Derivatives of 5-nitro-furan-2-carboxylic acid carbamoylmethyl ester inhibit RNase H activity associated with HIV-1 reverse transcriptase

Journal of Medicinal Chemistry

Volumn 52, Issue 5, 2009, Pages 1380-1387

  Fuji, Hideyoshi ^a   Urano, Emiko ^b,c   Futahashi, Yuko ^c   Hamatake, Makiko ^c   Tatsumi, Junko ^a   Hoshino, Tyuji ^a   Morikawa, Yuko ^b   Yamamoto, Naoki ^c   Komano, Jun ^c  

^a CHIBA UNIVERSITY   (Japan)

^b KITASATO UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

5 NITRO FURAN 2 CARBOXYLIC ACID [[4 (4 BROMO PHENYL) THIAZOL 2 YL] (TETRAHYDRO FURAN 2 YLMETHYL)CARBAMOYL] METHYL ESTER; 5 NITRO FURAN 2 CARBOXYLIC ACID ADAMANTAN 1 CARBAMOYLMETHYL ESTER; ANTIVIRUS AGENT; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; DRUG INHIBITION; DRUG STRUCTURE; ENZYME ACTIVITY; HUMAN IMMUNODEFICIENCY VIRUS 1; IC 50; STRUCTURE ACTIVITY RELATION; VIRUS REPLICATION;

ANIMALS; ANTI-HIV AGENTS; CELL LINE; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; FURANS; HIV-1; HUMANS; HYDROPHOBICITY; MODELS, MOLECULAR; PROTEIN CONFORMATION; REVERSE TRANSCRIPTASE INHIBITORS; RIBONUCLEASE H, HUMAN IMMUNODEFICIENCY VIRUS; STRUCTURE-ACTIVITY RELATIONSHIP; VIRUS REPLICATION;

EID: 64349084459     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm801071m     Document Type: Article

References (41)

