132
Views
19
CrossRef citations to date
0
Altmetric
Original Articles

Automated Docking and the Search for HIV Protease Inhibitors

&
Pages 273-285 | Received 02 Feb 1997, Accepted 17 May 1997, Published online: 05 Oct 2006

References

  • Ajay and Murcko , M. A. 1995 . Computational methods to predict binding free energy in ligand-receptor complexes . J. Med. Chem. , 38 : 4953 – 4967 .
  • Blaney , J. and Dixon , S. J. 1993 . A good ligand is hard to find . Perspect. Drug. Des. , 1 : 301 – 319 .
  • Bohm , H.-J. 1992a . The computer program LUDI: A new method for the de novo design of enzyme inhibitors . J. Comput. Aided Mol. Des. , 6 : 61 – 78 .
  • Bohm , H.-J. 1992b . LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads . J. Comp. Aided Mol. Design , 6 : 593 – 606 .
  • Bohm , H.-J. 1994 . The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known three-dimensional structure . J. Comput. Aided Mol. Des. , 8 : 243 – 256 .
  • Clark , D. E. and Westhead , D. R. 1996 . Evolutionary algorithms in computer-aided molecular design . J. Comput. Aided Mol. Des. , 10 : 337 – 358 .
  • DesJarlais , R. L. , Seibel , G. L. , Kuntz , I. D. , Furth , P. S. , Alvarez , J. C. , Ortiz de Montellano , P. R. , DeCamp , D. L. , Babe , L. M. and Carik , S. 1990 . Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease . Proc. Natl. Acad. Sci. USA , 87 : 6644 – 6648 .
  • DesJarlais , R. L. , Sheridan , R. P. , Dixon , J. S. , Kuntz , I. D. and Venkataraghavan , R. 1986 . Docking flexible ligands to macromolecular receptors by molecular shape . J. Med. Chem. , 29 : 2149 – 2153 .
  • DesJarlais , R. L. , Sheridan , R. P. , Seibel , G. L. , Dixon , J. S. , Kuntz , I. D. and Venkataraghavan , R. 1988 . Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure . J. Med. Chem. , 31 : 722 – 729 .
  • Goodsell , D. S. and Olson , A. J. 1990 . Automated docking of substrates to proteins by simulated annealing . Prot.: Struct., Funct., Genetics , 8 : 195 – 202 .
  • Harrison , R. W. and Weber , I. T. 1994 . Molecular dynamics simulations of HIV-1 protease with peptide substrate . Prot. Engin. , 7 : 1353 – 1363 .
  • Hart , T. N. and Read , R. J. 1992 . A multiple-start Monte Carlo docking method . Prot.: Struct., Funct. and Genetics , 13 : 206 – 222 .
  • Kuntz , I. D. , Blaney , J. M. , Oatley , S. , Langridge , R. and Ferrin , T. 1982 . A geometric approach to macromolecule-ligand interactions . J. Mol. Biol. , 161 : 269 – 288 .
  • Lam , P. Y. S. , Jadav , P. K. , Eyermann , C. , Hodge , C. N. , Lee , Y. R. , Bacheloer , L. T. , Meek , J. L. , Otto , M. J. , Rayner , M. M. , Wong , Y. N. , Chang , C.-H. , Weber , P. C. , Jackson , D. A. , Sharpe , T. R. and Erickson-Viitanen , S. E. 1994 . Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors . Science , 263 : 380 – 384 .
  • Leach , A. R. 1994 . Ligand docking to proteins with discrete side-chain flexibility . J. Mol. Biol. , 235 : 345 – 356 .
  • Leach , A. R. and Kuntz , I. D. 1992 . Conformational analysis of flexible ligands in macromolecular receptor sites . J. Comp. Chem. , 13 : 730 – 748 .
  • Lewis , R. 1990 . Automated site-directed drug design: approaches to the formation of 3D molecular graphs . J. Comput. Aided Mol. Des. , 4 : 205 – 210 .
  • Lewis , R. 1992 . Automated site-directed drug design: a method for the generation of general three-dimensional molecular graphs . J. Mol. Graphics , 10 : 131 – 143 .
  • Liu , H. , Muller-Plathe , F. and Van Gunsteren , W. F. 1996 . A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease . J. Mol. Biol. , 261 : 454 – 469 .
  • Miller , M. D. , Sheridan , R. P. , Kearsley , S. K. and Underwood , D. 1994, 1994 . “ Advances in automated docking applied to human immunodeficiency virus type 1 protease ” . In Methods in Enzymology , 354 – 355 . Academic Press .
  • Morris , G. M. , Goodsell , D. S. , Huey , R. and Olson , A. J. 1996 . Distributed automated docking of flexible ligands ot proteins: parallel applications of AutoDock 2.4 . J. Comp. Aided Mol. Design , 10 : 293 – 304 .
  • Pearlman , D. A. and Murcko , M. 1993 . CONCEPTS: New dynamic algorithm for de novo drug suggestion . J. Comp. Chem. , 14 : 1184 – 1193 .
  • Pearlman , D. and Murcko , M. A. 1996 . CONCERTS: Dynamic connection of fragments as an approach to de novo ligand design . J. Med. Chem. , 39 : 1651 – 1663 .
  • Pennisi , E. and Cohen , J. 1996 . Eradicating HIV from a patient not just a dream? . Science , 272 : 1884
  • Rosenfeld , R. , Vajda , S. and DeLisi , C. 1995 . Flexible docking design . Ann. Rev. Biophys. Biomol. Struct. , 24 : 677 – 700 .
  • Slee , D. H. , Laslo , K. L. , Elder , J. H. , Ollmann , I. R. , Gustchina , A. , Kervinen , J. , Zdano , V. , Wlodawer , A. and Wong , C.-H. 1995 . Selectivity in the inhibition of HIV and FIV protease: Inhibitory and mechanistic studies of pyrrolidine-containing alpha-keto amide and hydroxyethylamine core structures . J. Am. Chem. Soc. , 117 : 11867 – 11878 .
  • Solis , F. J. and Wets , R. J.-B. 1981 . Minimization by random search techniques . Mathematical Operations Res. , 6 : 19 – 30 .
  • Stouten , P. , Frommel , C. , Nakamura , H. and Sander , C. 1993 . An effective solvation term based on atomic occupancies for use in protein simulations . Molecular Simulations , 10 : 97 – 120 .
  • Walker , W. L. , Kopka , M. L. , Dickerson , R. E. and Goodsell , D. S. 1997 . Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method . J. Comput. Aided Mol. Des. , in press
  • Weber , I. T. and Harrison , R. W. 1996 . Molecular mechanics calculations on HIV-1 protease with peptide substrates correlate with experimental data . Prot. Engin. , 9 : 679 – 690 .
  • Weber , L. , Wallbaum , S. , Broger , C. and Gubernator , K. 1995 . Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm . Angew. Chem. Int. Ed. Engl. , 34 : 2280 – 2282 .
  • Wesson , L. and Eisenberg , D. 1992 . Atomic solvation parameters applied to molecular dynamics of proteins in solution . Prot. Sci. , 1 : 227 – 235 .
  • West , M. L. and Fairlie , D. P. 1995 . Targeting HIV-1 protease: a test of drug-design methodologies . Trends in Pharmacol. Sci. , 16 : 67 – 75 .
  • Williams , D. H. , Cox , J. P. L. , Doig , A. J. , Gardner , M. , Gerhard , U. , Kaye , P. T. , Lal , A. R. , Nicholls , I. A. , Salter , C. J. and Mitchell , R. C. 1991 . Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution . J. Am. Chem. Soc. , 113 : 7020 – 7030 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.