"Wide-open" 1.3 Å structure of a multidrug-resistant HIV-1 protease as a drug target

Structure

Volumn 13, Issue 12, 2005, Pages 1887-1895

  Martin, Philip ^a   Vickrey, John F ^d   Proteasa, Gheorghe ^a   Jimenez, Yurytzy L ^a   Wawrzak, Zdzislaw ^b   Winters, Mark A ^c   Merigan, Thomas C ^c   Kovari, Ladislau C ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c STANFORD UNIVERSITY   (United States)

^d UNIVERSITY OF TEXAS PAN AMERICAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIDRUG RESISTANCE PROTEIN; PROTEINASE; PROTEINASE INHIBITOR;

ARTICLE; BETA SHEET; CODON; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG TARGETING; HUMAN IMMUNODEFICIENCY VIRUS 1; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEIN VARIANT; WILD TYPE;

AMINO ACID SEQUENCE; BINDING SITES; CODON; CRYSTALLOGRAPHY; DRUG RESISTANCE, MULTIPLE, VIRAL; HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV-1; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; WATER;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 28844446162     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.11.005     Document Type: Article

References (42)

1. E.T. Baldwin, T.N. Bhat, B. Liu, N. Pattabiraman, and J.W. Erickson Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase Nat. Struct. Biol. 2 1995 244 249
2. J.A. Christopher SPOCK: The Structural Properties Observation and Calculation Kit (Program Manual) 1998 The Center for Macromolecular Design, Texas A&M University College Station, TX
3. J.M. Coffin HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy Science 267 1995 483 489
4. W.L. DeLano The PyMOL Molecular Graphics System 2002 Delano Scientific San Carlos, CA
5. M.A. DePristo, P.I. de Bakker, and T.L. Blundell Heterogeneity and inaccuracy in protein structures solved by x-ray crystallography Structure (Camb) 12 2004 831 838
6. P. Deutsch, H. Teppler, K. Squires, M. Saag, T. Pomerantz, T. Bjornsson, S. Waldman, B. Osborne, S. Justice, and J. Deloach Antiviral activity of L-735,524, an HIV protease inhibitor, in infected patients. (Abstr.) Intersci. Conf. Antimicrob. Agents Chemother. Proc. 34 1994 159
7. Fitzgerald, P.M. (1994). A generalized approach to the fitting of non-peptide electron density. From first map to final model. Proceedings of the CCP4 study weekend 35, 125-132.
8. H. Gatanaga, Y. Suzuki, H. Tsang, K. Yoshimura, M.F. Kavlick, K. Nagashima, R.J. Gorelick, S. Mardy, C. Tang, M.F. Summers, and H. Mitsuya Amino acid substitutions in Gag protein at non-cleavage sites are indispensable for the development of a high multitude of HIV-1 resistance against protease inhibitors J. Biol. Chem. 277 2002 5952 5961
9. M. Holodniy, D. Katzenstein, M. Winters, J. Montoya, R. Shafer, M. Kozal, M. Ragni, and T.C. Merigan Measurement of HIV virus load and genotypic resistance by gene amplification in asymptomatic subjects treated with combination therapy J. Acquir. Immune Defic. Syndr. 6 1993 366 369
10. J.R. Huff HIV protease: a novel chemotherapeutic target for AIDS J. Med. Chem. 34 1991 2305 2314
11. H. Jacobsen, K. Yasargil, D.L. Winslow, J.C. Craig, A. Krohn, I.B. Duncan, and J. Mous Characterization of human immunodeficiency virus type 1 mutants with decreased sensitivity to proteinase inhibitor Ro 31-8959 Virology 206 1995 527 534
12. V.A. Johnson, F. Brun-Vezinet, B. Clotet, B. Conway, R.T. D'Aquila, L.M. Demeter, D.R. Kuritzkes, D. Pillay, J.M. Schapiro, A. Telenti, and D.D. Richman Drug resistance mutations in HIV-1 Top. HIV Med. 11 2003 215 221
13. D.A. Katzenstein, and M. Holodniy HIV viral load quantification, HIV resistance, and antiretroviral therapy AIDS Clin. Rev. 1995 277 303
14. R.W. King, D.L. Winslow, S. Garber, H.T. Scarnati, L. Bachelor, S. Stack, and M.J. Otto Identification of a clinical isolate of HIV-1 with an isoleucine at position 82 of the protease which retains susceptibility to protease inhibitors Antiviral Res. 28 1995 13 24
15. N.E. Kohl, E.A. Emini, W.A. Schleif, L.J. Davis, J.C. Heimbach, R.A. Dixon, E.M. Scolnick, and I.S. Sigal Active human immunodeficiency virus protease is required for viral infectivity Proc. Natl. Acad. Sci. USA 85 1988 4686 4690
16. N. Kurt, W.R. Scott, C.A. Schiffer, and T. Haliloglu Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations Proteins 51 2003 409 422
17. U.K. Laemmli Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227 1970 680 685
