 37 and 91 can be synthesized according to the scheme. Compound 37 can be synthesized according to the procedures detailed below. Similar procedures can be used to synthesize compound 91. Variables R1 and R2 in the scheme are not the same as in the claims, and they are used in this scheme for purposes of this particular example.
Synthesis of Compound 31 from 1,5-dibromo-2-chloro-3-fluoro-benzene (2a)
A solution of 2,6-dibromo-3-chloro-4-fluoro-phenylamine (1a, 4.85 g, 16 mmol, 1 eq.) in DMF (20 mL) was added to a solution of isoamylnitrite (3.46 mL, 25.6 mmol, 1.6 eq.) in DMF (12 mL) at 70° C. The mixture was heated at 70° C. for 3 h before it was cooled to room temperature, quenched with 1 N NaOH aqueous solution (150 mL), and extracted with EtOAc (200 mL). The EtOAc extract was washed with brine (100 mL×2), dried over MgSO4, filtered and concentrated. The residue was purified by flash chromatography (heptane) to give desired product 2a as colorless oil (3.70 g, 80%).
Synthesis of [4-(3-bromo-4-chloro-5-fluoro-phenyl)-butyl]-carbamic acid benzyl ester (3a)
A solution of but-3-enyl-carbamic acid benzyl ester (5.00 g, 24.36 mmol, 1 eq) in anhydrous toluene (60 mL) was cooled under argon to 0-5° C. 9-BBN (0.50 M, solution in THF; 54.6 mL, 26.80 mmol, 1.1 eq.) was added dropwise, and the mixture was allowed to reach room temperature. After 24 h, the resulting solution was added dropwise at room temperature to a mixture of 2a (7.03 g, 24.36 mmol, 1 eq.), 1N NaOH/H2O (40 mL, 40 mmol, 1.6 eq.), and toluene (20 mL). The mixture was then degassed with argon and Pd(PPh3)4 (1.13 g, 0.98 mmol, 0.04 eq.) was added. The mixture was rapidly stirred under argon at 60° C. for 24 h, before cooling to room temperature. The mixture was partitioned between EtOAc (150 mL) and brine (150 mL). The organic phase was washed with brine (200 mL), dried over Na2SO4, filtered and concentrated. The crude product was purified by flash chromatography on silica gel (0-50% EtOAc in Heptane) to afford 3a as a colorless oil (3.54 g, 35%).
Synthesis of [4-(4-chloro-3-fluoro-5-trimethylsilanylethynyl-phenyl)-butyl]-carbamic acid benzyl ester (4a)
A mixture of 3a (4.78 g, 11.51 mmol, 1 eq.), CuI (175 mg, 0.92 mmol, 0.08 eq.), Pd(PPh3)2Cl2 (323 mg, 0.46 mmol, 0.04 eq.) and DMF (30 mL) was degassed. Trimethsilylacetylene (4.23 mL, 21.02 mmol, 2 eq.) was added under argon, followed by Et3N (4.81 mL, 34.53 mmol, 3 eq.). The resulting mixture was heated at 70° C. for 24 h. After cooling to room temperature, the reaction mixture was diluted with EtOAc (250 mL) was washed with brine (150 mL×2 containing 15 mL 28% NH4OH). The EtOAc solution was dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-50%, EtOAc in heptane) to afford 4a (4.50 g, 90%).
Synthesis of [4-(4-Chloro-3-ethynyl-5-fluoro-phenyl)-butyl]-carbamic acid benzyl ester (5a)
K2CO3 (2.76 g, 20 mmol, 2 eq.) was added to a solution of 4a (4.50 g, 10.36 mmol, 1 eq.) in degassed MeOH (200 mL). The suspension was stirred at room temperature for 30 min. before concentration. The residue was partitioned between EtOAc (200 mL) and brine (200 mL). The EtOAc layer was separated and washed further with brine (100 mL), dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-50%, EtOAc in heptane) to afford 5a as a colorless oil (3.60 g, 96%).
Synthesis of 6a
Intermediate 6a can generally be synthesized according to the scheme:




Synthesis of Compound 3b
Compound 2b (65.0 g, 373 mmol) was dissolved in ethanol (150 mL). The flask was purged with argon. Compound 1b (55.93 g, 373 mmol) was then added and the mixture was stirred at room temperature for 2 h. The reaction solution was then added via addition funnel, over 20 minutes, to a suspension of NaBH4 (14.18 g, 373 mmol) in toluene (150 mL), at 0° C. The ice bath was removed, and the resulting mixture was stirred at room temperature for 3 h. 1N HCl (750 mL) was added to the solution, and the mixture was stirred at room temperature for 30 min. K2CO3 (205.9 g, 1.49 mol), Boc2O (81.41 g, 373 mmol), and THF (200 mL) were added to the solution, and stirred at room temperature for 23 h. Reaction solution was partitioned between EtOAc and 1:1 brine/H2O. The aqueous layer was washed with EtOAc (2×300 mL). The combined organic layers were washed with brine (500 mL); dried over Na2SO4; filtered, and concentrated. The crude product was purified by Combi Flash chromatography, in 3 portions, affording the product as a white solid (119.43 g, 78%); 1H-NMR (300 MHz, CDCl3) δ 1.43 (bs, 18H), 1.63 (m, 2H), 2.95-3.30 (m, 4H), 4.45 (m, 2H), 5.93 (bs, 1H), 7.22 (bs, 1H), 7.34 (bs, 1H), 7.78 (d: 8 Hz, 1H), 8.19 (d: 8 Hz, 1H).
Synthesis of Compound 5b
To a mixture of compound 3b (42.28 g, 103.5 mmol) and compound 4b (24.54 g, 103.5 mmol) were added MeOH (3 L) and H2O (750 mL). The mixture was stirred vigorously open to air, at room temperature, for 30 min. Cu(OAc)2.H2O (20.67 g, 103.5 mmol) was then added followed by TMEDA (18.63 mL, 124.3 mmol). The solution was stirred open to air, at room temperature, for 5 h. Once the reaction was complete, the solution was concentrated to 0.7 L, and then partitioned between CH2Cl2 (700 mL) and 20% NH4OH/H2O saturated with NH4Cl (500 mL). The aqueous layer was washed with CH2Cl2 (500 mL, 200 mL). The combined organic layers were dried over MgSO4, filtered, and concentrated. The crude product was purified by Combi Flash chromatography: A: CH2Cl2 B: 15:1 CH2Cl2/2N NH3/MeOH, 0-100% B over 85 min. (two 330 g columns). This gave the product as a white solid (35.52 g, 58%); LCMS (ESI): m/e 600 (M+H)+.
Synthesis of Compound 6a
Compound 5b (10.0 g, 16.68 mmol) was dissolved in THF (40 mL). The flask was purged with argon. Pyridine (40 mL) was then added followed by BzCl (3.10 mL, 26.69 mmol). The solution was stirred at room temperature under argon atmosphere for 3 h. MeOH (4 mL) was added, the mixture was stirred at room temperature for 10 min, and then it was partitioned between EtOAc (200 mL), heptane (100 mL), and 5% KHCO3/H2O (200 mL). The aqueous layer was washed with EtOAc (100 mL, 50 mL). The combined organic layers were washed with 5% KHCO3/H2O (300 mL); dried over Na2SO4; filtered, and concentrated. The crude product was purified by Combi Flash chromatography: 0-100% EtOAc/heptane, over 55 min. (330 g column). The product was obtained as an off-white powder (9.81 g, 84%); LCMS (ESI): m/e 704 (M+H)+.







