A priori molecular descriptors in QSAR: A case of HIV-1 protease inhibitors: II. Molecular graphics and modeling

Journal of Molecular Graphics and Modelling

Volumn 21, Issue 6, 2003, Pages 499-515

  Kiralj, Rudolf ^a   Ferreira, Márcia M C ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

A priori and quantitative molecular modeling; A priori molecular descriptors; HIV 1 protease inhibitors; Partial least squares; Quantitative molecular graphics

Indexed keywords

CARRIER CONCENTRATION; DERIVATIVES; ENZYME INHIBITION; MOLECULAR GRAPHICS;

MOLECULAR DESCRIPTORS;

MOLECULAR BIOLOGY;

PROTEINASE INHIBITOR;

CONFERENCE PAPER; CRYSTAL STRUCTURE; DRUG ACTIVITY; DRUG PROTEIN BINDING; ENZYME INHIBITION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR SIZE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

BINDING SITES; HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV-1; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0037409261     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(02)00202-4     Document Type: Conference Paper

References (57)

1. N.C. Cohen, The molecular modeling perspective in drug design, in: N.C. Cohen (Ed.), Guidebook on Molecular Modeling in Drug Design, Academic Press, San Diego, 1996, pp. 1-17.
2. R.E. Hubbard, Molecular graphics and modeling: tools of the trade, in: N.C. Cohen (Ed.), Guidebook on Molecular Modeling in Drug Design, Academic Press, San Diego, 1996, pp. 19-54.
3. C.D. Selassie, T.E. Klein, Building bridges: QSAR and molecular graphics, in: H. Kubinyi (Ed.), 3D QSAR in Drug Design: Theory, Methods and Applications, Kluwer Academic Publisher, Dordrecht, The Netherlands, 2000, pp. 257-275.
4. H.P. Klung, L.E. Alexander, X-ray Diffraction Procedures for Polycrystalline and Amorphous Materials, 2nd ed., Wiley, New York, 1974.
5. R. Kiralj, M.M.C. Ferreira, QSAR of progestogens: use of a priori and computed molecular descriptors and molecular graphics, J. Chemometr., Quant. Struct.-Act. Relat., in press.
6. M.M.C. Ferreira, R. Kiralj, Molecular graphics-structural and molecular graphics-descriptors in a QSAR study of 17-α-acetylprogesterones, J. Braz. Chem. Soc., Web available since 19 November 2002.
7. Kiralj R., Kojic-Prodic B., Piantanida I., Zinic M. Crystal and molecular structures of diazapyrenes and a study of π···π interactions. Acta Cryst. B55:1999;55-69.
8. M.M.C. Ferreira, R. Kiralj, in: Proceedings of the 11th Simpósio Brasileiro de Química Teórica, Caxambu, MG, Brazil, 18-21 November 2001, p. 227.
9. K.R. Beebe, R.J. Pell, M.B. Seasholtz, Chemometrics: A Pratical Guide, Wiley, New York, NY, 1998.
10. Ferreira M.M.C., Kiralj R. A priori molecular descriptors in QSAR: a case of HIV-1 protease inhibitors. I. Chemometrics. J. Mol. Graphs. Mod. 21:2003;435-448.
11. Insight II, Version 95.0, 1995, Biosym/MSI Inc., San Diego, CA, USA.
12. WebLab Viewer, Version 2.01, 1997, Molecular Simulations Inc., San Diego, CA, USA.
13. 2 symmetry. J. Am. Chem. Soc. 113:1991;9382-9384.
14. Jones G., Willett P., Glen R.C., Leach A.R., Taylor R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267:1997;727-748. http://www.ccdc.cam.ac.uk/prods/gold/gold.html [accessed on 19 February 2002].
15. The Protein Data Bank (PDB), The Research Collaboratory for Structural Bioinformatics, Rutgers, NJ. http://www.rcsb.org/pdb/ [accessed on 18 February 2002].
16. J.J.P. Stewart, MOPAC, Version 6.0, 1990, Frank Seiler Research Laboratory at Air Force Academy, Colorado Springs, Colorado.