18. S. Leavitt, and E. Freire Direct measurement of protein binding energetics by isothermal titration calorimetry Curr. Opin. Struct. Biol. 11 2001 560 566
19. B.C. Logsdon, J.F. Vickrey, P.D. Martin, G. Proteasa, J.I. Koepke, S.R. Terlecky, Z. Wawrzak, M.A. Winters, T.C. Merigan, and L.C. Kovari Crystal structure of a multidrug-resistant human immunodeficiency virus type 1 protease reveals an expanded active-site cavity J. Virol. 78 2004 3123 3132
20. D.E. McRee XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
21. H. Ohtaka, A. Velazquez-Campoy, D. Xie, and E. Freire Overcoming drug resistance in HIV-1 chemotherapy: the binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of the HIV-1 protease Protein Sci. 11 2002 1908 1916
22. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
23. S. Palmer, R.W. Shafer, and T.C. Merigan Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development AIDS 13 1999 661 667
24. A.K. Patick, R. Rose, J. Greytok, C.M. Bechtold, M.A. Hermsmeier, P.T. Chen, J.C. Barrish, R. Zahler, R.J. Colonno, and P.F. Lin Characterization of a human immunodeficiency virus type 1 variant with reduced sensitivity to an aminodiol protease inhibitor J. Virol. 69 1995 2148 2152
25. A. Perrakis, T.K. Sixma, K.S. Wilson, and V.S. Lamzin wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models Acta Crystallogr. D Biol. Crystallogr. 53 1997 448 455
26. M. Prabu-Jeyabalan, N.M. King, E. Nalivaika, W.R.P. Scott, and C.A. Schiffer Drug resistance and substrate recognition in HIV-1 protease Antivir. Ther. 7 2002 S36
27. M. Prabu-Jeyabalan, E. Nalivaika, and C.A. Schiffer Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes Structure (Camb) 10 2002 369 381
28. M. Prabu-Jeyabalan, E.A. Nalivaika, N.M. King, and C.A. Schiffer Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy J. Virol. 77 2003 1306 1315
29. F.M. Richards Calculation of molecular volumes and areas for structures of known geometry Methods Enzymol. 115 1985 440 464
30. T. Ridky, and J. Leis Development of drug resistance to HIV-1 protease inhibitors J. Biol. Chem. 270 1995 29621 29623
31. D. Ringe, and G.A. Petsko Study of protein dynamics by X-ray diffraction Methods Enzymol. 131 1986 389 433
32. R.E. Rose, Y.F. Gong, J.A. Greytok, C.M. Bechtold, B.J. Terry, B.S. Robinson, M. Alam, R.J. Colonno, and P.F. Lin Human immunodeficiency virus type 1 viral background plays a major role in development of resistance to protease inhibitors Proc. Natl. Acad. Sci. USA 93 1996 1648 1653
33. R.W. Shafer, D. Stevenson, and B. Chan Human immunodeficiency virus reverse transcriptase and protease sequence database Nucleic Acids Res. 27 1999 348 352
34. G.M. Sheldrick, and T.R. Schneider SHELXTL: high resolution refinement Methods Enzymol. 277 1997 319 343
35. F.B. Straub Formation of the secondary and tertiary structure of enzymes Adv. Enzymol. Relat. Areas Mol. Biol. 26 1964 89 114
36. A.G. Tomasselli, J.O. Hui, T.K. Sawyer, D.J. Staples, C. Bannow, I.M. Reardon, W.J. Howe, D.L. DeCamp, C.S. Craik, and R.L. Heinrikson Specificity and inhibition of proteases from human immunodeficiency viruses 1 and 2 J. Biol. Chem. 265 1990 14675 14683
37. UNAIDS (2002). AIDS Epidemic Update (www.unaids.org/html/pub/ Publications/IRC-pub03/epiupdate2002_en_pdf.pdf).
38. A. Velazquez-Campoy, M.J. Todd, and E. Freire HIV-1 protease inhibitors: enthalpic versus entropic optimization of the binding affinity Biochemistry 39 2000 2201 2207
39. A. Velazquez-Campoy, Y. Kiso, and E. Freire The binding energetics of first- and second-generation HIV-1 protease inhibitors: implications for drug design Arch. Biochem. Biophys. 390 2001 169 175
40. J.F. Vickrey, B.C. Logsdon, G. Proteasa, S. Palmer, M.A. Winters, T.C. Merigan, and L.C. Kovari HIV-1 protease variants from 100-fold drug resistant clinical isolates: expression, purification and crystallization Protein Expr. Purif. 28 2003 165 172
41. J. Weber, J.R. Mesters, M. Lepsik, J. Prejdova, M. Svec, J. Sponarova, P. Mlcochova, K. Skalicka, K. Strisovsky, and T. Uhlikova Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains J. Mol. Biol. 324 2002 739 754
42. T.D. Wu, C.A. Schiffer, M.J. Gonzales, J. Taylor, R. Kantor, S. Chou, D. Israelski, A.R. Zolopa, W.J. Fessel, and R.W. Shafer Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments J. Virol. 77 2003 4836 4847