Synthesis of 7a
Pyrrolocytosine 7a was prepared from the coupling of common intermediate 6a and alkyne 5a according to the procedure describing this type of reaction. For example: compound 6a (1 eq) and compound 5a (1 eq) were placed in a pressure vessel, and anhydrous DMF was added. The solution was purged with argon, and then CuI (0.1 eq), Pd(PPh3)4 (0.05 eq), and Et3N (6 eq) were added, the vessel was sealed, and the mixture was stirred at 22° C., for 15 min. Subsequently, the temperature was increased to 80-85° C., and the mixture was stirred for 14 h. It was cooled to ambient temperature, MeOH was added, the vessel was sealed, and the mixture was stirred at 90° C. for 3 h. After cooling to ambient temperature, the mixture was partitioned between sat. KH2PO4/H2O and EtOAc, the organic phase was washed with brine, dried over Na2SO4, filtered and concentrated. The crude product was purified by flash chromatography on silica gel using 5% (2.5M NH3/MeOH)/CH2Cl2. Starting from 360 mg of 5a, 600 mg of the desired compound 7a was obtained as an orange-brown solid (72%); LCMS (ESI) m/e 813.2 (M+1)+.
Synthesis of 8a
Boc-deprotection of 7a (0.60 g, 0.72 mmol) was accomplished with 8 mL of 6N HCl in 25 mL EtOH at 60° C. (2 h). Following solvent evaporation, the crude residue was taken to the next step without further purification. LCMS (ESI) m/e 613.0 (M+1)+.
Synthesis of 9a
Guanidine formation was carried out by dissolving 8a in a 5:1 DMF/MeOH (0.1 M) at rt. After treating with diisopropylethylamine (8 eq), N,N-bis-boc-guanylpyrrazole (1.3 eq) was added as a solid. The reaction mixture was stirred for 6 h, and upon completion the solvents were removed by rotary evaporation. Crude 9a was used without further purification.
Synthesis of 10a (Compound 31)
Under argon, fully protected guanidine 9a (0.60-0.80 mmol) was dissolved in 25 mL of trifluoroacetic acid. Thioanisole (0.5 mL) was added dropwise and the solution was stirred at rt for 4 h. Upon completion, solvent was evaporated affording an oil. Diethyl ether was added and the liquid layer containing most of the residual thioanisole was decanted. Crude 10a was then dissolved in [(20% MeOH-80% H2O)+0.15% TFA] (10 mL). An aliquot (10 mL) was injected on a Dynamax 41.4 mm, C-18 prep HPLC Unit (guard+column), which was eluted with a gradient of solvents of 20%-80% (MeOH/H2O+0.15% TFA), over 45 min. The pure fractions were combined and concentrated with EtOH to dryness. This sample was treated with 1N HCl/H2O (5 mL) and EtOH (70 mL), and concentrated. This operation was repeated; the solid thus obtained was lyophilized from H2O-MeCN (4:1), affording compound 10a as a yellow powder (250 mg); LCMS (ESI) m/e 539.0 (M+1)+; 1H NMR (300 MHz, D2O) δ 1.50-1.60 (m, 4H), 1.82-1.95 (m, 2H), 2.57 (t, J=6.9 Hz, 2H), 2.86 (t, J=6.9 Hz, 2H), 3.06 (t, J=6.9 Hz, 2H), 3.17 (t, J=6.9 Hz, 2H), 4.23 (s, 2H), 6.78 (s, 1H), 7.08 (d, J=8.5 Hz, 1H), 7.18 (s, 1H), 7.44 (d, J=8.7, 2H), 7.58 (d, J=8.7 Hz, 2H), 8.48 (s, 1H).
Example 3
Synthesis of a Benzylic Methylated Fragment A Intermediate




Pyridine sulfurtrioxide complex (20 g, 125 mmol, 2.5 eq.) was added to a mixture of (3-hydroxy-propyl)-carbamic acid tert-butyl ester (8.75 g, 50 mmol, 1 eq.), Et3N (17.67 g, 175 mmol, 2.5 eq.), DMSO (25 mL) and CH2Cl2 (100 mL) at 0° C. The resulted mixture was stirred at 0° C. for 1 h and warmed up to room temperature and continuously stirred for 3 h. After concentration, the residue was diluted with EtOAc (200 mL) and washed with H2O (200 mL), brine (100 mL), dried over MgSO4, filtered and concentrated to give desired aldehyde as colorless oil (8.60 g, 99%).




A mixture of (3-oxo-propyl)-carbamic acid tert-butyl ester (8.94 g, 51.7 mmol, 1 eq.), (S)-(−)-1-(4-bromo-phenyl)-ethylamine (10.33 g, 51.7 mmol, 1.0 eq.) and MeOH (50 mL) was stirred at RT for 18 h. NaBH4 (1.98 mg, 52.1 mmol, 1.01 eq.) was added slowly to the above solution. The resulted mixture was stirred at RT for 1 h, additional (3-oxo-propyl)-carbamic acid tert-butyl ester (0.8 g, 4.6 mmol) was added and stirred for 2 h. additional NaBH4 (0.21 g, 5.53 mmol) was added and stirred for 1 h. EtOAc (120 mL) was added and washed with 1N NaOH (40 mL×2), 1N HCl (60 mL) and water, dried over MgSO4, filtered and concentrated. The crude product was dissolved in EtOAc (120 mL) and MeOH (20 mL), Et3N (10.8 mL, 77.52 mmol, 1.5 eq.) was added, followed by Boc2O (11.3 g, 51.8 mmol, 1.0 eq.). The resulted mixture was stirred at RT for 3 days (weekend), washed with H2O, dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (EtOAc:Heptane/1:5) to afford (3-{[1-(4-bromo-phenyl)-ethyl]-tert-butoxycarbonyl-amino}-propyl)-carbamic acid tert-butyl ester (17.5 g, 74%).




A mixture of (3-{[1-(4-bromo-phenyl)-ethyl]-tert-butoxycarbonyl-amino}-propyl)-carbamic acid tert-butyl ester (15.73 g, 34.42 mmol), bis(pinacolato)diborane (9.18 g, 36.14 mmol, 1.05 eq.), Pd(dppf)Cl2.CH2Cl2 (843 mg, 1.026 mmol, 0.03 eq.), KOAc (10.6 g, 108.42 mmol, 3.15 eq.) and dioxane (60 mL) was degassed and heated at 100° C. at Argon atmosphere overnight. The mixture was diluted with CH2Cl2 (150 mL), washed with H2O, dried over MgSO4, filtered and concentrated. The crude product was purified by chromatography (EtOAc:Heptane/1:5) to afford [3-(tert-butoxycarbonyl-{1-[4-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-phenyl]-ethyl}-amino)-propyl]-carbamic acid tert-butyl ester (16.77 g, 97%).




References for above rxn: Jacobsen, M. F.; Knudsen, M. M.; Gothelf, K. V. “Efficient N-Arylation and N-Alkenylation of the Five DNA/RNA Nucleobases” J. Org. Chem. 2006, 71, 9183-9190.

Dai, Q.; Ran, C.; Harvey, R. G. “Regioselective Arylation of 2′Deoxyribonucleosides on Amido or Imino Sites by Copper(II)-Mediated Direct Coupling with Arylboronic Acids” Tetrahedron 2006, 62, 1764-1771.

Cu(OAc)2 (6.02 g, 33.13 mmol, 1.1 eq.) was added to a mixture of [3-(tert-butoxycarbonyl-{1-[4-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-phenyl]-ethyl}-amino)-propyl]-carbamic acid tert-butyl ester (15.18 g, 30.12 mmol, 1 eq.), 4-amino-5-iodo-1H-pyrimidin-2-one (7.85 g, 33.13 mmol, 1.1 eq.), MeOH (400 mL) and H2O (100 mL), followed by N,N,N′,N′-tetramethyl-ethane-1,2-diamine (7.69 g, 66.26 mmol, 2.2 eq.). The Mixture was stirred at RT under air for 48 h (weekend) before concentrated to a volume ca. 130 mL. The residue was diluted with CH2Cl2 (200 mL). The CH2Cl2 extract was washed with brine and concentrated. The crude product was purified by flash chromatography (CH2Cl2:MeOH:NH4OH/35:1:0.01) to afford [3-({1-[4-(4-amino-5-iodo-2-oxo-2H-pyrimidin-1-yl)-phenyl]-ethyl}-tert-butoxycarbonyl-amino)-propyl]-carbamic acid tert-butyl ester (16.06 g, 87%).