17. Stewart J.J.P. Reply to comments on a comparison of am1 with the recently developed PM3 method. J. Comput. Chem. 11:1990;534-544.
18. Stewart J.J.P. Optimization of parameters for semiempirical methods. I. Method. J. Comput. Chem. 10:1989;209-220.
19. Stewart J.J.P. Optimization of parameters for semiempirical methods. II. Applicatons. J. Comput. Chem. 10:1989;221-264.
20. M.M.C. Ferreira, R. Kiralj, New methods for finding the best orientation in molecular graphics, unpublished results.
21. C.K. Clarke, Geography 115A/115AL: Introductory Air Photo Interpretation and Remote Sensing, Lecture 3: Scale and Area Measurement, Department of Geography, University of California, Santa Barbara, CA, USA. http://www.geog.ucsb.edu/~jeff/115a/ [accessed on 6 February 2002].
22. A.H. Robinson, Elements of Cartography, 2nd ed., Wiley, New York, 1966, p. 48.
23. PLATON, A Multipurpose Crystallographic Tool, Version 31000, 2000, Spek, A.L. Utrecht University, Utrecht, The Netherlands.
24. Allen F.K., Kennard O., Watson D.G., Brammer L., Orpen G., Taylor R. Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc., Perkin Trans. 2:1987;S1-S19.
25. A. Gavezzotti, Molecular packing and correlations between molecular and crystal properties, in: H.-B. Bürgi, J.D. Dunitz (Eds.), Structure Correlation, vol. 2, VCH Publishers, Weinheim, 1994, pp. 509-542.
26. Pastor M., Pérez C., Gago F. Simulation of alternative binding modes in a structure-binding based QSAR study of HIV-1 protease inhibitors. J. Mol. Graphics Mod. 15:1997;389.
27. Pastor M., Pérez C., Gago F. Simulation of alternative binding modes in a structure-binding based QSAR study of HIV-1 protease inhibitors. J. Mol. Graphics Mod. 15:1997;363-371.
28. Pácios L.F. Analytical density-dependent representation of Hartree-Fock atomic potentials. J. Comp. Chem. 14:1993;410-421.
29. 2 symmetry. J. Am. Chem. Soc. 113:1991;9382-9384.
30. R. Kiralj, M.M.C. Ferreira (Eds.), F77 Routines for Study of Inhibitor-Enzyme Interactions, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil, 2000.
31. Gavezzotti A. Are crystal structures predictable? Acc. Chem. Res. 27:1994;309-314.
32. Holloway M.K., Wai J.M., Halgren T.A., Fitzgerald P.M.D., Vacca J.P., Dorsey B.D., Levin R.B., Thompson W.J., Chen L.J., Desolms S.J., Gaffin N., Ghosh A.K., Giuliani E.A., Graham S.L., Guare J.P., Hungate R.W., Lyle T.A., Sanders W.M., Tucker T.J., Wiggins M., Wiscount C.M., Woltersdorf O.W., Young S.D., Darke P.L., Zugay J.A. A priori prediction of activiy for HIV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 38:1995;305-317.
33. Titan, Version 1, Wavefunction Inc., Irvine, CA, 2000.
34. Halgren T.A. Merck molecular force field. 1. Basis, form, scope, parameterization, and performance of MMFF94. J. Comp. Chem. 17:1996;490-519.
35. W.F. Bader, Atoms in Molecules, Clarendon Press, Oxford, 1990, p. 432.
36. M.R. Spiegel, Schaum's Outline of Theory and Problems of Theoretical Mechanics with Introduction to Langrange's Equation and Hamilton Theory, McGraw-Hill, New York, 1967, p. 255.
37. Kungl A.J., Visser N.V., von Hoek A., Visser A.J.W.G., Billich A., Schilk A., Gstach H., Auer M. Time-resolved fluorescence anisotropy of HIV-1 protease inhibitor complexes correlated with inhibitor activity. Biochemistry. 37:1998;2778-2786.
38. Wlodawer A., Vondrasek J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 27:1998;249-284.
39. Pérez C., Pastor M., Ortiz A.R., Gago F. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. J. Med. Chem. 41:1998;836-852.
