Structure-based evaluation of C5 derivatives in the catechol diether series targeting HIV-1 reverse transcriptase

Chemical Biology and Drug Design

Volumn 83, Issue 5, 2014, Pages 541-549

  Frey, Kathleen M ^a   Gray, William T ^a   Spasov, Krasimir A ^a   Bollini, Mariela ^b   Gallardo Macias, Ricardo ^b   Jorgensen, William L ^b   Anderson, Karen S ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

halogen bonds; HIV 1 reverse transcriptase; non nucleoside reverse transcriptase inhibitors; structure activity relationships; structure based drug design

Indexed keywords

CATECHOL DERIVATIVE; CHLORINE; DELAVIRDINE; EFAVIRENZ; ETRAVIRINE; HALOGEN; HYDROGEN; NEVIRAPINE; NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; RILPIVIRINE; RNA DIRECTED DNA POLYMERASE; URACIL; CATECHOL; REVERSE TRANSCRIPTASE, HUMAN IMMUNODEFICIENCY VIRUS 1; RNA DIRECTED DNA POLYMERASE INHIBITOR;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG CONFORMATION; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; ANTAGONISTS AND INHIBITORS; BINDING SITE; CHEMISTRY; DRUG DESIGN; ENZYMOLOGY; HUMAN IMMUNODEFICIENCY VIRUS 1; METABOLISM; MOLECULAR DYNAMICS; PROTEIN TERTIARY STRUCTURE;

HUMAN IMMUNODEFICIENCY VIRUS 1;

BINDING SITES; CATECHOLS; DRUG DESIGN; HIV REVERSE TRANSCRIPTASE; HIV-1; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, TERTIARY; REVERSE TRANSCRIPTASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP; URACIL;

EID: 84899489984     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12266     Document Type: Article

References (30)