Benzoic anhydride (5.26 g, 23.25 mmol, 1.05 eq.) was added to a solution of [3-({1-[4-(4-amino-5-iodo-2-oxo-2H-pyrimidin-1-yl)-phenyl]-ethyl}-tert-butoxycarbonyl-amino)-propyl]-carbamic acid tert-butyl ester (13.58 g, 22.15 mmol) in DMF (60 mL). The mixture was heated at 70° C. for 2 h and at RT for 20 h. EtOAc (150 mL) was added to the mixture and washed with saturated sodium bicarbonate and brine, dried over MgSO4, filtered and concentrated. The crude product was purified by chromatography (CH2Cl2:MeOH:NH4OH/50:1:0.01) to afford benzoic acid 1-(4-{1-[tert-butoxycarbonyl-(3-tert-butoxycarbonylamino-propyl)-amino]-ethyl}-phenyl)-5-iodo-2-oxo-1,2-dihydro-pyrimidin-4-yl ester (15.5 g, 98%).
Example 4
Synthesis of the Fragment B Intermediates
The preparation of the Fragment B intermediates 5b and 5c was carried out as described below. The Wittig Olefination can be performed according to methods known in the art or according to Gerpe, A., Convenient Route to Primary (Z)-Allyl Amines and Homologs.” Synth. Commun. 2009, 39, 29-47. In one aspect, the intermediates 5b and 5c were used to prepare compounds 27 and 100.
Synthesis of Phosphonium Bromide XXb




Synthesis of Phosphonium Bromide XXc




Synthesis of Fragment B Intermediates via Wittig Olefination 




Example 5
Synthesis of Compound 234
The preparation of compound 234 was carried out by coupling Fragment A (5) and Fragment B (H). The preparation of Fragment B involves the coupling of intermediates 1 and 2.
Synthesis of N-Cbz (S)-4-aminopentene 1 intermediate 




(R)-4-Hydroxy-1-pentene A (15.00 g, 174.15 mmol) was dissolved in CH2Cl2 (180 mL). To the solution, stirred/Ar at 0° C. was added triethylamine (30.4 mL, 217.69 mmol), followed by dropwise addition of methanesulfonyl chloride (14.43 mL, 186.35 mmol), over 10 min. After 5 min, the cold bath was removed and the mixture was stirred for 75 min, concentrated to 50 mL, and partitioned between heptane (80 mL), EtOAc (200 mL), H2O (100 mL) and brine (100 mL). The phases were separated, the organic phase was washed with H2O-brine (2:1; 150 mL), dried over Na2SO4, filtered and concentrated, affording intermediate B (28.6 g, yield=100%).
Compound B (28.6 g, 174.15 mmol) was dissolved in anhydrous DMF (250 mL) and NaN3 (48.46 g; 745.4 mmol) was added. The mixture was stirred/Ar at RT for 5 min, and then at 70-75° C. for 90 min. Afterwards, the mixture was cooled to RT and partitioned between ice (150 g), water (500 mL) and Et2O (150 mL). The phases were separated, the aqueous phase was extracted with Et2O (3×100 mL) (Note: Et2O could be substituted by 2-Me-THF). The organic extracts were combined and washed with brine (2×150 mL), resulting in a solution of compound C, which was used directly in the next step.
To the solution of C (174.15 mmol) was added THF (100 mL), followed by H2O (35 mL). The mixture was stirred at RT/Ar, and triphenylphosphine 58.65 g, 223.6 mmol) was added in small portions, over 5 min. Afterwards, the flask was equipped with a reflux condenser and the mixture was stirred at 40-42° C., for 16 hrs. Water (60 mL) was added, followed by dropwise addition of 3N HCl/H2O (57 mL) to achieve pH=ca. 2.0. The phases were separated, and the organic phase was washed with a mixture of H2O (40 mL) and 3N HCl/H2O (3.5 mL). The aqueous phases were combined and washed with EtOAc (2×70 mL), resulting in a solution of salt D, which was used directly in the next step.
The aqueous solution of D (174 mmol) was stirred under argon, while the flask was cooled in a water bath at 20° C. Na2CO3 (18.44 g, 174 mmol) was added in small portions, followed by KHCO3 (34.84 g, 348 mmol), and THF (150 mL). To this mixture, stirred rapidly, was dropwise added benzyl chloroformate (27.3 mL; 191.4 mmol), over 10 min. The mixture was stirred for 2 hrs. Next, water (150 mL) and EtOAc (200 mL) were added, and the mixture was stirred for 10 min. The phases were separated and the aqueous phase was extracted with EtOAc (2×70 mL). The organic layers were combined, washed with brine (100 mL), dried over Na2SO4, filtered and concentrated (50.5 g). This sample was purified by flash chromatography on Si-gel (230-400 mesh; 750 g), using 5% EtOAc/heptane (4 L) and then 10% EtOAc/heptane (5 L). This gave a colorless viscous oil of compound 1, which solidified upon standing (35.6 g; purity (NMR) 99%—contains 1% of heptane; yield=93.2% over 4 steps).
Synthesis of 1-bromo-3-chloro-2-fluoro-5-iodo-benzene 2 intermediate




N-Iodosuccinimide (286.2 g, 1.272 mol) was slowly added under argon to rapidly stirred DMF (0.85 L) (Note: It is important to do it in this order because if DMF is added to NIS, a very insoluble solid forms), and then methanesulfonic acid (1.90 mL, 29.3 mmol) was added. The mixture was stirred for 5 min and filtered, which gave a clear solution. Separately, 4-chloro-3-fluoroaniline E (176.3 g, 1.211 mol) was dissolved/Ar in DMF (1.10 L), the solution was cooled to 0° C., and methanesulfonic acid (2.03 mL, 31.3 mmol) was added. The mixture was stirred at 0° C./Ar and the above described solution of NIS in DMF was added dropwise, at 0-5° C., over 1 h 20 min. Subsequently, the mixture was stirred at 0-3° C. for 2.5 h, and then a solution of monosodium ascorbate (24.0 g, 0.121 mol) in H2O (70 mL) was added dropwise at 0-5° C., over 10 min. The mixture was stirred at 0-5° C. for 20 min, and then EtOAc (1.3 L) and heptane (0.2 L) are added, followed by 5% KHCO3/H2O (1.4 L). After 5 minutes of stirring, the phases are separated, and the aqueous phase is extracted with EtOAc (500 mL). The organic phases are combined, washed with water (1 L), dried/Na2SO4, filtered and concentrated (401 g). This material is purified by flash chromatography on Si-gel (230-400 mesh; 3.0 kg), using 7%-9% EtOAc/heptane. During the concentration of fractions, the product F precipitates; the solid was filtered and dried in vacuo to give aniline F as a crystalline solid (206.68 g, yield: 77.5%).
N-Bromosuccinimide (142.29 g, 799.43 mmol) was dissolved under argon in DMF-AcOH (5:1; 0.40 L), stirred for 5 min, which resulted in a clear solution.
Separately, compound F (206.68 g, 761.36 mmol) was dissolved under argon in DMF-AcOH (5:1; 1.40 L). The solution was cooled to 0-4° C. and the above described solution of NBS was added dropwise, at 0-4° C., over 20 min. The mixture was stirred at 0-4° C. for 30 min, and then at 12-14° C. (Note: it is important not to exceed the specified temperature range due to a sudden drop in selectivity at higher temperatures), for 5 h, with HPLC monitoring. Subsequently, the mixture was cooled to 0-5° C. and a solution of monosodium ascorbate (15.08 g, 76.14 mmol) in water (40 mL) is added at 0-10° C., over 10 min. The mixture is stirred at 5-10° C. for 10 min, and then EtOAc (1.6 L), heptane (0.2 L), H2O (3.2 L), and brine (0.6 L) are added, the mixture is stirred for 5 min, and the phases are separated. The aqueous phase is extracted with EtOAc (0.40 L), the organic phases are combined and washed with 10% KHCO3/H2O (2×1.1 L), dried over Na2SO4, and concentrated (320 g). The crude material is dissolved in minimal amount of CH2Cl2, and purified by flash chromatography on Si-gel (3.0 kg) using 2% EtOAc in heptane. The fractions are concentrated to ca. 600 g, at which point a solid precipitates. The mixture is cooled at 10-15° C. and stirred for 1 hr, the product is filtered, and dried to give aniline G (124.15 g, yield: 46.5%).
A solution of isoamyl nitrite (94.9 mL, 708.7 mmol) in DMF (500 mL) was stirred and heated under argon, at 65° C. To this solution was added dropwise a solution of aniline G in DMF (200 mL), over 40 min, while maintaining the temperature at 65-75° C. The mixture was stirred at 65-70° C. for 30 min, and then cooled to 30-40° C. Heptane (0.80 L), EtOAc (0.40 L) and 0.5 N HCl/H2O (1.6 L) were added, after extraction the phases were separated, and the aqueous phase was washed with a mixture of heptane (0.20 L) and EtOAc (0.30 L). The organic phases were combined, washed with 2N HCl/H2O (0.70 L), and then with water (0.50 L), dried over Na2SO4, filtered, and concentrated (brown oil, 160 g). This sample was purified by flash chromatography on Si-gel (3.0 kg) using 100% heptane as the eluent. This gave a solidifying, thick oil (90.5 g), which was dissolved at 40° C. in heptane (100 mL), and then crystallized from the solution at 0° C. After filtration, the filtrate was recrystallized under similar conditions, and the crystals were combined. This gave compound 2 (67.0 g, yield: 56.4%; HPLC purity (PDA)>93%) as colorless crystals (Note: The major impurity (3-5%) is identified as 1,5-dibromo-3-chloro-2-fluoro-benzene, which is expected to show utility in the present synthesis, essentially similar to compound 2).
Synthesis of alkyne Fragment B intermediate 5




