Towards a MIP-based alignment and docking in computer-aided drug design

Proteins: Structure, Function and Genetics

Volumn 56, Issue 3, 2004, Pages 585-594

  Barbany, Montserrat ^a   Gutiérrez De Terán, Hugo ^a   Sanz, Ferran ^a   Villà Freixa, Jordi ^a  

^a INST MUNIC D INVESTIGACIO MEDICA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CAPRAVIRINE; CARBOXANILIDE; DIHYDROFOLATE REDUCTASE; EFAVIRENZ; METHOTREXATE; RNA DIRECTED DNA POLYMERASE INHIBITOR; TNK 6123; TNK 651; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER AIDED DESIGN; CONFORMATION; DRUG DESIGN; ENERGY; ENZYME ACTIVE SITE; GEOMETRY; MOLECULAR INTERACTION; PHARMACOPHORE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS;

BINDING SITES; COMPUTER-AIDED DESIGN; DRUG DESIGN; FOLIC ACID ANTAGONISTS; HIV-1 REVERSE TRANSCRIPTASE; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REVERSE TRANSCRIPTASE INHIBITORS; SOFTWARE; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 3142759982     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20153     Document Type: Article

References (41)

1. Liljefors T, Pettersson I. Computer-aided development of three dimensional pharmacofore models. In: A textbook of drug design and development. Harwood Academic Publishers, 1996. Krogsgaard-Larsen P, Madsen U, eds.
2. Perez C, Ortiz A. Evaluation of docking functions for protein-ligand docking. J Med Chem 2001;44:3768-3785.
3. Kubinyi H. 3D QSAR in Drug Design: Theory, Methods and Applications. Lenden: ESCOM; 1993.
4. Murray J, Brinck T, Grice M, Politzer P. Correlations between molecular electrostatic potentials and some experimentally-based indices of reactivity. J Mol Struct (Theochem) 1992;256:29-45.
5. Goodford P. A computational procedure for determining energetically favourable binding sites on biologically important macromolecules. J Med Chem 1985;28:849-857.
6. Pastor M, Cruciani G, McLay I, Pickett S, Clementi S. GRid-INdependent Descriptors (GRIND): A novel class of alignment-independent three-dimensional molecular descriptors. J Med Chem 2000;43:3233-3243.
7. Rodrigo J, Barbany M, Gutiérrez-de Terán H, Centeno N. B, de Càceres M, Dezi C, Fontaine F, Lozano JJ, Pastor M, Villà J, Sanz F. Comparison of biomolecules on the basis of molecular interaction potentials. J Braz Chem Soc 2002;13:795-799.
8. Barbany M, Gutiérrez-de Terán H, Sanz F, Villà-Freixa J, Warshel A. Pharmacophore approach for hapten design in catalytic antibodies generation. ChemBioChem 2003;4:277-285.
9. Berman H, et al. The Protein Data Bank. Acta Crystallogr. D Biol Crystallogr 2002;58:899-907.
10. de Cáceres M, Villà J, Lozano JJ, Sanz F. MIPSIM: Similarity analysis of molecular interaction potentials. Bioinformatics 2000;16:568-569.
11. Bagdassarian CK, Schramm VL, Schwartz SD. Molecular electrostatic potential analysis for enzymatic substrates, competitive inhibitors, and transition-state inhibitors. J Am Chem Soc 1996;118:8825-8836.
12. Sanz F, Manaut F, Rodríguez J, Lozoya E, López de Briñas, E. MEPSIM: a computational package for analysis and comparison of molecular electrostatic potentials. J Comput Aid Mol Des 1993;7:337-347.
13. GRID v. 21. Molecular discovery. London:2003.
14. Russell RB, Barton GJ. Multiple protein sequence alignment from tertiary structure comparison. Proteins 1992;14:309-323.
15. Zhou J, Tits A, Lawrence C. FFSQP program, version 3.7. Maryland: AEM Design, University of Maryland. 1997.
16. Morris G, Goodsell D, Halliday R, Huey R, Hart W, Belew R, Olson A. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662 FS.
17. Huennekens F. Adv Enzyme Regul 1994;34:397-419.
18. Roth B, Stammers D. The design of drugs to macromolecular targets. New York: John Wiley & Sons, Inc; 1992.
19. Manaut F, Lozoya E, Sanz F. Automatic determination of maximum electrostatic alignment between methotrexate and dihydrofolic acid. In: Silipo C, Vittoria A, editors. QSAR: rational approaches to the design of bioactive compounds. Amsterdam: Elsevier Science; 1991.
20. Lemmen C, Lengauer T, Klebe G. Flexs: A method for fast flexible ligand superposition. J Med Chem 1998;41:4502-4520.
