Higher desolvation energy reduces molecular recognition in multi-drug resistant HIV-1 protease

Biology

Volumn 1, Issue 1, 2012, Pages 81-93

  Wang, Yong ^a   Dewdney, Tamaria G ^a   Liu, Zhigang ^a   Reiter, Samuel J ^a   Brunzelle, Joseph S ^b   Kovari, Iulia A ^a   Kovari, Ladislau C ^a  

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

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Desolvation energy; Multi drug resistant HIV 1 protease; X ray crystallography

Indexed keywords

EID: 84865430118     PISSN: None     EISSN: 20797737     Source Type: Journal    
DOI: 10.3390/biology1010081     Document Type: Article

References (25)

1. Nalam, M.N.L.; Ali, A.; Altman, M.D.; Reddy, G.S.K.K.; Chellappan, S.; Kairys, V.; Ozen, A.; Cao, H.; Gilson, M.K.; Tidor, B.; Rana, T.M.; Schiffer, C.A. Evaluating the substrate-envelope hypothesis: Structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J. Virol. 2010, 84, 5368-5378.
2. Prabu-Jeyabalan, M.; Schiffer, C.A.; Nalivaika, E. Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes. Structure 2002, 10, 369-381.
3. Ozen, A.; Haliloglu, T.; Schiffer, C.A. Dynamics of preferential substrate recognition in HIV-1 protease: Redefining the substrate envelope. J. Mol. Biol. 2011, 410, 726-744.
4. Luque, I.; Todd, M.J.; Gomez, J.; Semo, N.; Freire, E. Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis. Biochemistry 1998, 37, 5791-5797.
5. Tie, Y.; Boross, P.I.; Wang, Y.F.; Gaddis, L.; Liu, F.; Chen, X.; Tozser, J.; Harrison, R.W.; Weber, I.T. Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. FEBS J. 2005, 272, 5265-5277.
6. Ohtaka, H.; Freire, E. Adaptive inhibitors of the HIV-1 protease. Prog. Biophys. Mol. Biol. 2005, 88, 193-208.
7. Palmer, S.; Shafer, R.W.; Merigan, T.C. Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development. AIDS 1999, 13, 661-667.
8. Wang, Y.; Liu, Z.; Brunzelle, J.S.; Kovari, I.A.; Dewdney, T.G.; Reiter, S.J.; Kovari, L.C. The higher barrier of darunavir and tipranavir resistance for HIV-1 protease. Biochem. Biophys. Res. Commun. 2011, 412, 737-742.
9. Logsdon, B.C.; Vickrey, J.F.; Martin, P.; Proteasa, G.; Koepke, J.I.; Terlecky, S.R.; Wawrzak, Z.; Winters, M.A.; Merigan, T.C.; Kovari, L.C. Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity. J. Virol. 2004, 78, 3123-3132.
10. Vondrasek, J.; Wlodawer, A. HIVdb: A database of the structures of human immunodeficiency virus protease. Proteins 2002, 49, 429-431.
11. HHS. Panel on Antiretroviral Guidelines for Adults and Adolescents, Guidelines for the Use of Antiretroviral Agents in HIV-1-infected Adults and Adolescents; Department of Health and Human Services: Washington, DC, USA, 2011.
12. Ozer, N.; Schiffer, C.A.; Haliloglu, T. Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophys. J. 2010, 99, 1650-1659.
13. Szeltner, Z.; Polgar, L. Rate-determining steps in HIV-1 protease catalysis-The hydrolysis of the most specific substrate. J. Bio. l Chem. 1996, 271, 32180-32184.
14. Pettit, S.C.; Moody, M.D.; Wehbie, R.S.; Kaplan, A.H.; Nantermet, P.V.; Klein, C.A.; Swanstrom, R. The P2 domain of human-immunodeficiency-virus Type-1 gag regulates sequential proteolytic processing and is required to produce fully infectious virions. J. Virol. 1994, 68, 8017-8027.
15. Vickrey, J.F.; Logsdon, B.C.; Proteasa, G.; Palmer, S.; Winters, M.A.; Merigan, T.C.; Kovari, L.C. HIV-1 protease variants from 100-fold drug resistant clinical isolates: Expression, purification, and crystallization. Protein Expr. Purif. 2003, 28, 165-172.
16. Galiano, L.; Ding, F.; Veloro, A.M.; Blackburn, M.E.; Simmerling, C.; Fanucci, G.E. Drug pressure selected mutations in HIV-1 protease alter flap conformations. J. Am. Chem. Soc. 2009, 131, 430-431.
17. Otwinowski, Z.; Minor, W. Processing of X-ray Diffraction Data Collected in Oscillation Mode. In Methods in Enzymology; Carter, C.W., Sweet, R.M., Eds.; Academic Press, Inc.: New York, NY, USA, 1997; Volume 276, pp. 307-326.
18. Collaborative Computational Project Number 4, The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 1994, 50, 760-763.
19. Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics 2006, 22, 195-201.
20. Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781-1802.
21. Darden, T.; York, D.; Pedersen, L. Particle mesh ewald-an N. Log(N) method for ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
22. Hazuda, D.J.; Felock, P.; Witmer, M.; Wolfe, A.; Stillmock, K.; Grobler, J.A.; Espeseth, A.; Gabryelski, L.; Schleif, W.; Blau, C.; Miller, M.D. Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells. Science 2000, 287, 646-650.
23. Baker, N.A.; Sept, D.; Joseph, S.; Holst, M.J.; McCammon, J.A. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 2001, 98, 10037-10041.
24. 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.
25. Sitkoff, D.; Sharp, K.A.; Honig, B. Accurate calculation of hydration free-energies using macroscopic solvent models. J. Phys. Chem. 1994, 98, 1978-1988.