1. Nikolenko, G. N.; Svarovskaia, E. S.; Delviks, K. A.; Pathak, V. K. Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template-switching frequency. J. Virol. 2004, 78, 8761-8770.
2. Nikolenko, G. N.; Palmer, S.; Maldarelli, F.; Mellors, J. W.; Coffin, J. M.; Pathak, V. K. Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision. Proc. Natl. Acad. Sci. U.S.A 2005,102, 2093-2098. Epub 2005 Jan 2031.
3. Luo, G. X.; Taylor, J. Template switching by reverse transcriptase during DNA synthesis. J. Virol. 1990, 64, 4321-4328.
4. Peliska, J. A.; Benkovic, S. J. Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science 1992, 258,1112-1118.
5. DeStefano, J. J.; Mallaber, L. M.; Rodriguez-Rodriguez, L.; Fay, P. J.; Bambara, R. A. Requirements for strand transfer between internal regions of heteropolymer templates by human immunodeficiency virus reverse transcriptase. J. Virol. 1992, 66, 6370-6378.
6. DeStefano, J. J.; Roberts, B.; Shriner, D. The mechanism of retroviral recombination: the role of sequences proximal to the point of strand transfer. Arch. Virol. 1997, 142, 1797-1812.
7. DeStefano, J. J.; Bambara, R. A.; Fay, P. J. The mechanism of human immunodeficiency virus reverse transcriptase-catalyzed strand transfer from internal regions of heteropolymeric RNA templates. J. Biol. Chem. 1994, 269, 161-168.
8. Klumpp, K.; Mirzadegan, T. Recent progress in the design of small molecule inhibitors of HIV RNase H. Curr. Pharm. Des. 2006, 12, 1909-1922.
9. Borkow, G.; Fletcher, R. S.; Barnard, J.; Arion, D.; Motakis, D.;
10. Dmitrienko, G. I.; Parniak, M. A. Inhibition of the ribonuclease H and DNA polymerase activities of HIV-1 reverse transcriptase by N-(4-tert- butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone. Biochemistry 1997, 36, 3179-3185.
11. Sluis-Cremer, N.; Arion, D.; Parniak, M. A. Destabilization of the HIV-1 reverse transcriptase dimer upon interaction with N-acylhydrazone inhibitors. Mol. Pharmacol. 2002, 62, 398-405.
12. Marchand, C.; Beutler, J. A.; Wamiru, A.; Budihas, S.; Mollmann, U.; Heinisch, L.; Mellors, J. W.; Le Grice, S. F.; Pommier, Y. Madurahydroxylactone derivatives as dual inhibitors of human immunodeficiency virus type 1 integrase and RNase H. Antimicrob. Agents Chemother. 2008, 52, 361-364. Epub 2007 Oct 2029.
13. Tramontano, E.; Esposito, F.; Badas, R.; Di Santo, R.; Costi, R.; La Colla, P. 6-[1-(4-Huorophenyl)methyl-1H-pyrrol-2-yl)]-2,4-dioxo-5- hexenoic acid ethyl ester a novel diketo acid derivative which selectively inhibits the HIV-1 viral replication in cell culture and the ribonuclease H activity in vitro. Antivir. Res. 2005, 65, 117-124.
14. Tarrago-Litvak, L.; Andreola, M. L.; Fournier, M.; Nevinsky, G. A.; Parissi, V.; de Soultrait, V. R.; Litvak, S. Inhibitors of HIV-1 reverse transcriptase and integrase: classical and emerging therapeutical approaches. Curr. Pharm. Des. 2002, 8, 595-614.
15. Moelling, K.; Schulze, T.; Diringer, H. Inhibition of human immunodeficiency virus type 1 RNase H by sulfated polyanions. J. Virol. 1989, 63, 5489-5491.
16. Loya, S.; Hizi, A. The interaction of illimaquinone, a selective inhibitor of the RNase H activity, with the reverse transcriptases of human immunodeficiency and murine leukemia retroviruses. J. Biol. Chem. 1993, 268, 9323-9328.
17. Tan, C. K.; Civil, R.; Mian, A. M.; So, A. G.; Downey, K. M. Inhibition of the RNase H activity of HIV reverse transcriptase by azidothymidylate. Biochemistry 1991, 30, 4831-4835.
18. Davis, W. R.; Tomsho, J.; Nikam, S.; Cook, E. M.; Somand, D.; Peliska, J. A. Inhibition of HIV-1 reverse transcriptase-catalyzed DNA strand transfer reactions by 4-chlorophenylhydrazone of mesoxalic acid. Biochemistry 2000, 39, 14279-14291.
19. Klumpp, K.; Hang, J. Q.; Rajendran, S.; Yang, Y.; Derosier, A.; Wong Kai In, P.; Overton, H.; Parkes, K. E.; Cammack, N.; Martin, J. A. Two-metal ion mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV RNase H inhibitors. Nucleic Acids Res. 2003, 31, 6852-6859.
20. Shaw-Reid, C. A.; Munshi, V.; Graham, P.; Wolfe, A.; Witmer, M.; Danzeisen, R.; Olsen, D. B.; Carroll, S. S.; Embrey, M.; Wai, J. S.; Miller, M. D.; Cole, J. L.; Hazuda, D. J. Inhibition of HIV-1 ribonuclease H by a novel diketo acid, 4-[5-(benzoylamino)thien-2-