1. Adamson C.S., Freed E.O., (2009) Anti-HIV-1 therapeutics: from FDA-approved drugs to hypothetical future targets. Mol Interv; 9: 70-74.
2. Adamson C.S., Freed E.O., (2010) Novel approaches to inhibiting HIV-1 replication. Antiviral Res; 85: 119-141.
3. Pomerantz R.J., Horn D.L., (2003) Twenty years of therapy for HIV-1 infection. Nat Med; 9: 867-873. (Pubitemid 36889928)
4. Roberts J.D., Bebenek K., Kunkel T.A., (1988) The accuracy of reverse-transcriptase from Hiv-1. Science; 242: 1171-1173.
5. Owen A., (2006) The impact of host pharmacogenetics on antiretroviral drug disposition. Curr Infect Dis Rep; 8: 401-408. (Pubitemid 44445715)
6. Vandamme A.M., Van Vaerenbergh K., De Clercq E., (1998) Anti-human immunodeficiency virus drug combination strategies. Antivir Chem Chemother; 9: 187-203. (Pubitemid 28273053)
7. Boyer J., Arnoult E., Medebielle M., Guillemont J., Unge J., Jochmans D., (2011) Difluoromethylbenzoxazole pyrimidine thioether derivatives: a novel class of potent non-nucleoside HIV-1 reverse transcriptase inhibitors. J Med Chem; 54: 7974-7985.
8. Das K., Bauman J.D., Clark A.D. Jr, Frenkel Y.V., Lewi P.J., Shatkin A.J., Hughes S.H., Arnold E., (2008) High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations. Proc Natl Acad Sci U S A; 105: 1466-1471. (Pubitemid 351346537)
9. De Clercq E., (2009) Anti-HIV drugs: 25 compounds approved within 25 years after the discovery of HIV. Int J Antimicrob Agents; 33: 307-320.
10. Lansdon E.B., Brendza K.M., Hung M., Wang R., Mukund S., Jin D., Birkus G., Kutty N., Liu X., (2010) Crystal structures of HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278): implications for drug design. J Med Chem; 53: 4295-4299.
11. Bollini M., Domaoal R.A., Thakur V.V., Gallardo-Macias R., Spasov K.A., Anderson K.S., Jorgensen W.L., (2011) Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents. J Med Chem; 54: 8582-8591.
12. Frey K.M., Bollini M., Mislak A.C., Cisneros J.A., Gallardo-Macias R., Jorgensen W.L., Anderson K.S., (2012) Crystal structures of HIV-1 reverse transcriptase with picomolar inhibitors reveal key interactions for drug design. J Am Chem Soc; 134: 19501-19503.
13. Auwerx J., Van Nieuwenhove J., Rodriguez-Barrios F., de Castro S., Velazquez S., Ceccherini-Silberstein F., De Clercq E., Camarasa M.J., Perno C.F., Gago F., Balzarini J., (2005) The N137 and P140 amino acids in the p51 and the P95 amino acid in the p66 subunit of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase are instrumental to maintain catalytic activity and to design new classes of anti-HIV-1 drugs. FEBS Lett; 579: 2294-2300. (Pubitemid 40569494)
14. Ceccherini-Silberstein F., Gago F., Santoro M., Gori C., Svicher V., Rodriguez-Barrios F., d'Arrigo R., Ciccozzi M., Bertoli A., d'Arminio Monforte A., Balzarini J., Antinori A., Perno C.F., (2005) High sequence conservation of human immunodeficiency virus type 1 reverse transcriptase under drug pressure despite the continuous appearance of mutations. J Virol; 79: 10718-10729. (Pubitemid 41098611)
15. Bauman J.D., Das K., Ho W.C., Baweja M., Himmel D.M., Clark A.D. Jr,., Oren D.A., Boyer P.L., Hughes S.H., Shatkin A.J., Arnold E., (2008) Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design. Nucleic Acids Res; 36: 5083-5092.
16. Otwinowski Z., Minor W., (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol; 276: 307-326. (Pubitemid 27085611)
17. Mccoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J., (2007) Phaser crystallographic software. J Appl Crystallogr; 40: 658-674. (Pubitemid 47080256)
18. Emsley P., Lohkamp B., Scott W.G., Cowtan K., (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr; 66: 486-501.
19. Adams P.D., Afonine P.V., Bunkoczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., et al,. (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr; 66: 213-221.
20. Terwilliger T.C., Grosse-Kunstleve R.W., Afonine P.V., Moriarty N.W., Adams P.D., Read R.J., Zwart P.H., Hung L.W., (2008) Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallogr D Biol Crystallogr; 64: 515-524. (Pubitemid 351653937)
21. Das K., Clark A.D. Jr, Lewi P.J., Heeres J., De Jonge M.R., Koymans L.M., Vinkers H.M., et al,. (2004) Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants. J Med Chem; 47: 2550-2560. (Pubitemid 38580092)
22. Wisniewski M., Palaniappan C., Fu Z., Le Grice S.F., Fay P., Bambara R.A., (1999) Mutations in the primer grip region of HIV reverse transcriptase can increase replication fidelity. J Biol Chem; 274: 28175-28184.
23. Kertesz D.J., Brotherton-Pleiss C., Yang M., Wang Z., Lin X., Qiu Z., Hirschfeld D.R., Gleason S., Mirzadegan T., Dunten P.W., Harris S.F., Villaseñor A.G., Hang J.Q., Heilek G.M., Klumpp K., (2010) Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-benzyl derivatives with broad potency against resistant mutant viruses. Bioorg Med Chem Lett; 20: 4215-4218.
24. Himmel D.M., Das K., Clark A.D. Jr, Hughes S.H., Benjahad A., Oumouch S., Guillemont J., Coupa S., Poncelet A., Csoka I., Meyer C., Andries K., Nguyen C.H., Grierson D.S., Arnold E., (2005) Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: a new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains. J Med Chem; 48: 7582-7591. (Pubitemid 41698799)
25. Pelemans H., Esnouf R., De Clercq E., Balzarini J., (2000) Mutational analysis of trp-229 of human immunodeficiency virus type 1 reverse transcriptase (RT) identifies this amino acid residue as a prime target for the rational design of new non-nucleoside RT inhibitors. Mol Pharmacol; 57: 954-960. (Pubitemid 30253379)
26. Wilcken R, Zimmermann MO, Lange A, Joerger AC, Boeckler FM, (2013) Principles and applications of halogen bonding in medicinal chemistry and chemical biology. J Med Chem; 56: 1363-1388.
27. Boas F.E., Harbury P.B., (2007) Potential energy functions for protein design. Curr Opin Struct Biol; 17: 199-204. (Pubitemid 46575252)
28. Davis A.M., Teague S.J., (1999) Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis. Angew Chem Int Edit; 38: 737-749. (Pubitemid 129701960)
29. Atkins P., de Paula J., (2006) Physical Chemistry for the Life Sciences. Oxford, UK: Oxford University Press.
30. La Regina G., Coluccia A., Silvestri R., (2010) Looking for an active conformation of the future HIV type-1 non-nucleoside reverse transcriptase inhibitors. Antivir Chem Chemother; 20: 213-237.