The Suzuki-coupling reaction is preformed according to methods known in the art e.g., Al-Hellani, R.; Schluter, A. D. “On the Synthesis and Selective Deprotection of Low-Generation Dendrons with Orthogonally Protected Peripheral Amine Groups and a Possible Impact of the Deprotection Conditions on the Stability of Dendronized Polymers' Skeletons.”Helv. Chim. Acta. 2006, 89, 2745-2763.
A solution of olefin 1 (18.62 g, 84.06 mmol) in dry toluene (185 mL) was purged with argon, and then cooled to 0° C. under argon, at which point 9-BBN (11.08 g, 90.80 mmol) was added in a few portions. The mixture was stirred at 0-5° C. for 20 min, and then at RT for 21 h, which gave a solution of the trialkylborane.
To a solution of iodide 2 (28.19 g, 84.06 mmol) in toluene (65 mL) was added 1N NaOH/H2O (142.9 mL, 142.9 mmol). The mixture was purged with argon, and the above described solution of trialkylborane was added under argon, followed by tetrakis(triphenylphosphine)Pd(0) (4.86 g, 4.20 mmol). The mixture was purged with argon, the flask was transferred to an oil bath (60-64° C.), and the mixture was stirred under argon for 9 h. After cooling to RT, EtOAc (150 mL) and brine (150 mL) were added, the phases were separated, the organic phase was washed with 1N NaOH/H2O (100 mL), and with brine (100 mL). The organic layer was dried over Na2SO4, filtered, and concentrated (56.1 g). This sample was purified by flash chromatography on Si-gel (750 g) using 15% EtOAc in heptane as the eluent. The fractions were combined and concentrated to ca. 300 mL, at which point crystallization occurred. The solid was filtered and dried. This gave compound 3 as a white solid (27.9 g; yield: 77.4%).
The bromide 3 (27.85 g; 64.96 mmol) was dissolved in DMF (220 mL), the solution was purged with argon. Under a gentle stream of argon, trimethylsilyl acetylene (27.5 mL, 194.9 mmol) was added, followed by CuI (990 mg, 5.2 mmol), Pd (PPh3)4 (3.0 g, 2.6 mmol) and triethylamine (stored under argon; 72.5 mL, 519.7 mmol). The flask was equipped with a reflux condenser, and the mixture was stirred under argon, at 70° C. for 2.5 h. After cooling the mixture to RT, brine (300 mL), water (1.0 L) and EtOAc (0.75 L) were added, and after extraction the phases were separated. The organic layer was washed with H2O (0.75 L), dried over Na2SO4, filtered and concentrated. The crude product was purified by flash chromatography on Si-gel (750 g) using 15% EtOAc in heptane. This purification was repeated under the same conditions (Note: due to the potential for ready dimer formation in the next step, it is essential to eliminate from 4 as much transition metal residues as possible). This gave compound 4 as a pale-yellow, thick oil (29.8 g).
This sample was dissolved in MeOH (previously purged with argon; 350 mL), K2CO3 (19 g, 137.47 mmol) was added, the mixture was stirred under a stream of argon for 5 min, and then it was stirred in darkness, under argon, at 45° C. After 35 min the mixture was cooled/Ar to RT, concentrated, and purified by flash chromatography on Si-gel (750 g) using 17% EtOAc in heptane (Note: these operations are performed quickly to avoid alkyne dimerization; after chromatographic purification the alkyne is stable). This afforded alkyne 5 as a white, crystalline solid (20.20 g, yield: 83.2%).
Synthesis of Compound 234







The Fragment A intermediate H was prepared according to methods described herein. H (38.77 g, 54.03 mmol) and alkyne 5 (20.20 g, 54.03 mmol) were dissolved in acetonitrile and the solution was stirred under gentle stream of argon. Copper(I) iodide (617 mg, 3.24 mmol) and Pd(PPh3)4 (1.87 g, 1.62 mmol) were added, followed by diisopropylethyl amine (26.8 mL, 162.1 mmol). The mixture was stirred under Ar, at RT, for 5 min, and then it was heated at 72-75° C. for 4.5 h. Afterwards, MeOH (100 mL) was added and the mixture was stirred/Ar, at 72-75° C., for 15 h. After cooling to RT, the mixture was concentrated, the gummy solid thus obtained was dissolved in EtOAc (300 mL), and the solution was washed with NH4Cl/NH4OH (3×200 mL). The organic phase was concentrated and purified by flash chromatography on Si-gel (750 g) using 5% (2.5M NH3/MeOH) in CH2Cl2. The chromatography was repeated under similar conditions, thus affording a red-brown, gummy solid (41.5 g). To a solution of this sample in MeOH (300 mL), was added charcoal (Aldrich No. 242276; 45 g) and the mixture was stirred for 2 h at RT. Afterwards, the mixture was filtered through a silica gel plug prepared in MeOH, the solids were washed with MeOH (1.0 L), concentrated, and dried in vacuo to give compound 6 as a light-brown solid (32.5 g, 70%).
The pyrrolocytosine 6 (32.5 g, 37.82 mmol) was dissolved under argon in EtOH (200 proof; 200 mL), 6N HCl/H2O 75.6 mL, 453.8 mmol) was added, and the mixture was stirred under argon, at 70-72° C., for 1 h 40 min. Afterwards, the mixture was cooled to 40-45° C., and IPA (200 mL) was added. After 3 min, abundant precipitation occurred—more IPA (350 mL) was added, the mixture was stirred for 10 min, and then filtered. The solid was washed with IPA (2×80 mL), and dried in vacuo overnight, affording salt 7 as a crystalline solid (20.7 g, yield: 75%).
Salt 7 (20.7 g, 28.3 mmol) was added under argon to rapidly stirred MeOH (350 mL), followed by addition of triethylamine (15.8 mL, 113.2 mmol). After the solid dissolved completely (pH ca. 9.5), N,N′-bis-Boc-1-guanylpyrazole (10.54 g, 33.96 mmol) was added and the mixture was stirred for 1 h, at which time more N,N′-bis-Boc-1-guanylpyrazole (0.88 g, 2.83 mmol) was added. The stirring was continued for 1 h; the mixture was concentrated, and the thus obtained semi-solid was purified by flash chromatography on Si-gel (750 g) using 3% MeOH-2% Et3N-95% CH2Cl2. (Note: it is believed that during this chromatography most of palladium residues are removed in the form of a complex with the by-product pyrazole) This gave a partially purified product (29.0 g) which was additionally purified by flash chromatography on Si-gel (750 g) using 3% (2.5M NH3/MeOH) in CH2Cl2. This gave compound 8 as a bright-yellow, solid foam (21.6 g, yield: 84.5%); ICP-OES Pd: 8 ppm, Cu<1 ppm.
Compound 8 (21.30 g) was placed under argon in a 1 L round-bottom flask. With stirring, a pre-formed mixture of thioanisole (8.32 mL, 70.9 mmol) and TFA (300 mL) was added. The reaction mixture was stirred/Ar, at 40-45° C., for 2 h 40 min, and then it was cooled to RT, concentrated, and dried in vacuo. The thus obtained glassy solid was treated with 6N HCl/H2O (50 mL) and EtOH (200 proof, 200 mL), and the mixture was concentrated to a semi-solid. This material was again treated with 6N HCl/H2O (50 mL) and EtOH (200 mL), and the mixture was concentrated, and dried to a solid. This solid was dissolved in 3N HCl/H2O (45 mL), the solution was stirred/Ar, and THF (80 mL) was added dropwise to precipitate an oil. The mixture was rapidly stirred for 5 min, and then the phases were separated. The bottom phase (64.5 g) was placed under argon in a 500 mL flask, stirred at RT under argon, and then the product was precipitated by addition of EtOH (150 mL) and isopropanol (50 mL), and the mixture was stirred at RT for 1 h. The solid was filtered, washed with IPA (4×40 mL), dried with suction, and then dried in vacuo (1 mm Hg, RT) overnight. This gave the product (14.40 g), which contained 1 equivalent IPA (by 1H-NMR), in addition to some ethanol and THF. This sample (14.0 g) was dissolved in 1N HCl/H2O (21 mL), and solvents (5 mL) were distilled-off. The sample remaining in the flask was diluted with EtOH (40 mL), and solvents (35 mL) were distilled-off. The residue was stirred/Ar at RT, EtOH (150 mL) was added dropwise, the resulting thick suspension was stirred for 1.5 h at RT, and then filtered. The canary-yellow solid was washed with EtOH (3×30 mL), dried in vacuo at RT for 2 h, and then dried in an oven at 70° C., for 40 h. This gave compound 234 as a yellow powder (11.94 g; Yield: 75% from 8; HPLC Purity (PDA): 98.9%; Solvents: EtOH 0.3%wt).
Example 6
Synthesis of Compound 248
The preparation of compound 248 was carried out by coupling Fragment A (10) and Fragment B (9).
Synthesis of Fragment B Intermediate 9




