Rifamycin analogs and uses thereof

1. A compound having the formula:

or a pharmaceutically acceptable salt thereof, wherein

(a) A is H, OH, O—(C 1-6 alkyl), O—(C 1-4 alkaryl), O—(C 6-12 aryl), O—(C 1-9 heteroaryl), or O—(C 1-4 alkheteroaryl);

W is O, S, or NR 1 , wherein R 1 is H, C 1-6 alkyl, C 1-4 alkaryl, or C 1-4 alkheteroaryl;

X is H or COR 2 , wherein R 2 is C 1-6 alkyl, which can be substituted with 1-5 OH groups, O—(C 3-7 alkyl), which can be substituted with 1-4 OH groups, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl, wherein each alkyl carbon is bonded to no more than one oxygen atom;

Y is H, Hal, or OR Y3 , wherein R Y3 is C 1-6 alkyl, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl;

Z is H, Hal, or OR Z3 wherein R Z3 is C 1-6 alkyl, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl; and

R 4 has the formula:

wherein

R 5 is H, C 1-6 alkyl, C 1-4 alkaryl, C 1-4 alkheteroaryl, COR 10 , CO 2 R 11 , CONR 10 R 11 CSR 10 , COSR 11 , CSOR 10 , CSNR 10 R 11 , SO 2 R 11 , or SO 2 NR 10 R 11 , wherein R 10 is H, C 1-6 alkyl, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl, R 11 is H, C 1-6 alkyl, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl, or R 10 and R 11 together form a C 2-6 linkage, optionally containing a non-vicinal O;

R 6 is H, C 1-6 alkyl, C 1-4 alkaryl, C 1-4 alkheteroaryl;

R 7 is H, C 1-6 alkyl, C 6-12 aryl, C 1-9 heteroaryl, C 2-9 heterocyclyl, C 1-4 alkaryl, C 1-4 alkheteroaryl, OR 12 , or NR 12 R 13 , wherein R 12 is H, C 1-6 alkyl, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl, R 13 is C 1-6 alkyl, C 6-12 aryl, C 1-4 alkaryl, C 1-9 heteroaryl, or C 1-4 alkheteroaryl, or R 12 and R 13 together from a C 2-6 linkage, optionally containing a non-vicinal O;

T is O, S, NR 5 , or a bond;

each of R 8 and R 9 is, independently H, C 1-6 alkyl, C 6-12 aryl, C 1-9 heteroaryl, C 2-9 heterocyclyl, C 1-4 alkaryl, or C 1-4 alkheteroaryl, or R 8 and R 5 together form a 3-8-membered ring, with the ring optionally containing a non-vicinal oxygen;

and each of r and s is, independently, 1 or 2,

wherein said C 1-9 heteroaryl is selected from the group consisting of furanyl, thienyl, pyrrolyl, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, triazolyl, tetrazolyl, oxadiazolyl, oxatriazolyl, pyridyl, pyridazyl, pyrimidyl, pyrazyl, triazyl, benzofuranyl, isobenzofuranyl, benzothienyl, indole, indazolyl, indolizinyl, benzisoxazolyl, quinolinyl, isoquinolinyl, cinnolinyl, quinazolinyl, naphtyridinyl, phthalazinyl, phenanthrolinyl, purinyl, and carbazolyl, and

wherein,

when W is O or NR 1 , T is a bond, R 8 and R 9 are H, and X is COR 2 , R 4 is not

and

when W is O, and X is COR 2 , R 4 is not

2. A compound selected from the group consisting of:

3. A pharmaceutical composition comprising a pharmaceutically acceptable carrier or diluent and the compound of claim 1 .

4. A method of treating a bacterial infection in an animal, or a condition caused by a bacterial infection in an animal, said method comprising administering to said animal the compound of claim 1 in an amount sufficient to treat said bacterial infection.

5. The method of claim 4 , wherein said said compound is administered orally, topically, intravenously, intramuscularly, or subcutaneously.

6. The method of claim 4 , wherein said animal is a human.

7. The method of claim 4 , wherein said condition is selected from the group consisting of community-acquired pneumonia, upper and lower respiratory tract infections, skin and soft tissue infections, bone and joint infections, and hospital-acquired lung infections.

8. The method of claim 4 , wherein said infection is a persistent infection.

9. The method of claim 4 , wherein said infection is an ear infection.

10. The method of claim 4 , wherein said microbial infection is an intracellular infection.

11. The method of claim 4 , wherein said infection is caused by a Gram positive coccus.

12. The method of claim 4 , wherein said infection is caused by N. gonorrhoeae.

13. The method of claim 4 , wherein said infection is caused by C. difficile.

14. The method of claim 4 , wherein said infection is caused by C. pneumoniae.

15. The method of claim 4 , wherein said infection is caused by H. pylori.

16. The method of claim 15 , wherein said method further comprises administering to said animal a proton pump inhibitor or bismuth preparation.

17. The method of claim 4 , wherein said microbial infection is caused by a bacterium selected from the group consisting of Anaplasma bovis, A. caudatum, A. centrale, A. marginale A. ovis, A. phagocytophila, A. platys, Bartonella bacilliforrnis, B. clarridgeiae, B. elizabethae, B. henselae, B. henselae phage, B. quintana, B. taylorii, B. vinsonii, Borrelia afielii, B. andersonii, B. anserina, B. bissettii, B. burgdorferi, B. crocidurae, B. garinii, B. hermsii, B. japonica, B. miyamotoi, B. parkeri, B. recurrentis, B. turdi, B. turicatae, B. valaisiana, Brucella abortus, B. melitensis, C. psittaci, C. trachomatis, Cowdria ruminantium, Coxiella burnetii, Ehrlichia canis, E. chaffeensis, E. equi, E. ewingii, E. muris, E. phagocytophila, E. platys, E. risticii, E. rurninantium, E. sennetsu, Haemobartonella canis, H. felis, H. muris, Mycoplasma arthriditis, M. buccale, M. faucium, M. fermentans, M. genitalium, M. hominis, M. laidlawii, M. lipophilum, M. orale, M. penetrans, M. pirum, M pneumoniae, M. salivarium, M. spermatophilum, Rickettsia australis, R. conorii, R. felis, R. helvetica, R. japonica, R. massiliae, R. montanensis, R. peacockii, R. prowazekii, R. rhipicephali, R. rickettsii, R. sibirica , and R. typhi.

18. The method of claim 4 , wherein said method further comprises administering to said animal a second agent selected from the group consisting of:

antifungal agent, antiviral agent, antibacterial agent, and antiprotozoan agent.