Chemical fragments that hydrogen bond to Asp, Glu, Arg, and his side chains in protein binding sites

Journal of Medicinal Chemistry

Volumn 53, Issue 8, 2010, Pages 3086-3094

  Chan, A W Edith ^a   Laskowski, Roman A ^b   Selwood, David L ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; ASPARTIC ACID; GLUTAMINE; HISTIDINE; IMIDAZOLE; OXYGEN;

ARTICLE; BINDING SITE; HYDROGEN BOND; LIGAND BINDING; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION; STRUCTURE ANALYSIS;

ARGININE; ASPARTIC ACID; BINDING SITES; DATABASES, FACTUAL; GLUTAMIC ACID; HISTIDINE; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE;

EID: 77951107242     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm901696w     Document Type: Article

References (53)

1. Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent developments in fragment-based drug discovery J. Med. Chem. 2008, 51, 3661-3680
2. Hajduk, P. J.; Greer, J. A decade of fragment-based drug design: strategic advances and lessons learned Nat. Rev. Drug Discovery 2007, 6, 211-219
3. Warr, W. A. Fragment-based drug discovery J. Comput.-Aided Mol. Des. 2009, 23, 453-451
4. Murray, C. W.; Rees, D. C. The rise of fragment-based drug discovery Nature Chem. 2009, 1, 187-192
5. Joseph-McCarthy, D. Challenges of fragment screening J. Comput.-Aided Mol. Des. 2009, 23, 453-458
6. See examples in special issue: Fragment-based drug discovery. J. Comput.-Aided Mol. Des. 2009, 23, 449 - 620.
7. Clark, M.; Meshkat, S.; Talbot, G. T.; Carnevali, P.; Wiseman, J. S. Fragment-based computation of binding free energies by systematic sampling J. Chem. Inf. Model 2009, 49, 1901-1913
8. Mauser, H.; Stahl, M. Chemical fragment spaces for de novo design J. Chem. Inf. Model. 2007, 47, 318-324
9. Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 1996, 39, 2887-2893
10. Lameijer, E. W.; Kok, J. N.; Back, T.; Ijzerman, A. P. Mining a chemical database for fragment co-occurrence: discovery of "chemical cliches" J. Chem. Inf. Model. 2006, 46, 553-562
11. Hendlich, M.; Bergner, A.; Günther, J.; Klebe, G. Relibase - design and development of a database for comprehensive analysis of protein-ligand interactions J. Mol. Biol. 2003, 326, 607-620
12. Laskowski, R. A. PDBsum: summaries and analyses of PDB structures Nucleic Acids Res. 2001, 29, 221-222
13. PDBsum on the web. http://www.ebi.ac.uk/pdbsum/.
14. Velankar, S.; Best, C.; Beuth, B.; Boutselakis, C. H.; Cobley, N.; Sousa Da Silva, A. W.; Dimitropoulos, D.; Golovin, A.; Hirshberg, M.; John, M.; Krissinel, E. B.; Newman, R.; Oldfield, T.; Pajon, A.; Penkett, C. J.; Pineda-Castillo, J.; Sahni, G.; Sen, S.; Slowley, R.; Suarez-Uruena, A.; Swaminathan, J.; van Ginkel, G.; Vranken, W. F.; Henrick, K.; Kleywegt, G. J. PDBe: Protein databank in Europe Nucleic Acids Res. 2010, 38, D308-D317
15. Protein databank in Europe (PDBe) on the web. http://www.ebi.ac.uk/pdbe/.
16. Kirchmair, J.; Markt, P.; Distinto, S.; Schuster, D.; Spitzer, G. M.; Liedl, K. R.; Langer, T.; Wolber, G. The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery J. Med. Chem. 2008, 51, 7021-7040
17. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
18. Chalk, A. J.; Worth, C. L.; Overington, J. P.; Chan, A. W. E. PDBLIG: classification of small molecular protein binding in the Protein Data Bank J. Med. Chem. 2004, 47, 3807-3816
19. Verdonk., M. L.; Cole, J. C.; Taylor, R. SuperStar: A knowledge-based approach for identifying interaction sites in proteins J. Mol. Biol. 1999, 289, 1093-1108
20. Moriaud, F.; Doppelt-Azeroual, O.; Martin, L.; Oguievetskaia, K.; Koch, K.; Vorotyntsev, A.; Adcock, S. A.; Delfaud, F. Computational fragment-based approach at PDB scale by protein local similarity J. Chem. Inf. Model. 2009, 49, 280-294
21. Vietg, M.; Siegel, M. G.; Higgs, R. E.; Watson, I. A.; Robertson, D. H.; Savin, K. A.; Durst, G. L.; Hopskind, P. A. Characteristic physical properties and structural fragments of marketed oral drugs J. Med. Chem. 2004, 47, 224-232
22. Villar, H. O.; Kauvar, L. M. Amino acid preferences at protein binding sites FEBS Lett. 1994, 349, 125-130
23. Bartlett, G. J.; Porter, C. T.; Borkakoti, N.; Thornton, J. M. Analysis of catalytic residues in enzyme active sites J. Mol. Biol. 2002, 324, 105-121
24. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Hot spots - a review of the protein-protein interface determinant amino acid residues Proteins 2007, 68, 803-812
25. Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 1995, 8, 127-134
26. Muegge, I. Selection criteria for drug-like compounds Med, Res. Rev. 2003, 23, 302-321
27. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A "Rule of three" for fragment-based lead discovery? Drug Discovery Today 2003, 8, 876-877
28. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug. Delivery Rev. 1997, 23, 3-25
29. Onufriev, A.; Case, D. A.; Ullmann, G. M. A novel view of pH titration in biomolecules Biochemistry 2001, 40, 3413-3419
30. Trujillo, J. I.; Huang, H.-C.; Neumann, W. L.; Mahoney, M. W.; Long, S.; Huang, W.; Garland, D. J.; Kusturin, C.; Abbas, Z.; South, M. S.; Reitz, D. B. Design, synthesis, and biological evaluation of pyrazinones containing novel P1 needles as inhibitors of TF/VIIa Bioorg. Med. Chem. Lett. 2007, 17, 4568-4574
31. Quan, M. L.; Lam, P. Y.; Han, Q.; Pinto, D. J.; He, M. Y.; Li, R.; Ellis, C. D.; Clark, C. G.; Teleha, C. A.; Sun, J. H.; Alexander, R. S.; Bai, S.; Luettgen, J. M.; Knabb, R. M.; Wong, P. C.; Wexler, R. R. Discovery of 1-(3′-aminobenzisoxazol-5′-yl)-3-trifluoromethyl- N -[2-fluoro-4- [(2′-dimethylaminomethyl)imidazol-1-yl]phenyl]-1 H -pyrazole-5- carboxyamide hydrochloride (razaxaban), a highly potent, selective, and orally bioavailable factor Xa inhibitor J. Med. Chem. 2005, 48, 1729-1744
32. Baglin, T. P.; Carrell, R. W.; Church, F. C.; Esmon, C. T.; Huntington, J. A. Crystal structure of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11079-11084
33. Brenk, R.; Naerum, L.; Gradler, U.; Gerber, H. D.; Garcia, G. A.; Reuter, K.; Stubbs, M. T.; Klebe, G. Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis J. Med. Chem. 2003, 46, 1133-1143
34. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry, Part I; W. H. Freeman: San Francisco, 1980; pp 49.
35. Cotton, F. A.; Hazen, E. E., Jr.; Legg, M. J. Staphylococcal nuclease: Proposed mechanism of action based on structure of enzyme-thymidine 3′,5′-bisphosphate-calcium ion complex at 1.5-Å resolution Proc. Natl. Acad. Sci. U.S.A. 1979, 76, 2551-2555
36. Kim, E. E.; Wyckoff, H. W. Structure of alkaline phosphatases Clin. Chim. Acta 1990, 186, 175-187
37. Tamaru, S.; Hamachi, I. Recent progress of phosphate derivatives recognition utilizing artificial small molecular receptors in aqueous media. In Recognition of Anions; Vilar, R., Ed; Springer: Berlin, Heidelberg, 2008; pp 95 - 127.
38. Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level Nucleic Acids Res. 2001, 29, 2860-2874
39. Harding, M. M. The architecture of metal coordination groups in proteins Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 849-859
40. Wang, G.; Dunbrack, R. L., Jr. PISCES: a protein sequence culling server Bioinformatics 2003, 19, 1589-1591
41. Chothia, C.; Lesk, A. M. The relation between the divergence of sequence and structure in proteins EMBO J. 1986, 5, 823-826
42. Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. An overview of halogen bonding J. Mol. Model. 2007, 13, 305-311
43. Politzer, P.; Murray, J. S.; Concha, M. C. Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors J. Mol. Model. 2007, 13, 643-650
44. Zhou, P.; Zou, J.; Tian, F.; Shang, Z. Fluorine bonding - how does it work in protein-ligand interactions? J. Chem. Inf. Model. 2009, 49, 2344-2355
45. Brown, I. D. Hydrogen bonds. In The Chemical Bond in Inorganic Chemistry: The Bond Valence Model; International Union of Crystallography Monographs on Crystallography, 12; Oxford University Press: Oxford, UK, 2006; pp 75 - 90.
46. Hubbard, R. E.; Chen, I.; Davis, B. Informatics and modeling challenges in fragment-based drug discovery Curr. Opin. Drug Discovery Dev. 2007, 10, 289-297
47. Vangrevelinghe, E.; Rudisser, S. Computational approaches for fragment optimization Curr. Comput.-Aided Drug Des. 2007, 3, 69-83
48. Boda, K.; Johnson, A. P. Molecular complexity analysis of de novo designed ligands J. Med. Chem. 2006, 49, 5869-5879
49. Cheeseright, T. The identification of bioisosteres as drug development candidates. Innovations in Pharmaceutical Technology, March, 2009, 22 - 26.
50. Maass, P.; Schulz-Gasch, T.; Stahl, M.; Rarey, M.; Recore, A Fast and versatile method for scaffold hopping based on small molecule crystal structure conformations J. Chem. Inf. Model. 2007, 27, 390-399
51. McDonald, I. K.; Thornton, J. M. Satisfying hydrogen bonding potential in proteins J. Mol. Biol. 1994, 238, 777-793
52. Dalby, A.; Nourse, J. G.; Hounshell, W. D.; Gushurst, A. K. I.; Grier, D. L.; Leland, B. A.; Laufer, J. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited J. Chem. Inf. Comput. Sci. 1992, 32, 244-255
53. Oprea, T. I.; Allu, T. K.; Fara, D. C.; Rad, R. F.; Ostopovici, L.; Bologa, C. G. Lead-like, drug-like or pub-like: how different are they? J. Comput.-Aided Mol. Des. 2007, 21, 113-119