21. yl]-2,4-dioxobutanoic acid. J. Biol. Chem. 2003, 278, 2777-2780. Epub 2002 Dec 2711.
22. Himmel, D. M.; Sarafianos, S. G.; Dharmasena, S.; Hossain, M. M.; McCoy-Simandle, K.; Ilina, T.; Clark, A. D., Jr.; Knight, J. L.; Julias, J. G.; Clark, P. K.; Krogh-Jespersen, K.; Levy, R. M.; Hughes, S. H.; Parniak, M. A.; Arnold, E. HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. ACS Chem. Biol. 2006, 1, 702-712.
23. Parniak, M. A.; Min, K. L.; Budihas, S. R.; Le Grice, S. F.; Beutler, J. A. A fluorescence-based high-throughput screening assay for inhibitors of human immunodeficiency virus-1 reverse transcriptase- associated ribonuclease H activity. Anal. Biochem. 2003, 322, 33-39.
24. Chan, K. C.; Budihas, S. R.; Le Grice, S. F.; Parniak, M. A.; Crouch, R. J.; Gaidamakov, S. A.; Isaaq, H. J.; Wamiru, A.; McMahon, J. B.; Beutler, J. A. A capillary electrophoretic assay for ribonuclease H activity. Anal. Biochem. 2004, 331, 296-302.
25. Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 1998, 282, 1669-1675.
26. 2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site. Proteins 1993, 17, 337-346.
27. Nowotny, M.; Gaidamakov, S. A.; Ghirlando, R.; Cerritelli, S. M.; Crouch, R. J.; Yang, W. Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol. Cell 2007, 28, 264-276.
28. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11 (5), 425-45.
29. Smith, J. S.; Roth, M. J. Purification and characterization of an active human immunodeficiency virus type 1 RNase H domain. J. Virol. 1993, 67, 4037-4049.
30. Sarafianos, S. G.; Das, K.; Tantillo, C.; Clark, A. D. Jr.; Ding, J.; Whitcomb, J. M.; Boyer, P. L.; Hughes, S. H.; Arnold, E. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J. 2001, 20, 1449-1461.
31. Schatz, O.; Cromme, F. V.; Gruninger-Leitch, F.; Le Grice, S. F. Point mutations in conserved amino acid residues within the C-terminal domain of HIV-1 reverse transcriptase specifically repress RNase H function. FEBS Lett. 1989, 257, 311-314.
32. Nikolenko, G. N.; Delviks-Frankenberry, K. A.; Palmer, S.; Maldarelli, F.; Fivash, M. J.; Coffin, J. M.; Pathak, V. K. Mutations in the connection domain of HIV-1 reverse transcriptase increase 3′-azido- 3′-deoxythymidine resistance. Proc. Natl. Acad. Sci. U.S.A. 2007,104, 317-322. Epub 2006 Dec 2019.
33. Brehm, J. H.; Koontz, D.; Meteer, J. D.; Pathak, V.; Sluis-Cremer, N.; Mellors, J. W. Selection of mutations in the connection and RNase H domains of human immunodeficiency virus type 1 reverse tran- scriptase that increase resistance to 3′-azido-3′-dideoxythymidine. J. Virol. 2007, 81, 7852-7859. Epub 2007 May 7816.
34. Delviks-Frankenberry, K. A.; Nikolenko, G. N.; Barr, R.; Pathak, V. K. Mutations in human immunodeficiency virus type 1 RNase H primer grip enhance 3′-azido-3′-deoxythymidine resistance. J. Virol. 2007, 81, 6837-6845. Epub 2007 Apr 6811.
35. Radzio, J.; Sluis-Cremer, N. Efavirenz accelerates HIV-1 reverse transcriptase ribonuclease H cleavage, leading to diminished zidovu- dine excision. Mol. Pharmacol. 2008, 73, 601-606. Epub 2007 Nov 2016.
36. Hirakawa, K.; Midorikawa, K.; Oikawa, S.; Kawanishi, S. Carcinogenic semicarbazide induces sequence-specific DNA damage through the generation of reactive oxygen species and the derived organic radicals. Mutat. Res. 2003, 536, 91-101.
37. Kim, B.; Hathaway, T. R.; Loeb, L. A. Human immunodeficiency virus reverse transcriptase. Functional mutants obtained by random mutagenesis coupled with genetic selection in Escherichia coli. J. Biol. Chem. 1996, 271, 4872-4878.
38. Kim, B.; Hathaway, T. R.; Loeb, L. A. Fidelity of mutant HIV-1 reverse transcriptases: interaction with the single-stranded template influences the accuracy of DNA synthesis. Biochemistry 1998, 37, 5831-5839.
39. Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.; Baker, N. A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004, 32, W665-W667.
40. Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 2007, 35, W522-W525. Epub 2007 May 2008.
41. Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Improved protein-ligand docking using GOLD. Proteins 2003, 52 (4), 609-623.