Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies

Journal of Chemical Information and Modeling

Volumn 46, Issue 2, 2006, Pages 903-911

  Kämper, Andreas ^a   Apostolakis, Joannis ^b   Rarey, Matthias ^c   Marian, Christel M ^d   Lengauer, Thomas ^a  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF HAMBURG   (Germany)

^d HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTER SOFTWARE; CONFORMATIONS; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; SUPRAMOLECULAR CHEMISTRY;

CONFORMATIONAL SAMPLING; FLEXIBLE SYNTHETIC RECEPTORS; INVERSE DOCKING; LIGANDS;

MOLECULAR STRUCTURE;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 33646244470     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050467z     Document Type: Conference Paper

References (37)

1. Lehn, J.-M. Supramolecular Chemistry; VCH Publishers: Weinheim, 1995.
2. Steed, J. W.; Atwood, J. L. Supramolecular Chemistry; John Wiley & Sons: Chinchester, 2000.
3. Lavigne, J. J.; Anslyn, E. V. Sensing A Paradigm Shift in the Field of Molecular Recognition: From Selective to Differential Receptors. Angew. Chem., Int. Ed. 2001, 40, 3118-3130.
4. Apostolakis, J.; Caflisch, A. Computational Ligand Design. Comb. Chem. High Througput Screening 1999, 2, 91-104.
5. Muegge, I.; Rarey, M. Small molecule docking and scoring. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Wiley-VCH: New York, 2001, Vol. 17, Chapter 1, pp 1-60.
6. Brooijmans, N.; Kuntz, I. D. Molecular Recognition and Docking Algorithms. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 335-373.
7. Rarey, M.; Lemmen, C.; Matter, H. Algorithmic Engines in Virtual Screening. In Chemoinformatics in Drug Discovery; Oprea, T. I., Ed.; Wiley-VCH: Weinheim, 2005; pp 59-115.
8. Lengauer, T.; Rarey, M. Computational Methods for Biomolecular Docking. Curr. Opin. Struct. Biol. 1996, 6, 402-406.
9. Leach, A. R.; Kuntz, I. D. Conformational Analysis of Flexible Ligands in Macromolecular Receptor Sites, J. Comput. Chem. 1992, 13, 730-748.
10. 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.
11. Rarey, M.; Kramer, B.; Lengauer, T. Multiple Automatic Base Selection: Protein-Ligand Docking Based on Incremental Construction Without Manual Intervention. J. Comput.-Aided Mol. Des. 1997, 11, 369-384.
12. de Jong, M. R.; Knegtel, R. M. A.; Grootenhuis, P. D. J.; Huskens, J.; Reinhoudt, D. N. A Method to Identify and Screen Libraries of Guests that Complex to a Synthetic Host. Angew. Chem., Int. Ed. 2002, 41, 1004-1008.
13. Hamilton, A. D.; van Engen, D. Induced Fit in Synthetic Receptors: Nucleotide Base Recognition by a "Molecular Hinge". J. Am. Chem. Soc. 1987, 109, 5035-5036.
14. Klebe; G.; Mietzner; T. A Fast and Efficient Method to Generate Biologically Relevant Conformations. J. Comput.-Aided Mol. Des. 1994, 8, 583-606.
15. Sadowski, J.; Gasteiger, J. From Atoms and Bonds to Three-Dimensional Atomic Coordinates: Automatic Model Builders. Chem. Rev. 1993, 93, 2567-2581.
16. Böhm, H.-J. 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. 1994, 8, 243-256.
17. Confort. Tripos Inc., 1699 South Hanley Road, St. Louis, MO 63144-2913, U.S.A.
18. Kämper, A.; Apostolakis, J.; Lengauer, T. Docking of Bacterial Cell-Wall Fragments into Glycopeptide Antibiotics. In From Genes to Drugs via Crystallography; Borkakoti, N., Ed.; Erice Crystallography Publications: Padova, 2002; p 49.
