Interactions of the Dimeric Triad of HIV-1 Aspartyl Protease with Inhibitors

References

• De Clercq, E. (1995). Toward improvement anti-HIV chemotherapy: Therapeutic strategies for intervention with HIV-1 infections. J. Med. Chem., 38, 2491–2517.
   PubMed Web of Science ®Google Scholar
• Toh, H., Ono, M., Saigo, K., and Miyata, T. (1985). Retroviral protease-like sequence in the yeast transposon Ty1. Nature, 315, 691–692.
   Web of Science ®Google Scholar
• Power, M. C., Marx, P. A., Bryant, M. L., Gardner, M. B., Barr, P. J., and Luciew, P. A. (1986). Nucleotide sequence of SRV-1: A type-D simian acquired immune deficiency syndrome retrovirus. Science, 231, 1567–1572.
   PubMed Web of Science ®Google Scholar
• Pearl L. H., and Taylor, W. R. A. (1987). A structural model for the retroviral proteases. Nature, 329, 351–354.
   PubMed Web of Science ®Google Scholar
• Lee, H., Darden, T. A., and Pedersen, L. G. (1996). An ab initio quantum mechanical model for the catalytic mechanism of HIV-1 protease. J. Am. Chem. Soc., 118, 3946–3950.
   Web of Science ®Google Scholar
• Roberts, N. A., Martin, J. A., Kinchington, D., Broadhurst, A. V., Craig, J. C., Duncan, I. B., Galpin, S. A., Handa, B. K., Kay, J., Kröhn, A., Lambert, R. W., Merrett, J. H., Mills, J. S., Parkes, K. E. B., Redshaw, S., Ritchie, A. J., Taylor, D. L., Thomas, G. J., and Machin, P. J. (1990). Rational design of peptide-based HIV proteinase inhibitors. Science, 248, 358- 361.
   PubMed Web of Science ®Google Scholar
• Prasad, J. V. N. V., Lunney, E. A., Para, K. S., Tummino, P. J., Ferguson, D., Hupe, D., Domagala, J. M., and Erickson, J. W. (1996). Nonpeptide potent HIV-1 protease inhibitors. Drug Design Discovery, 13,15-28.
   Google Scholar
• Hoog, S. S., Zhao, B., Winborne, E., Fisher, S., Green, D. W., DesJarlais, R. L., Newlander, K. A., Callahan, J. F., Moore, M. L., Huffman, W. F., and Abdel-Meguid, S. S. (1995). A check on rational drug design: Crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel γ-turn mimetic inhibitor. J. Med. Chem., 38, 3246–3252.
   PubMed Web of Science ®Google Scholar
• March, D. R., Abbenante, G., Bergman, D. A., Brinkwworth, R. I., Wickramasinghe, W., Begun, J., Martin, J. L., and Fairlie, D. P. (1996). Substrate-based cyclic peptidomimetics of Phe-IleVal that inhibit HIV-1 protease using a novel enzyme-binding mode. J. Am. Chem. Soc., 118, 3375–3379.
   Web of Science ®Google Scholar
• Humber, D. C., Bamford, M. J., Bethell, R. C., Cammack, N., Cobley, K., Evans, D. N., Gray, N. M., Hann, M. M., Orr, D. C., Saunders, J., Shenoy, B. E., Storer, R., Weingarten, G. G., and Wyatt, P. G. (1993). A series of penicillin derived C2-symmetric inhibitors of HIV-1 proteinase: Synthesis, mode of interaction, and structure-activity relationships. J. Med. Chem., 36, 3120- 3128.
   PubMed Web of Science ®Google Scholar
• Yu, Z., Caldera, P., McPhee, F., De Voss, J. J., Jones, P. R., Burlingame, A. L., Kuntz, I. D., Craik, C. S., and de Montellano, P. R. O. (1996). Irreversible inhibition of the HIV-1 protease: Targeting alkylating agents to the catalytic aspartate groups. J. Am. Chem. Soc., 118, 5846- 5856.
   Web of Science ®Google Scholar
• Komai, T., Yagi, R., Suzuki-Sunagawa, H., Ishikawa, Y., Katsuya, A., Miyamoto, S., Handa, H., and Nishigaki, T. (1997). Inhibition of HIV-1 protease by oxime derivatives. Biochem. Biophys. Res. Commun., 230, 557–561.
