De novo ligand design to an ensemble of protein structures

Proteins: Structure, Function and Genetics

Volumn 64, Issue 1, 2006, Pages 43-59

  Todorov, N P ^a   Buenemann, C L ^b   Alberts, I L ^a  

^a De Novo Pharmaceuticals Ltd   (United Kingdom)

^b Novartis Forschungsinstitut GmbH   (Austria)

Author keywords

Drug design; Free energy; Homology models; Molecular design; Protein ligand interaction; Structure generation

Indexed keywords

COLLAGENASE; LIGAND; PROTEINASE; RECEPTOR;

ARTICLE; COMBINATORIAL CHEMISTRY; ENZYME ACTIVE SITE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTON TRANSPORT; RECEPTOR AFFINITY;

BINDING SITES; COMPUTER SIMULATION; DRUG DESIGN; HIV PROTEASE; HIV-1; LIGANDS; MATRIX METALLOPROTEINASE 1; MODELS, THEORETICAL; PROTEIN CONFORMATION; PROTEINS; X-RAY DIFFRACTION;

EID: 33744827370     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20928     Document Type: Article

References (62)

1. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
2. Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Mol Pharm 2000;57:213-218.
3. Vieira E, Binggeli A, Breu V, et al. Substituted piperidines-highly potent renin inhibitors due to induced fit adaptation of the active site. Bioorg Med Chem Lett 1999;9:1397-1402.
4. Teague SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2003;2:527-540.
5. Fischer E. Einfluss der Configuration auf die Wirkung der Enzyme. Ber Dtsch Chem Ges 1894;27:2985-2993.
6. Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958;44:98-104.
7. Tsai CJ, Kumar S, Ma B, Nussinov R. Folding funnels, binding funnels and protein function. Protein Sci 1999;8:1179-1188.
8. Böhm H-J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 1992;6:61-78.
9. Eisen MB, Wiley DC, Karplus M, Hubbard RE. HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins 1994;19:199-221.
10. Gillet V, Johnson AP, Mata P, Sike S, Williams P. SPROUT: a program for structure generation. J Comput Aided Mol Des 1994;7:127-153.
11. Stahl M, Todorov NP, James T, Mauser H, Boehm HJ, Dean PM. A validation study of the practical use of automated de novo design. J Comput Aided Mol Des 2002;16:459-478.
12. Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 2001;15:411-428.
13. Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
14. Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489.
15. Jones G, Willet P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
16. Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739-1749.
17. Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997;Suppl 1:215-220.
18. Schnecke V, Kuhn LA. Virtual screening with solvation and ligand-induced complementarity. Perpect Drug Discov 2000;20:171-190.
19. Leach AR. Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol 1994;235:345-356.
20. Frimurer TM, Peters GH, Iversen LF, Andersen HS, Moller NP, Olsen OH. Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. Biophys J 2003;84:2273-2281.
21. Taylor RD, Jewsbury PJ, Essex JW. FDS: flexible ligand and receptor docking with a continuum solvent and soft core energy function. J Comput Chem 2003;24:1637-1656.
22. Källblad P, Dean PM. Efficient sampling of local side-chain flexibility. J Mol Biol 2003;326:1651-1665.
23. Desmet J, De Maeyer M, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
24. Murray CW, Baxter CA, Frenkel AD. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des 1999;13:547-562.
25. Najmanovich R, Kuttner J, Sobolev V, Edelman M. Side-chain flexibility in proteins upon ligand binding. Proteins 2000;39:261-268.
26. Bouzida D, Rejto PA, Arthurs S, et al. Computer simulations of ligand-protein binding with ensembles of protein conformations: a Monte Carlo study of HIV-1 protease binding energy landscapes. Int J Quant Chem 1999;72:73-84.
27. Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 2004;337:1161-1182.
28. Claussen H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure variation. J Mol Biol 2001;308:377-395.
29. Apostolakis J, Pluckthun A, Caflisch A. Docking small ligands in flexible binding sites. J Comp Chem 1998;19:21-37.
30. Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 2004;337:209-225.
31. Knegtel RMA, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. J Mol Biol 1997;266:424-440.