Synthesis of 7
A solution of (S)—N-Cbz-4-aminopentene (16.425 g, 75 mmol) and 9-BBN (dimer, 10.065 g, 41.25 mmol) in toluene was stirred at RT under argon for 16 hrs. 1N NaOH (120 mL), compound 6 (22.79 g, 75 mmol) in toluene (100 mL) and Pd(PPh3)4 (3.5 g, 3.0 mmol) was added. The mixture was stirred under argon at 60° C. for 18 hrs, The mixture was diluted with EtOAc (150 mL), washed with brine (150 mL), dried over MgSO4, filtered and concentrated. The crude product was purified by chromatography on silica gel (0-20% EtOAc in Heptane) to afford 7 as a colorless oil (31.5 g, 95%). Note the procedure to prepare the starting material (S)—N-Cbz-4-aminopentene is described herein.
Synthesis of 8
A mixture of 7 (31.5 g, 70.96 mmol), CuI (674 mg, 3.55 mmol), PdCl2 (PPh3)2 (996 mg, 1.42 mmol) and DMF (110 mL) was degassed. Et3N (19.8 mL, 142.12 mmol) and trimethsilylacetylene (10.43 g, 106.42 mmol) was added under argon. The resulting mixture was heated at 70° C. for 24 h. After cooling to room temperature, the reaction mixture was diluted with EtOAc (250 mL), washed with 15% NH4OH and brine (100 mL×2). The EtOAc solution was dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-10%, EtOAc in heptane) to afford 8 as a light yellow oil (28.10 g, 86%).
Synthesis of 9
The suspension of 8 (28.10 g, 60.96 mmol) and K2CO3 (4.4 g, 31.88 mmol) in MeOH (100 mL) was stirred at room temperature for 1 h. The reaction was diluted with CH2Cl2 (150 mL), washed with water, dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (5-20%, EtOAc in heptane) to afford 9 as a light brown oil (22.60 g, 95%).







Synthesis of 11
Compound 9 (13.0 g, 33.38 mmol) and compound 10 (23.47 g, 33.38 mmol) were dissolved in anhydrous DMF (80 mL). The solution was purged with argon, and then CuI (381 mg, 2.0 mmol), Pd(PPh3)4 (1.157 g, 1.0 mmol), and Et3N (13.95 mL, 100.15 mmol) were added. After stirring at 70° C. for 18 h, MeOH (30 mL) was added, and the mixture was stirred at 90° C. for 3 h. After cooling to ambient temperature, the mixture was diluted with EtOAc (200 mL), washed with 15% NH4OH and brine (150 mL), dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (1-4%, 2.5M NH3/MeOH in CH2Cl2) to give product 11 (22.94 g, 80%).
Synthesis of 12
To a solution of 11 (20.94 g, 24.38 mmol) in MeOH (200 mL) and CH2Cl2 (200 mL) was added 4N HCl in dioxane (150 mL) at 0° C. The reaction was concentrated after stirring at RT for 16 h. The residue was dissolved in DMF (200 mL). Diisopropylethyl amine (21 mL) was added, followed by N,N-bis-boc-guanylpyrrazole (7.56 g, 24.38 mmol). After stirring at RT for 2 days, the reaction was diluted with EtOAc (250 mL), washed with brine (100 mL×2), The EtOAc solution was dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-5%, 2.5M NH3/MeOH in CH2Cl2) to give product 12 (15.76 g, 72%) as a yellow foam. 12 was further treated with charcoal (1.5 g) in EtOAc (200 mL) at RT for 4 hrs before next step use.
Synthesis of 13
To a solution of 12 (10.42 g, 11.55 mmol) in CH2Cl2 (70 mL) was added Boc2O (3.07 g, 14.07 mmol). The reaction was concentrated after stirring at RT for 3 h. The residue was purified by flash chromatography (25-90%, EtOAc in Heptane) to give product 13 (11.08 g, 96%) as a yellow foam.
Synthesis of Compound 248
To a solution of 13 (10.42 g, 10.40 mmol) in TFA (20 mL) was added thioanisole (3.9 g, 31.45 mmol). The reaction was concentrated after stirring at 50° C. for 8 h. MeOH (20 mL) and 3N HCl/H2O (40 mL) were added, the resulted solution was concentrated (this sequence was repeated once). The residue was dissolved in 1N HCl (120 mL), washed with diethyl ether (80 mL×3). The acidic aqueous solution was concentrated and recrystallized from MeOH/water/ethanol (2 mL/2 mL/20 mL) to afford the final product 248 (5.8 g, >99% purity, 82% yield).
Example 7
Synthesis of Compounds 387 and 388
Compounds 387 and 388 were prepared according to the procedure below.







Example 8
Synthesis of Compounds 389 and 390
Compounds 389 and 390 were prepared according to the procedure below.







Example 9
Synthesis of Compound 399
Compound 399 was prepared according to the procedure below.




Example 10
Synthesis of Compound 404
Compound 404 was prepared according to the procedure below.




Example 11
Synthesis of Compound 390




Synthesis of [1-Methyl-4-(4-trifluoromethyl-pyridin-2-yl)-butyl]-carbamic acid benzyl ester (2)
A solution of but-3-enyl-carbamic acid benzyl ester (3.06 g, 14.0 mmol, 1 eq) in anhydrous toluene (40 mL) was cooled under argon to 0-5° C. 9-BBN (0.50 M, solution in THF; 30.8 mL, 1504 mmol, 1.1 eq.) was added dropwise, the mixture was stirred and allowed to reach room temperature. After 24 h, 1N NaOH/H2O (23.8 mL, 23.8 mmol, 1.7 eq.) was added, followed by 2-bromo-4-trifluoromethyl-pyridine (3.16 g, 14.0 mmol, 1 eq.) and toluene (25 mL). The resulting mixture was degassed and Pd(PPh3)4 (0.89 g, 0.70 mmol, 0.05 eq.) was added. The mixture was rapidly stirred under argon at 60° C. for 24 h, and then it was cooled to room temperature. Afterwards, the mixture was partitioned between EtOAc (100 mL) and brine (100 mL). The organic phase was washed with brine (100 mL), dried over Na2SO4, filtered and concentrated. The crude product was purified by flash chromatography on silica gel (0-50% EtOAc in Heptane) to afford 2 as colorless oil (5.1 g, 99%).




Synthesis of [1-methyl-4-(1-oxy-4-trifluoromethyl-pyridin-2-yl)-butyl]-carbamic acid benzyl ester (3)
To a solution of 2 (5.1 g, 13.94 mmol, 1 eq.) in CH2Cl2 (50 ml) was added m-chloroperoxybenzoic acid (2.88 g, 16.72 mmol, 1.2 eq.). The mixture was stirred at room temperature for 18 h before quenching with NaHCO3 (sat. 50 ml). The organic solution was washed with brine (50 mL×2), dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-10%, MeOH in CH2Cl2) to afford 3 (5.30 g, 99%).
Synthesis of [4-(6-Chloro-4-trifluoromethyl-pyridin-2-yl)-1-methyl-butyl]-carbamic acid benzyl ester (4)
A solution of 3 (1.52 g, 4.0 mmol) in POCl3 (6 ml) was heated at 110° C. for 15 h before cooling to room temperature. The reaction mixture was quenched with ice, basified with NaOH to pH ca. 10, and extracted with EtOAc (50 mL×2). The EtOAc solution was washed with brine (50 mL×2), dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-10%, MeOH in CH2Cl2) to afford the 2-chloropyridine derivative (360 mg). The resulting product was dissolved in CH2Cl2 (10 ml). Hunig's base (520 mg, 4.03 mmol) was added at 0° C. followed by CbzCl (343 mg, 2.02 mmol). The mixture was stirred for 3 h at 0° C., then concentrated and purified by flash chromatography (0-50%, EtOAc in heptane) to afford 4 (470 mg, 32%).
Synthesis of [4-(6-Ethynyl-4-trifluoromethyl-pyridin-2-yl)-1-methyl-butyl]-carbamic acid benzyl ester (5)
A mixture of 4 (470 mg, 1.17 mmol, 1 eq), CuI (23 mg, 0.117 mmol, 0.1 eq.), Pd(PPh3)4 (68 mg, 0.058 mmol, 0.05 eq.) and DMF (8 mL) was degassed. Trimethsilyacetylene (173 mg, 1.760 mmol, 1.5 eq.) was added under Argon, followed by Et3N (356 mg, 4.81 mL, 3.52 mmol, 3 eq.). The mixture was heated at 70° C. for 24 h. After being cooled to room temperature, the reaction mixture was diluted with EtOAc (50 mL) and washed with brine (20 mL×2). The EtOAc solution was dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-30%, EtOAc in heptane) to afford the desired trimethsilyacetylene derivative (500 mg, 92%). The product was dissolved in MeOH (20 mL), and K2CO3 (138 mg, 1 mmol) was added. The reaction mixture was stirred at room temperature for 30 min before concentration. The residue was partitioned between EtOAc (20 mL) and H2O (20 mL). The EtOAc layer was washed with brine (10 mL), dried over MgSO4, filtered and concentrated. The crude product was purified by flash chromatography (0-50%, EtOAc in heptane) to afford 5 as colorless oil (423 mg, 100%).