   PubMed Web of Science ®Google Scholar
• De Voss, J., Zui, Z., De Camp, D. L., Salto, R., Babe, L. M., Craik, C. S., and Ortiz de Montellano, P. R. (1994). Haloperidol-based irreversible inhibitors of the HIV-1 and HIV-2 protease. J. Med. Chem., 37, 665–673.
   PubMed Web of Science ®Google Scholar
• Ro, S., Baek, S. G., Lee, B., Park, C., Choy, N., Lee, C. S., Son, Y. C., Choi, H., Koh, J. S., Yoon, H., Kim, S. C., and Ok, J. H. (1998). NMR and topochemical studies on peptidomimetic HIV-1 protease inhibitors containing a cis-epoxide amide isostere. Bioorg. Med. Chem. Lett., 8, 2423–2436.
   PubMed Web of Science ®Google Scholar
• Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc., 117, 5179–5197.
   Web of Science ®Google Scholar
• Corrections to MM+ calculations were downloaded from http://www.hyper.com/mmpfix45.exe.
   Google Scholar
• Frey, R. F., Coffin, J., Newton, S. Q., Ramek, M., Cheng, V. K. W., Momany, F. A., and Schäfer, L. (1992). Importance of correlation-gradient geometry optimization for molecular conformational analyses. J. Am. Chem. Soc., 114, 5369–5377.
   Web of Science ®Google Scholar
• Gasteiger, J., and Marsili, M. (1980). Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron, 36, 3219–3288.
   Web of Science ®Google Scholar
• Pople, J. A., and Beveridge, D. L. (1970). Approximate Molecular Orbital Theory. New York: McGraw-Hill.
   Google Scholar
• Montgomery, J. A., Jr., Ochterski, J. W., and Petersson, G. A., (1994). A complete basis set model chemistry: IV. An improved atomic pair orbital method. J. Chem Phys., 101, 5900- 5909.
   Web of Science ®Google Scholar
• Meylan, W. M., and Howard, P. H. (1995). Atom/fragment contribution method for estimating octanol-water partition coefficients. J. Pharm. Sci., 84,83-92.
   Web of Science ®Google Scholar
• Dixon, S. L., and Jurs, P. C. (1993). Estimation of pKa, for organic oxyacids using calculated atomic charges. J. Comput. Chem., 14, 1460–1467.
   Web of Science ®Google Scholar
• Weber, I. T., Miller, M., Jaskolski, M., Leis, J., Skalka, A. M., and Wlodawer, A. (1989). Molecular modeling of the HIV-1 protease and its substrate binding site. Science, 243, 928- 931.
   PubMed Web of Science ®Google Scholar
• Yamazaki, T., Hinck, A. P., Wang, Y. X., Nicholson, L. K., Torchia, D. A., Wingfield, P., Stahl, S. J., Kaufman, J. D., Chang, C. H., Domaille, P. J., and Lam, P. Y. (1996). Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy. Protein Sci., 5, 495–506.
   PubMed Web of Science ®Google Scholar
• Abbenante, G., March, D. R., Bergman, D. A., Hunt, P. A., Garnham, H., Dancer, R. J., Martin, J. I., and Fairlie, D. P. (1995). Regioselective structural and functional mimicry of peptides. Design of hydrolytically-stable cyclic peptidomimetic inhibitors of HIV-1 protease. J. Am. Chem. Soc., 117, 10220–10226.
   Web of Science ®Google Scholar
• Schaal, W., Karlsson, A., Ahlsen, G., Lindberg, J., Andersson, H. O., Danielson, U. H., Classon, B., Unge, T., Samuelsson, B., Hulten, J., Hallberg, A., and Karlen, A. (2001). Synthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfonamide HIV-1 protease inhibitors. J. Med. Chem., 44, 155–169.
   PubMed Web of Science ®Google Scholar
• Wang, S., Milne, G. W. A., Yan, X., Posey, I. J., Nicklaus, M. C., Graham, L., and Rice, W. G. (1996). Discovery of novel, non-peptide HIV-1 protease inhibitors by pharmacophore searching. J. Med. Chem., 39, 2047–2054.
   PubMed Web of Science ®Google Scholar