Flexible ligand docking using conformational ensembles

Protein Science

Volumn 7, Issue 4, 1998, Pages 938-950

  Lorber, David M ^a   Shoichet, Brian K ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Conformation; Flexibility; Molecular docking; Structure based drug design

Indexed keywords

DIHYDROFOLATE REDUCTASE; THYMIDYLATE SYNTHASE;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEPTOR BINDING; X RAY CRYSTALLOGRAPHY;

EID: 0031965676     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070411     Document Type: Article

References (65)

1. Abad-Zapatero C, Griffith JP, Sussman JL, Rossmann MG. 1987. Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol 198:445-467.
2. Bartlett PA, Shea GT, Telfer ST, Waterman S. 1989. CAVEAT: A program to facilitate the structure-derived design of biologically active molecules. In: Roberts SM, ed. Molecular recognition. London: Royal Society of Chemistry. pp 182-196.
3. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structure. J Mol Biol 112:535-542.
4. Blaney JM, Hansch C, Silipo C, Vittoria A. 1984. Structure-activity relationships of dihydrofolate reductase inhibitors. Chem Rev 84:333-407.
5. Bodian DL, Yamasaki RB, Buswell RL, Stearns JF, White JM, Kuntz ID. 1993. Inhibition of the fusion-inducing conformational change of the influenza hemagglutinin by bensoquinones and hydroquinones. Biochemistry 32:2967-2978.
6. Bohm HJ. 1992. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. J Comput-Aided Mol Des 6:61-78.
7. Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J. 1982. Crystal structures of E. coli and L. casei DHFR refined to 1.7 Å resolution. 1: General features and binding of Methotrexate. J Biol Chem 257:13650-13662.
8. Bystroff C, Oatley SJ, Kraut J. 1990. Crystal structures of Escherichia coli dihydrofolate eductase. The NADP holoenzyme complex and the folate/ NADP ternary complex. Substrate binding and a model for the transition state. Biochemistry 29:3263-3277.
9. Caflisch A, Niederer P, Anliker M. 1992. Monte Carlo docking of oligopeptides to proteins. Proteins 13:223-230.
10. Connolly ML. 1983. Analytical molecular surface calculations. J Appl Crystallogr 16:548-558.
11. Connolly ML. 1985. Shape complementarity at the hemoglobin α1β1 subunit interface. Biopolymers 25:1229-1247.
12. DesJarlais RL, Seibel GL, Kuntz ID, Montellano POd, Furth PS, Alvarez JC, DeCamp DL, Babé LM, Craik CS. 1990. Structure-based design of non-peptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci USA 87:6644-6648.
13. DesJarlais RL, Sheridan RP, Dixon JS, Kuntz ID, Venkataraghavan R. 1986. Docking flexible ligands to macromolecular receptors by molecular shape. J Med Chem 29:2149-2153.
14. DesJarlais R, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, 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.
15. Dunn CR, Wilks HM, Halsall DJ, Atkinson T, Clarke AR, Muirhead H, Holbrook J. 1991. Design and synthesis of new enzymes based on the lactate dehydrogenase framework. Phil Trans Royal Soc B 332:177-184.
16. Ewing TJ, Kuntz ID. 1997. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 18:1175-1189.
17. Ferrin TE, Huang CC, Jarvis LE, Langridge R. 1988. The MIDAS display system. J Mol Graph 6:13-27.
18. Gilson MK, Honig BH. 1987. Calculation of electrostatic potentials in an enzyme active site. Nature 330:84-86.
19. Goodsell DS, Morris GM, Olson AJ. 1996. Automated docking of flexible ligands: Applications of AutoDock. J Mol Recogn 9:1-5.
20. Goodsell DS, Olson AJ. 1990. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202.
21. Guner OF, Hughes DW, Dumont LM. 1991. An integrated approach to three dimensional information management with MACCS-3D. J Chem Inf Comput Sci 31:408-414.
22. Ho CMW, Marshall GR. 1993. Foundation: A program to retrieve all possible structures containing a user-defined minimum number of matching elements from three-dimensional databases. J Comput-Aided Mol Des 7:3-22.
23. Huang C. 1989. Computer graphics [Ph.D. thesis]. University of California.
24. Janin J. 1995. Protein-protein recognition. Prog Biophys Mol Biol 64:145-166.
25. Jiang F, Kim SH. 1991. Soft docking: Matching of molecular surface cubes. J Mol Biol 201:79-102.
26. Jones G, Willett P, Glen RC, Leach AR, Taylor R. 1997. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748.
27. Kuhl FS, Crippen GM, Friesen DK. 1984. A combinatorial algorithm for calculating ligand binding. J Comput Chem 5:24-34.
28. Kuntz ID. 1992. Structure-based strategies for drug design and discovery. Science 257:1078-1082.
29. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. 1982. A geometric approach to macromolecule-ligand interactions. J Mol Biol 161:269-288.
30. Kuntz ID, Meng EC, Shoichet BK. 1994. Structure-based molecular design. Accts Chem Res 27:117-123.
31. Leach AR, Kuntz ID. 1992. Conformational analysis of flexible ligands in macromolecular receptor sites. J Comput Chem 13:730-748.
32. Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. 1992. Automated site-directed drug design using molecular lattices. J Mol Graph 10:66-78.
33. Malby RL, Tulip WR, Harley VR, McKimm-Breschkin JL, Laver WG, Webster RG, Coleman PM. 1994. The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody. Structure 2:733-746.
34. Marquart M, Walter J, Deisenhofer J, Bode W, Huber R. 1983. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr B 39:480-490.
35. Meng EC, Shoichet B, Kuntz ID. 1992. Automated docking with grid-based energy evaluation. J Comput Chem 13:505-524.
36. Miller MD, Kearsley SK, Underwood DJ, Sheridan RP. 1994. FLOG: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure. J Comput-Aided Mol Des 8:153-174.
37. Miranker A, Karplus M. 1991. Functionality maps of binding sites: A multicopy simultaneous search method. Proteins 11:29-34.
38. Miranker A, Karplus M. 1995. An automated method for dynamic ligand design. Proteins 23:472-490.
39. Moon JB, Howe WJ. 1991. Computer design of bioactive molecules: A method for receptor-based de novo ligand design. Proteins Struct Funct Genet 11:314-328.
40. Olson AJ, Goodsell DS. 1993. Soluble proteins: Size, shape and function. Trends Biochem Sci 18:65-68.
41. Oshiro CM, Kuntz ID, Dixon JS. 1995. Flexible ligand docking using a genetic algorithm. J Comput-Aided Mol Des 9:113-130.
42. Perry KM, Fouman EB, Finer-Moore JS, Montfort WR, Maley GF, Maley F, Stroud RM. 1990. Plastic adaptation toward mutations in proteins: Structural comparison of thymidylate synthase. Proteins Struct Funct Genet 8:315.
43. Rarey M, Kramer B, Lengauer T. 1996. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489.
44. Rashin AA. 1990. Hydration phenomena, classical electrostatics and the boundary element method. J Phys Chem 94:1725-1733.
45. Ring CS, Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE. 1993. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci USA 90:3583-3587.
46. Rose GD. 1978. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature 272:586-590.
47. Rusinko A, Skell JM, Balducci R, Pearlman RS. 1987. CONCORD manual and description. St. Louis. MO: Tripos Associates.
48. Rutenber E, Fauman EB, Keenan RJ, Fong S, Furth PS, Ortiz de Montellano PR, Meng E, Kuntz ID, DeCamp DL, Salto R, Rose JR, Craik CS, Stroud RM. 1993. Structure of a non-peptide inhibitor complexed with HIV-1 protease. J Biol Chem 268:15343-15346.
49. Sandak B, Wolfson HJ, Nussinov R. 1995. An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching. Comput Appl Biosci 11:87-89.
50. Shoichet B, Bodian DL, Kuntz ID. 1992. Molecular docking using sphere descriptors. J Comput Chem 13:380-397.
51. Shoichet B, Kuntz ID. 1991. Protein docking and complementarity. J Mol Biol 221:327-346.
52. Shoichet BK. 1996. Docking ligands to proteins. In: Sternberg MJE, ed. Protein structure prediction. New York: Oxford University Press. pp 263-290.
53. Shoichet BK, Kuntz ID. 1993. Matching chemistry and shape in molecular docking. Protein Eng 6:723-732.
54. Shoichet BK, Kuntz ID. 1996. Predicting the structures of protein complexes: A step in the right direction. Chem Biol 3:151-156.
55. Shoichet BK, Perry KM, Santi DV, Stroud RM, Kuntz ID. 1993. Structure-based discovery of inhibitors of thymidylate synthase. Science 259:1445-1450.
56. Stoddard BL, Koshland DE. 1992. Prediction of the structure of a receptor-protein complex using a binary docking method. Nature 358:774-776.
57. Stout TJ, Stroud RM. 1996. The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 Å resolution: Implications for a new mode of inhibition. Structure 5:67-77.
58. Strynadka NC, Jensen SE, Johns K, Blanchard H, Page M, Matagne A, Frere JM, James MN. 1994. Structural and kinetic characterization of a beta-lactamase-inhibitor protein. Nature 368:657-660.
59. Strynadka NCJ, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abazyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MNG. 1996a. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to tem-1 beta-lactamase. Nature Struct Biol 3:233-239.
60. Strynadka NCJ, Jensen SE, Alzari PM, James MNG. 1996b. A potent new mode of β-lactamase inhibition revealed by the 1.7 Å X-ray crystallographic structure of the TEM-1-β-lactamase complex. Nature Struct Biol 3:290-297.
61. Verkhivker GM, Rejto PA, Gehlhaar DK, Freer ST. 1996. Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes. Proteins 25:342-353.
62. Walter J, Steigemann W, Singh TP, Bartunik H, Bode W, Huber R. 1982. On the disordered activation domain in trypsinogen. Acta Crystallog B 38:1462.
63. Wasserman ZR, Hodge CN. 1996. Fitting an inhibitor into the active site of thermolysin: A molecular dynamics study. Proteins 24:227-237.
64. Welch W, Ruppert J, Jain AN. 1996. Hammerhead: Fast, fully automated docking of flexible ligands into protein binding sites. Chem Biol 3:449-462.
65. Wodak SJ, Janin J. 1978. Docking BPTI and trypsin. J Mol Biol 124:323-342.