Synthesis of 7
Pyrrolocytosine 7 was prepared from the coupling of common intermediate 6 and alkyne 5 according to the procedure described previously. Starting from 230 mg of 5, 320 mg of the desired compound was obtained as an orange-brown solid (62%); LCMS (ESI) m/e 876.2 (M+1)+.
Synthesis of Compound 390
Boc-deprotection of 7 (0.32 g) was accomplished with 2 mL of 4N HCl in dioxane and CH2Cl2 (10 mL) at room temperature (2 h). Following solvent evaporation, the crude residue was taken to the next step without further purification. LCMS (ESI) m/e 613.0 (M+1)+. Guanidine formation was carried out according to the protocol used to prepare the other described compounds (bis-Boc-guanylpyrrazole, Et3N, MeOH, RT). Deprotection was found to work best using a stepwise procedure to first remove the Boc-groups (trifluoroacetic acid in 10 mL of CH2Cl2). Following concentration, the Cbz group was removed by redissolving the yellow-brown solid in 5 mL of trifluoroacetic acid and adding thioanisole (0.1 mL) dropwise. The solution was stirred at rt overnight, and upon completion solvent was evaporated affording the final compound as a brown oil. Diethyl ether was added and the liquid layer containing most of the residual thioanisole was decanted. Crude product was then dissolved in [(20% MeOH-90% H2O)+0.15% TFA] (10 mL). An aliquot (10 mL) was injected on a Dynamax 41.4 mm, C-18 prep HPLC Unit (guard+column), which was eluted with a gradient of solvents of 15%-70% (MeOH/H2O+0.15% TFA), over 45 min. The pure fractions were combined and concentrated with EtOH to dryness. This sample was treated with 1N HCl/H2O (5 mL) and EtOH (10 mL), and concentrated. This operation was repeated; the solid thus obtained was lyophilized from H2O-MeCN (4:1), affording compound 390 as a yellow powder (86 mg); LCMS (ESI) m/e 584.1 (M+1)+; 1H NMR (300 MHz, D2O) δ 1.20 (d, J=6.6 Hz, 3H), 1.56 (m, 2H), 1.65 (d, J=6.8 Hz, 3H), 1.85 (m, 2H), 2.87 (m, 1H), 2.89 (t, J=6.9 Hz, 2H), 3.00 (m, 1H), 3.15 (t, J=6.9 Hz, 2H), 3.31 (q, J=6.8 Hz, 1H), 4.47 (q, J=6.6 Hz, 1H), 7.05 (s, 1H), 7.50 (d, J=8.1 Hz, 2H), 7.51 (s, 1H), 7.61 (d, J=8.1 Hz, 2H), 7.94 (s, 1H), 8.51 (s, 1H).
Example 12
Synthesis of Compound 322




Synthesis of Mesylate 2 from Aldehyde 1 
Aldehyde 1 (11.8 g, 46.6 mmol) was dissolved in MeOH (70 mL) and the solution was cooled to 0° C. NaBH4 (2.13 g, 56 mmol) was added slowly as a solid in several portions. After 30 minutes, the mixture was warmed to RT, resulting in the formation of a clear solution. Stirring for an addition 1.5 h at RT led to complete consumption of starting material. MeOH was then evaporated and the residue was partitioned between EtOAc and H2O. The organic layer was collected, dried over MgSO4, and concentrated to a viscous, colorless oil (12.5 g, 99%). This oil was then redissolved in CH2Cl2 at 0° C., and Et3N was added. The dropwise addition of MsCl produced a slightly yellow solution that was allowed to gradually warm to RT. Upon completion, the reaction was quenched with NaHCO3. The organic layer was separated and the aqueous phase was extracted 2× with fresh CH2Cl2. The combined organics were dried over Na2SO4 and concentrated to give an oil (8.10 g, 53%) that was used directly in the next step.
Synthesis of Aryl THP Ether 4
To a flask containing NaH (4.2 g, 105.7 mmol, 60% dispersion in oil) in 20 mL of THE at 0° C. was added THP-protected ether 3 (16.9 g, 105.7 mmol) in 30 mL THF. An additional 20 mL of solvent was added to reduce foaming. After 5 min, the ice bath was removed and the mixture was brought to RT and stirring was continued for 1 h. Mesylate 2 (4.4 g, 13.21 mmol) in 50 mL of THF was then added dropwise at RT and the resulting solution was heated for 1.5 h at 45-50° C. Complete conversion was observed by LCMS, so the reaction was quenched with NH4Cl. EtOAc was added and the phases were separated. The aqueous layer was extracted 2× with fresh EtOAc and the combined organics were dried over MgSO4 and concentrated. The crude material was purified by column chromatography (5-30% EtOAc in heptanes) to provide 2.10 g of product (40%).
Synthesis of Aryl Alcohol 5
THP-protected aryl ether 4 (2.10 g, 5.28 mmol) was dissolved in 35 mL of MeOH and treated with cat. TsOH (0.1 eq). After 5 h at RT, the reaction was complete as indicated by LCMS and TLC. MeOH was removed and the mixture was partitioned between EtOAc and H2O. The organic layer was separated, dried over MgSO4, and concentrated to a slightly yellow-colored oil (1.54 g, 93%). This material was used without further purification.
Synthesis of Cbz-Protected Aryl Amine 6
The same procedure for mesylation was used that was part of the two step conversion starting from aldehyde 1. From 0.86 g (2.73 mmol) of alcohol 5, 1.29 g of crude mesylate was obtained and used directly for azide formation.
This residue (1.29 g) was dissolved in DMF (10 mL) and treated with a single portion of NaN3 (0.6 g. 9.3 mmol). The resulting mixture was then allowed to stir overnight at RT. Upon completion, ether was added and the organic layer was separated. The aqueous phase was washed 3× with additional ether and the organics were combined, washed 4× with H2O, dried over MgSO4, and concentrated. The crude oil ( ̃1 g) was used directly in the next step without purification.
For the reduction to amine, the azide material ( ̃3 mmol) was then dissolved in 10 mL THF along with 1 mL of H2O and triphenylphosphine (1.6 g, 6.0 mmol). The contents were heated from 55-60° C. overnight to obtain complete consumption of starting material. THF was then removed in vacuo.
Cbz-protection was then accomplished by placing the amine in 15 mL of CH2Cl2 and 15 mL of sat. NaHCO3. The solution was cooled to 0° C. prior to the addition of CbzCl (0.64 mL, 4.5 mmol, 1.5 eq). After 4 h at RT, the organic layer was separated. The aqueous phase was washed 2× with fresh CH2Cl2 and the combined organics were dried over Na2SO4 and concentrated. The crude material was purified by column chromatography (3:1 heptanes/EtOAc) to produce 1.2 g of desired compound (97% yield from aryl alcohol 5).
Note: The remainder of the synthesis (i.e. alkyne formation, Sonogashira/cyclization, and guanidine installation) is according the procedures described above for compounds 234 and 248).
Example 13
Antimicrobial Activity
The compounds of the present invention were tested for antimicrobial activity. These data are presented in Table 3, Table 4, Table 5, and Table 6. The compounds were run against Escherichia coli strain ATCC25922 using a standard microdilution assay to determine minimum inhibitory concentrations (MICs). The data is presented whereby a “+” indicates that the compound has an MIC value of 16 micrograms/ml or less and a “−” indicates that the compound has an MIC value greater than 16 micrograms/ml. A “N/A” means that data is unavailable. It will be recognized by one skilled in the art that the compounds can be assessed against other bacterial organisms and that the presentation of data for activity against Escherichia coli is illustrative and in no way is intended to limit the scope of the present invention. The compounds of the present invention can be assayed against a range of other microorganisms depending upon the performance activity desired to be gathered. Furthermore, the “+”, “−”, and “N/A” representation and the selection of a cutoff value of 16 micrograms/ml is also illustrative and in no way is intended to limit the scope of the present invention. For example, a “−” is not meant to indicate that the compound necessarily lacks activity or utility, but rather that its MIC value against the indicated microorganism is greater than 16 micrograms/ml.