21. De Clercq E. The role of non-nucleoside reverse transcriptase inhibitors (NNRTI) in the therapy of HIV-1 infection. Antivir Res 1998;38:153-179.
22. Kohlstaedt L, Wang J, Friedman J, Rice P, Steitz T. Crystal structure at 3.5A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 1992;256:1783-1790.
23. Ren J, Esnouf R, Garman E, Somers D, Ross C, Kirby I, Keeling J, Darby G, Jones Y, Stuart D, Stammers D. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat Struct Biol 1995;2:293-302.
24. Esnouf R, Ren JS, Ross C, Jones Y, Stammers D, Stuart D. Mechanism of inhibition of HIV-1 reverse-transcriptase by nonnucleoside inhibitors. Nat Struct Biol 1995;2:303-308.
25. Hopkins AL, Ren JS, Esnouf RM, Wilcox BE, Jones EY, Ross C, Miyasaka T, Walker RT, Tanaka H, et al. Complexes of HIV-1 reverse-transcriptase with inhibitors of the hept series reveal conformational-changes relevant to the design of potent nonnucleoside inhibitors. J Med Chem 1996;39:1589-1600.
26. Ren JS, Esnouf R, Hopkins A, Ross C, Jones Y. The structure of HIV-1 reverse-transcriptase complexed with 9-chloro-tibo-lessons for inhibitor design. Structure 1995;3:915-926.
27. Chimirri A, Grasso S, Molica C, Monforte A, Monforte P, Zapplà M, Bruno G, Nicolò R, Witvrouw M, Jonckeere H, Balzarini J, De Clercq E. Antiviral Chem Chemother 1997;8:363.
28. Matthews B. Comparison of the predicted and observed secondary structure of t4 phage lysozyme. Biochim Biophys Acta 1975;405:442-451.
29. Åqvist J, Medina C, Samuelsson JE. A new method for predicting binding affinity in computer-aided drug design. Prot Eng 1994;7:385-391.
30. Sham Y, Chu Z. T, Tao H, Warshel A. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins 2000;39:393-407.
31. Dunn WJ, Wold S, Edlund U, Hellberg S, Gasteiger J. Multivariate structure-activity relationship between data from a battery of biological tests and an ensemble of chemical descriptors: The pls methodol. Quant Struct Act Relat 1973;3:131-137.
32. Cocco L, Roth B, Temple Jr C, Montgomery J, London R, Blakley R. Protonated state of methotrexate, trimethoprim, and pyrimethamine bound to dihydrofolate reductase. 1983;226(2):567-577.
33. Cody V, Galitsky N, Luft J, Pangborn W, Blakley R, Gangjee A. Comparison of ternary crystal complexes of f31 variants of human dihydrofolate reductase with nadph and a classical antitumor furopyrimidine. Anticancer Drug Des 1998;13(4):307-315.
34. Davies JF, n, Delcamp T, Prendergast N, Ashford V, Freisheim J, Kraut J. Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate. Biochemistry 1990;29(40):9467-9479.
35. Chan J, et al. 2-Amino-6-arylsulfonylbenzonitriles as nonnucleoside reverse transcriptase inhibitors of HIV-1. J Med Chem 2001;44:1866-1882.
36. Ren J, Diprose J, Warren J, Esnouf R, Bird L, Ikemizu S, Slater M, Milton J, Balzarini J, Stuart D, Stammers D. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. J Biol Chem 2000;275:5633-5639.
37. Hopkins AL, Ren J, Tanaka H, Baba M, Okamato M, Stuart D, Stammers D. Design of MKC-442 (Emivirine) analogues with improved activity against drug-resistant HIV mutants. J Med Chem 1999;42:4500-4505.
38. Baba M, Shigeta S, Yuasa S, Takashima H, Sehila K, Ubasaka M, Tanaka H, Miyasaka T, Walker R, De Clercq E. Preclinical evaluation of MKC-442, a highly potent and specific inhibitor of human immunodeficiency virus type 1 in vitro. Antimicrob Agents Chemother 1994;38:688-692.
39. Mertens A, Zilch H, Zonig B, Schafer W, Poll T, Kampe W, Seidel H, Leser U, Leinert H. Selective non-nucleoside HIV-1 reverse transcriptase inhibitors. New 2,3-dihydrothiazolo[2,3-a]isoindol-5(9bH)-ones and related compounds with anti-HIV activity. J Med Chem 1993;36:2526-2535.
40. Young S, Emini E. L-743, 726 (DMP-266): a novel, highly potent non-nucleoside inhibitor of the human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother 1995;39:2609-2605.
41. Fujiwara T, Sato A, El-Farrash M, Miki S, Abe K, Isaka Y, Kodama M, Wu Y, Chen L, Harada H, Sugimoto H, Hatanaka M, Hinuma Y. S-1153 inhibits replication of known drug-resistant strains of human immunodeficiency virus type 1. Antimicrob Agents Chemother 1998;42:1340-1345.