32. Österberg F, Morris GM, Sanner MF, Olsen AJ, Goodsell DS. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002;46:34-40.
33. Broughton HB. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. J Mol Graph Model 2000;18:247-257.
34. Bursavich MG, Rich EH. Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles. J Med Chem 2002;45:541-558.
35. Carlson HA. Protein flexibility is an important component of structure-based drug discovery. Curr Pharm Dis 2002;8:1571-1578.
36. Vella S. HIV therapy advances. Update on a proteinase inhibitor. AIDS 1994;8(Suppl 3):S25-29.
37. 2′ amide bond isostere. J Med Chem 1994;37:3100-3107.
38. Lam PYS, Jadhav PK, Eyermann CJ, et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994;263:380-384.
39. Coussence LM, Fingleton B, Matrisian LM. Matrix metalloproteinase inhibitors and cancer: trials and tribulations. Science 2002;295:2387-2392.
40. Cleutjens JP. The role of matrix metalloproteinases in heart disease. Cardiovasc Res 1996;30:816-821.
41. Beckett RP, Whittaker M. Matrix metalloproteinase inhibitors. Expert Opin Ther Pat 1998;8:259-282.
42. Källblad P, Todorov NP, Willems HMG, Alberts IL. Receptor flexibility in the in silico screening of reagents in the S1′ pocket of human collagenase. J Med Chem 2004;47:2761-2767.
43. Hodge CN, Aldrich PE, Bacheler LT, et al. Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450. Chem Biol 1996;3:301-314.
44. Kim EE, Baker CT, Dwyer MD, et al. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme. J Am Chem Soc 1995;117:1181-1182.
45. Baldwin ET, Bhat TN, Gulnik S, et al. Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analogue containing allophenylnorstatine. Structure 1995;3:581-590.
46. Hosur MV, Bhat TN, Kempf D, et al. Influence of stereochemistry on activity and binding modes for C2 symmetry-based diol inhibitors of HIV-1 protease. J Am Chem Soc 1994;116:847-855.
47. Kempf DJ, Marsh KC, Denissen JF, et al. ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans. Proc Natl Acad Sci USA 1995;92:2484-2488.
48. Lapatto R, Blundell T, Hemmings A, et al. X-ray analysis of HIV-1 proteinase at 2.7Å resolution confirms structural homology among retroviral enzymes. Nature 1989;342:299-302.
49. Swain AL, Miller MM, Green J, et al. X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc Natl Acad Sci USA 1990;87:8805-8809.
50. Skulnick HI, Johnson PD, Aristoff PA, et al. Structure based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyramones. J Med Chem 1997;40:1149-1164.
51. Borkakoti N, Winkler FK, Williams DH, et al. Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor. Nat Struct Biol 1994;1:106-110.
52. Moy FJ, Chanda PK, Cosmi S, et al. High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast determined by multidimensional NMR. Biochemistry 1998;37:1495-1504.
53. Moy FJ, Chanda PK, Chen JM, et al. Solution structure of the catalytic fragment of human fibroblast collagenase complexed with a sulphonamide derivative of a hydroxamic acid compound. Biochemistry 1999;38:7085-7096.
54. Todorov NP, Dean PM. An evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. J Comput Aided Mol Des 1997;11:175-192.
55. Todorov NP, Dean PM. Computational ligand design by free energy minimization. In: Frauenfelder H, Hummer G, Garcia R, editors. Biological physics. Melville, NY: American Institute of Physics; 1999.
56. Kirkpatrick S, Gellat CD, Vecchi MP. Optimization by simulated annealing. Science 1983;220:671-680.
57. Stahl M, Rarey M. Detailed analysis of scoring functions for virtual screening. J Med Chem 2001;44:1035-1042.
58. Gehlhaar DK, VerKhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem Biol 1995;2:317-324.
59. Lewell XQ, Judd DB, Watson SP, Hann MM. RECAP: retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J Chem Inf Comput Sci 1998;38:511-522.
60. Appelt K. Crystal structures of HIV-1 protease-inhibitor complexes. Perspectives Drug Discov Des 1993;1:23-48.
61. Abdel-Meguid SS. Inhibitors of aspartyl proteinases. Med Res Rev 1993;13:731-778.
62. Silva AM, Cachau RE, Sham HL, Erickson JW. Inhibition and catalytic mechanism of HIV-1 aspartic protease. J Mol Biol 1996;255:321-346.