19. Harriman, D. J.; Deslongchamps, G. Reverse-Docking as a Computational Tool for the Study of Asymmetric Organocatalysis. J. Comput.-Aided Mol. Des. 2004, 18, 303-308.
20. Allen, F. H. The Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising. Acta Crystallogr., Sect. B: Struct. Sci. 2002, 58, 380-388.
21. Garcia-Tellado, F.; Goswami, S.; Chang, S.-K.; Geib, S. J.; Hamilton, A. D. Molecular Recognition: A Remarkably Simple Receptor for the Selective Complexation of Dicarboxylic Acids. J. Am. Chem. Soc. 1990, 112, 7393-7394.
22. +. Angew. Chem., Int. Ed. Engl. 1999, 38, 2756-2759.
23. Ballester, P.; Capo, M.; Costa, A.; Deyá, P. M.; Gomila, R., Decken, A., Deslongchamps, G. Selective Binding of cis-1,3,5-Cyclohexane Tricarboxylic Acid vs its Epimeric trans Isomer by a Tripodal Amidopyridine Receptor: Crystal Structures of the 1:1 Complex. Org. Lett. 2001, 3, 267-270.
24. Pascal, R. A.; Ho, D. M. Molecular Structures of Host-Guest Complexes with Rebek's Diacid. Tetrahedron 1994, 50, 8559-8568.
25. Berl, V.; Huc, I.; Lehn, J.-M.; DeCian, A.; Fischer, J. Induced Fit Selection of a Barbiturate Receptor from a Dynamic Structural and Conformational/Configurational Library. Eur. J. Org. Chem. 1999, 3089, 9-3094.
26. Bell, T. W.; Hou, Z.; Luo, Y.; Drew, M. G. B.; Chapoteau, E.; Czech, B. P.; Kumar, A. Detection of Creatinine by a Designed Receptor. Science 1995, 269, 671-674.
27. Kneeland, D. M.; Ariga, K.; Lunch, V. M.; Huang, C.-Y.; Anslyn, E. V. Bis(alkylguanidinium) Receptors for Phosphodiesters: Effect of Counterions, Solvent Mixtures, and Cavity Flexibility on Complexation. J. Am. Chem. Soc. 1993, 115, 10042-10055.
28. Grossel, M. C.; Merckel, D. A. S.; Hutchings, M. G. The Effect of Preorganisation on the Solid State Behaviour of Simple 'Aromatic-Cored' Bis(guanidinium) Sulfates. CrystEngComm 2003, 5, 77-81.
29. Waldvogel, S. R.; Fröhlich, R.; Schalley, C. A. First Artificial Receptor for Caffeine: A New Concept for the Complexation of Alkylated Oxopurines. Angew. Chem., Int. Ed. 2000, 39, 2472-2475.
30. Clark, M.; Cramer, R. D., III.; van Opdenbosch, N. Validation of the General Purpose Tripos 5.2 Force Field. J. Comput. Chem. 1989, 10, 982-1012.
31. Leach, A. R. A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Wiley-VCH: New York, 1991; Vol. 2, Chapter 1, pp 1-55.
32. Kämper, A.; Kaspar, M.; Lengauer, T. Efficient Conformational Analysis of Synthetic Receptors with Macrocyclic and Fused Ring Systems. In Synthetic Receptors 2005, Proceedings of the Second World Congress on Synthetic Receptors; Elsevier Publishers: Oxford, 2005; p O4.
33. Raub, S.; Marian, C., work in progress.
34. Bruno, I. J.; Cole, J. C.; Lommerse, J. P. M.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. IsoStar: A Library of Information about Nonbonded Interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
35. Jones, D. R.; Lindoy, L. F.; Sargeson, A. M.; Snow, M. R. Structure and Synthesis of Isomers of Novel Binuclear Cobalt(III)-Phenyl Phosphate Complexes. Inorg. Chem. 1982, 21, 4155-4160.
36. Gajda, T.; Krämer, R.; Janscó, A. Structure, Equilibrium and Ribonuclease Activity of Copper(II) and Zinc(II) Complexes Formed with a Dinucleating Bis-Imidazole Ligand. Eur. J. Inorg. Chem. 2000, 1635-1644.
37. Böhm, H.-J. LUDI: Rule-Based Automatic Design of new Substituents for Enzyme-Inhibitor Leads. J. Comput.-Aided Mol. Des. 1992, 6, 593-606.