40. Pattabiram N. Occluded molecular surface analysis of ligand-macromolecule contacts: application to HIV-1 protease inhibitor complexes. J. Med. Chem. 42:1999;3821-3834.
41. Zhang C., Vasmatzis G., Cornette J.L., DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267:1997;707-716.
42. Lian C.Y., Robinson H., Wong A.H.-J. J. Am. Chem. Soc. 118:1996;8791-8801.
43. Garg R., Gupta S.P., Gao H., Baby M.S., Debnath A.K., Hansch C. Comparative quantitative structure-activity relationship studies on anti-HIV drugs. Chem. Rev. 99:1999;3526-3601.
44. Friedman S.H., DeCamp D.L., Sijbesma R.P., Srdanov G., Wudl F., Kenyon G.L. Inhibition of the HIV-1 protease by Fullerene derivatives: model building studies and experimental verification. J. Am. Chem. Soc. 115:1993;6506-6509.
45. Debnath A.K. Three-dimensional quantitative structure-activity relationship study on cyclic urea derivatives as HIV-1 protease inhibitor: application of comparative molecular field analysis. J. Med. Chem. 42:1999;249-259.
46. Lunney E.A., Hagen S.E., Domagola J.M., Humblet C., Kosinski J., Tait B.D., Warmus J.S., Wilson M., Ferguson D., Hupe D., Tummino P.J., Baldwin E.T., Bhat T.N., Liu B., Erickson J.W. A novel nonpeptide HIV-1 protese-inhibitor: elucidation of the binding mode and its application in the design of related analogs. J. Med. Chem. 37:1994;2664-2677.
47. Liang J., Edelsbrunner H., Woodward C. Anatomy of protein pockets and cavities - measurement of binding site geometry and implications for ligand design. Protein Sci. 7:1998;1884-1897.
48. Sakurai M., Higashida S., Sugano M., Handa H., Komai T., Yagi R., Nishigaku T., Yabe Y. Studies of human immunodeficiency virus type 1 (HIV-1) protease inhibitors. III. Structure-activity relationship of HIV-1 protease inhibitors containing cyclohexylalanylalanine hydroxyethane dipeptide isostere. Chem. Pharm. Bull. 42:1994;534-540.
49. Rellick L.M., Becktel W.J. Comparison of van der Waals and semiempirical calculations of the molecular volumes of small molecules and proteins. Biopolymer. 42:1997;191-202.
50. Bondi A., van der Waals J. Volumes and radii. Chem. Phys. 68:1964;441-451.
51. Pácios L.F. Atomic radii Scales and electron properties deduced from the charge density. J. Comp. Chem. 16:1995;133-145.
52. Mulichack A.M., Hui J.O., Tomasselli A.G., Heinrikson R.L., Curry K.A., Tomich C.-S., Thaisrivongs S., Sawyer T.K., Watenpaugh K.D. The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptide transition state analog inhibitors. J. Biol. Chem. 268:1993;13103-13109.
53. Stahl M., Böhm H.-J. Development of filter functions for protein-ligand docking. J. Mol. Graph. 16:1998;121-132.
54. Abdel-Meguid S.S., Metcalf B.W., Carr T.J., Demarsh P., DesJarlais R.L., Fisher S., Green D.W., Ivanoff L., Lambert D.M., Murthy K.H.M., Petterway S.R. Jr., Pitts W.J., Tomaszek T.A. Jr., Winborne E., Zhao B., Dreyer G.B., Meek T.D. An orally bioavailable HIV-1 protease inhibitors containing and imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis. Biochemistry. 33:1994;11671-11677.
55. G. Klebe, Structure correlation and ligand/receptor binding, in: H.-B. Bürgi, J.D., Dunitz (Eds.), Structure Correlation, vol. 2, VCH, Weinheim, Germany, 1994, pp. 543-603.
56. HIV Protease Database, National Cancer Institute at Frederick, Frederick, NW. http://www.ncifcrf.gov/HIVdb/ [accessed on 19 February 2002].
57. Database for anti-HIV compounds, National Institute for Allergy and Infectious Deseases, Bethesda, MA, US. http://www.niaid.nih.gov/daids/dtpdb/ [accessed on 19 February 2002].