TABLE 3








E. coli




ATCC25922



Compound no.
MIC



















1
+



2
+



3
+



4
+



5
+



6
+



7
+



8
+



9
+



10
+



11
+



12
+



13
+



14
+



15
+



16
+



17
+



18
+



19
+



20
+



21
+



22
+



23
+



24
+



25
+



26
+



27
+



28
+



29
+



30
+



31
+



32
+



33
+



34
+



35
+



36
+



37
+



38
+



39
+



40
+



41
+



42
+



43
+



44
+



45
+



46
+



47
+



48
+



49
+



50
+



51
+



52
+



53
+



54
+



55
+



56
+



57
+



58
+



59
+



60
−



61
+



62
+



63
+



64
+



65
+



66
−



67
+



68
+



69
+



70
+



71
+



72
+



73
+



74
+



75
+



76
+



77
+



78
+



79
+



80
+



81
+



82
+



83
+



84
+



85
+



86
+



87
+



88
+



89
+



90
+



91
+



92
+



93
+



94
+



95
+



96
+



97
+



98
+



99
+



100
+



101
+



102
+



103
+



104
+



105
+



106
+



107
+



108
+



109
+



110
+



111
+



112
+



113
+



114
+



115
+



116
+



117
+



118
+



119
+



120
+



121
+



122
+



123
+



124
+



125
+



126
+



127
+



128
+



129
+



130
+



131
+



132
+



133
+



134
+



135
+



136
+



137
+



138
+



139
+



140
+



212
+



213
+



214
+



215
+



216
+



217
+



218
+



219
+



220
+



221
+



222
+



223
+



224
+



225
+



226
+



227
+



228
+



229
+



230
+



231
+



232
+



233
+



234
+



235
+



236
+



237
+



238
+



239
+



240
+



241
+



242
+



243
+



244
+



245
+



246
+



247
+



248
+



249
+



250
+



251
+



252
+



253
+



254
+



255
+



256
+



257
+



258
+



259
+



260
+



261
+



262
+



263
+



264
+



265
+



266
+



267
+



268
+



269
+



270
+



271
+



272
+



273
+



274
+



275
+



276
+



277
+



278
+



279
+



280
+



281
+



282
+



283
+



284
+



285
+



286
+



287
+



288
+



289
+



290
+



291
+



292
+



293
+



294
+



295
+



296
+



297
+



298
+



299
+



300
+



301
+



302
+



303
+



304
+



305
+



306
+



307
+



308
+



309
+



310
+



311
+



312
+



313
+



314
+



315
+



316
+



317
+



318
+



319
+



320
+



321
+



322
+



323
+



324
+



325
+



326
+



327
+




















TABLE 4








E. coli




ATCC25922



Compound no.
MIC



















150
−



151
+



152
+



153
+



154
+



155
+



156
+



157
+



158
+



159
+



160
+



161
+



162
+



163
+



164
+



165
−



166
+



167
+



168
+



169
+



170
+



171
+



172
+



173
+



174
+



175
+



176
+



177
−



178
+



179
+



180
+



181
+



182
+



183
−



184
+



185
−



186
−



187
−



188
+



189
−



190
−




















TABLE 5








E. coli




ATCC25922



Compound no.
MIC



















333
+



334
+



335
+



336
+



337
+



338
+



339
+



340
+



341
+



342
+



343
+



344
+



345
+



346
+



347
+



348
+



349
+



350
+



351
−



352
−



353
−



354
−



355
−



356
−



357
−



358
−



359
+



360
+



361
+



362
+



363
+



364
+



365
−



366
−



367
−



368
+



369
+



370
+



371
−



372
−



373
−



374
+



375
+



376
+



377
+



378
+



379
+



380
+



381
+



382
+



383
+



384
+



385
+



386
−



387
+



388
+



389
+



390
+



391
+



392
+



393
+



394
+



395
+



396
+



397
+



398
+



399
+



400
+



401
+



402
+



403
+



404
+



405
−



406
−



407
+



408
+



409
−



410
+



411
+



412
+



413
+



414
+



415
+



416
+



417
+



418
+



419
+



420
+



421
+



522
+



423
+



424
+



425
+



426
+



427
+



428
+



429
+



430
+



431
+



432
+



433
+



434
+



435
+



436
+



437
+



438
+



439
+



440
+



441
+



442
+



443
+



444
+



445
+



446
+



447
+



448
+



449
+



450
+



451
+



452
+



453
+



454
+



455
+



456
+



457
+



458
+



459
+



460
+



461
+



462
+



463
+



464
+



465
+



466
+



467
+



468
+




















TABLE 6








E. coli




ATCC25922



Compound no.
MIC









469
+



470
+



471
+



472
+



473
+



474
+



475
+



476
+



477
+



478
+



479
+



480
+



481
+



482
+



483
+



484
+



485
+



486
+



487
+



488
+



489
+



490
−



491
+



492
−



493
+



494
+



495
+



496
+



497
−



498
+



499
+



500
+



501
+



502
+



503
−



504
+



505
+



506
+



507
+










INCORPORATION BY REFERENCE
The entire disclosure of each of the patent documents and scientific articles referred to herein is incorporated by reference for all purposes.
EQUIVALENTS
The invention can be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.

## Claims

1. A compound having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, wherein
X1 is CR1 or N; X2 is CR2 or N; X3 is CR3 or N; X4 is CR4 or N; X5 is CR5 or N; with the proviso that X1, X2, X3, X4, and X5 are not all N;
Y6 is CR6 or N; Y7 is CR7 or N; Y8 is CR8 or N; Y9 is CR9 or N; Y10 is CR10 or N; with the proviso that Y6, Y7, Y8, Y9, and Y10 are not all N; wherein
R1, R2, R4, R5, R6, R7, R8 and R10 are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) Br, (e) I, (f) —CF3, (g) —CF2H, (h) —CFH2, (i) —OCF3, (j) —OCF2H, (k) —OCFH2, (l) —OCH3, (m) —CN, (n) —N3, (o) —NO2, (p) —NR11R11, (q) —NR11C(O)R11, (r) —C(O)NR11R11, (s) —OR11, (t) —COH, (u) —CO(C1-C8 alkyl), (v) —COR11, (w) —NR11(CNR11)NR11R11, (x) —S(O)pR11, (y) —NR11S(O)pR11, (z) —SR11, (aa) —SCF3, (bb) —C(CF3)H—NH—CHR11R11, (cc) —COOR11, (dd) —(OCH2CH2)tR11, (ee) —(OCH2CH2)tOR11, (ff) —C1-C8 alkyl, (gg) —C2-C8 alkenyl, (hh) —C2-C8 alkynyl, (ii) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (jj) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (kk) -haloalkyl, (ll) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (mm) -3-14 membered saturated, unsaturated, or aromatic carbocycle, and (nn) —CHR11—NH-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one of more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur);
wherein each (ff) through (nn) is optionally substituted with one or more R12;

alternatively, wherein two substituents selected from R6, R7, and R8 are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur; wherein each (a) through (b) is optionally substituted with one or more R12;
each R11 is independently selected from (a) hydrogen, (b) halogen, (c) —OH, (d) —SH, (e) —(C1-C8 alkyl)OH, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —OR12, (k) —COR12, (l) —CN, (m) —NO2, (n) —CONH2, (o) —CONR12R12, (p) —COCH3, (q) —S(O)pCH3, (r) —S(O)pNR12R12, (s) —SR12, (t) —C(O)OH, (u) —C(O)OR12, (v) —N3, (w) —NH2, (x) —NR12C(O)R12, (y) —NH(C1-C8 alkyl), (z) —N(C1-C8 alkyl)2, (aa) —C1-C8 alkyl, (bb) —C2-C8 alkenyl, (cc) —C2-C8 alkynyl, (dd) -haloalkyl, (ee) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (ff) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (gg) —3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (hh) —3-14 membered saturated, unsaturated, or aromatic carbocycle, and (ii) —(C═NH)NR12R12;
wherein each (y) through (hh) is optionally substituted with one or more R12;
alternatively two R11 substituents are taken together to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, wherein each (a) through (b) is optionally substituted with one or more R12;
R3 is selected from:




wherein R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l are each independently selected from (a) hydrogen, (b) halogen, (c) —CN, (d) —N3, (e) —NO2, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —OR11, (k) —C(O)R11, (l) —C(O)NR11R11, (m) —NH2, (n) —NR11R11, (o) —NR11C(O)R11, (p) —S(O)pR11, (q) —C(O)OH, (r) —C(O)OR11, (s) —C1-C8 alkyl, (t) —C2-C8 alkenyl, (u) —C2-C8 alkynyl, (v) haloalkyl, (w) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (x) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (s) through (x) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R3a and R3b, R3c and R3d, R3e and R3f, R3g and R3h, R3i and R3j, and R3k and R3l are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic, (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, wherein two substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms to form a substituted or unsubstituted carbon-carbon double bond, or wherein four substituents selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms to form a carbon-carbon triple bond;
U is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p—, —NR11S(O)pNR11—, and —NR11C(O)NR11—;
T is selected from —NR11R11, —NR11(C═O)OR11, —NR11(C═NR11)NR11R11, and OR11;
alternatively, one R11 and one substituent selected from R3a, R3b, R3c, R3d, R3e, R3f, R3g, R3h, R3i, R3j, R3k, and R3l are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R9 is selected from:




wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CN, (d) —N3, (e) —NO2, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —OR11, (k) —NH2, (l) —NR11R11, (m) —C(O)R11, (n) —C(O)OR11, (o) —C(O)NR11R11, (p) —NR11C(O)R11, (q) —S(O)pR11, (r) —C1-C8 alkyl, (s) —C2-C8 alkenyl, (t) —C1-C8 alkynyl, (u) haloalkyl, (v) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (w) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
wherein each (r) through (w) is optionally substituted with one or more R12;
alternatively, one or more pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) 3-7 membered saturated or unsaturated carbocyclic, (b) 3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (c) an exo carbon-carbon double bond, (d) carbonyl group, or (e) thiocarbonyl group;
wherein each (a) through (c) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on different carbon atoms are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
alternatively, two substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a substituted or unsubstituted carbon-carbon double bond, or four substituents selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t on two adjacent carbon atoms are taken together with the bond between said adjacent carbon atoms form a carbon-carbon triple bond;
Z is selected from —O—, —S(O)p—, —NR11—, —(C═O)—, —NR11(C═O)—, —(C═O)NR11—, —S(O)pNR11—, —NR11S(O)p—, —NR11S(O)pNR11—, and —NR11C(O)NR11—;
W is selected from —NR11R11, —NR11(CO)OR11, —NR11(C═NR11)NR11R11, and —OR11;
alternatively, one R11 and one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are taken together with the intervening atoms to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur;
wherein each (a) through (b) is optionally substituted with one or more R12;
R12 is independently selected from (a) hydrogen, (b) halogen, (c) —OH, (d) —SH, (e) —(C1-C8 alkyl)OH, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —O(C1-C8 alkyl), (k) —CN, (l) —NO2, (m) —CONH2, (n) C(O)NH(C1-C8 alkyl), (o) C(O)N(C1-C8 alkyl)2, (p) —COH, (q) —COCH3, (r) —S(O)pCH3, (s) —S(O)pN(C1-C8 alkyl)2, (t) —S(C1-C8 alkyl), (u) —C(O)OH, (v) —C(O)O(C1-C8 alkyl), (w) —N3, (x) —NHC(O)(C1-C8 alkyl), (y) —N(C1-C8 alkyl)C(O)(C1-C8 alkyl), (z) —NH2, (aa) —NH(C1-C8 alkyl), (bb) —N(C1-C8 alkyl)2, (cc) —C1-C8 alkyl, (dd) —C2-C8 alkenyl, (ee) —C2-C8 alkynyl, (ff) -haloalkyl, (gg) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur), (hh) —(C1-C8 alkyl)-(3-14 membered saturated, unsaturated, or aromatic carbocycle), (ii) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (jj) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (kk) —(C═NH)NH2, (ll) —C(═NH)NH2, (mm) —C(O)R13, (nn) ═O, and (oo) ═NR13;
wherein each (aa) through (jj) is optionally substituted with one or more R13;

R13 is independently selected from (a) hydrogen, (b) halogen, (c) —C1-C8 alkyl, (d) —C2-C8 alkenyl, (e) —C2-C8 alkynyl, (f) -haloalkyl, (g) —OH, (h) —OC1-C8 alkyl, (i) —OC2-C8 alkenyl, (j) —OC2-C8 alkynyl, (k) —OCF3, (l) —OCH3, (m) —OCF2H, (n) —OCFH2, (o) —NH2, (p) —CN, (q) —N3, (r) —S(O)pC1-C8 alkyl, (s) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (t) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
p is 0, 1, or 2; and
t is 0, 1, or 2.

2. The compound according to claim 1 having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

3. The compound according to claim 2 having the formula:




or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

4. The compound according to claim 3 having a formula selected from:










or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

5. The compound according to claim 3 having a formula selected from:










or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

6. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 1, wherein at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen.

7. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 2 wherein R1, R2, R4, and R5 are each hydrogen.

8. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 3, wherein R3a and R3b are each independently selected from (a) hydrogen, (b) F, (c) Cl, (d) —CH3, (e) —CF3, (f) —CF2H, (g) —CFH2, (h) —OCF3, (i) —OCF2H, (j) —OCFH2, (k) —OCH3, and (l) —OH.

9. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 1, wherein R10 is selected from hydrogen, F and Cl.

10. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 1, wherein R6 and R7 are each independently selected from (a) F, (b) Cl, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OCF3, (g) —OCF2H, (h) —OCFH2, (i) —OCH3, (j) —CN, (k) —OR11, (l) —S(O)pR11, (m) —SCF3, (n) —C1-C8 alkyl, (o) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, (p) -3-14 membered saturated, unsaturated, or aromatic carbocycle, (q) —CHCHCN and (r) —CHCH—C(O)NH-t-butyl.

11. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 1, wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (c) —CF3, (d) —CF2H, (e) —CFH2, (f) —OCF3, (g) —OCH3, (h) —OCF2H, (i) —OCFH2, (j) —OR11, (k) —C1-C8 alkyl, (l) haloalkyl, (m) -3-14 membered saturated, unsaturated, or aromatic heterocycle containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur, and (n) -3-14 membered saturated, unsaturated, or aromatic carbocycle;
alternatively, one or more of pairs of substituents selected from R9k and R9l, R9m and R9n, R9o and R9p, R9q and R9r, and R9s and R9t are taken together with the carbon atom to which they are attached to form (a) -3-7 membered saturated or unsaturated carbocyclic or (b) -3-7 membered saturated or unsaturated heterocyclic ring containing one or more heteroatoms selected from the group consisting of nitrogen, oxygen, and sulfur; and
at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen.

12. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 11 wherein R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t are each independently selected from (a) hydrogen, (b) halogen, (d) —CF3, (e) —CF2H, (f) —CFH2, (g) —OCF3, (h) —OCH3, (i) —OCF2H, (j) —OCFH2, (k) —OH, (c) —OCH3, (l) methyl, (m) ethyl, (n) isopropyl, and (o) t-butyl; and
at least one substituent selected from R9k, R9l, R9m, R9n, R9o, R9p, R9q, R9r, R9s, and R9t is not hydrogen.

13. The compound according to claim 1 having a formula selected from:







or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer.

14. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 13, wherein R9o, R9p, R9q, and R9r are each independently selected from —C1-C6 alkyl and hydrogen;
R6 and R8 are each independently selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3; and
R3a is selected from halogen and C1-C6 alkyl; and
p is 0, 1, or 2.

15. The compound or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, according to claim 13, wherein R9o, R9p, R9q, and R9r are each independently selected from C1-C6 alkyl and hydrogen;
R6 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, and —CF3;
R7 is selected from hydrogen, F, Cl, Br, I, —C1-C6 alkyl, —CH2F, —CHF2, —CF3, —OC1-C6 alkyl, —S(O)p—C1-C6 alkyl, —OCH2F, —OCHF2, —OCF3, —S(O)p—CH3, —S(O)p—CH2F, and —S(O)p—CF3;
R8 is hydrogen;
R3a is selected from halogen and —C1-C6 alkyl; and
p is 0, 1, or 2.

16. The compound of claim 1, or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer selected from:













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17. A pharmaceutical composition comprising a compound according to claim 1 or a tautomer thereof, or a pharmaceutically acceptable salt, ester, or prodrug of said compound or tautomer, and a pharmaceutically acceptable carrier.