Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site

Journal of Medicinal Chemistry

Volumn 47, Issue 14, 2004, Pages 3502-3511

  Huang, Niu ^a   Nagarsekar, Ashish ^a   Xia, Guanjun ^a   Hayashi, Jun ^a   MacKerell Jr , Alexander D ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOSUPPRESSIVE AGENT; PHOSPHOTYROSINE; PROTEIN KINASE LCK; PROTEIN P56; PROTEIN SH2; PROTEIN TYROSINE KINASE INHIBITOR;

ARTICLE; BINDING SITE; CELLULAR IMMUNITY; COMPUTER MODEL; DRUG ACTIVITY; DRUG BINDING; DRUG IDENTIFICATION; DRUG PROTEIN BINDING; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; ENZYME INHIBITION; FLUORESCENCE; IMMUNE RESPONSE; LYMPHOCYTE CULTURE; MOLECULAR WEIGHT; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SRC HOMOLOGY DOMAIN; T LYMPHOCYTE; TITRIMETRY;

ANIMALS; BINDING SITES; CELL SURVIVAL; CELLS, CULTURED; DATABASES, FACTUAL; ENZYME INHIBITORS; HUMANS; LYMPHOCYTE ACTIVATION; LYMPHOCYTE SPECIFIC PROTEIN TYROSINE KINASE P56(LCK); LYMPHOCYTES; MICE; MICE, INBRED BALB C; MICE, INBRED C57BL; MODELS, MOLECULAR; MOLECULAR WEIGHT; PEPTIDES; PHOSPHORYLATION; SPECTROMETRY, FLUORESCENCE; SRC HOMOLOGY DOMAINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 3042590341     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm030470e     Document Type: Article

References (47)

1. Tong, L.; Warren, T. C.; King, J.; Betageri, R.; Rose, J.; et al. Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 Å and 1.8 Å resolution. J. Mol. Biol. 1996, 256, 601-610.
2. Broadbridge, R. J.; Sharma, R. P. The Src homology-2 domains (SH2 domains) of the protein tyrosine kinase p56lck: structure, mechanism and drug design. Curr. Drug Targets 2000, 1, 365-386.
3. Straus, D. B.; Weiss, A. Genetic evidence for the involvement of the lck tyrosine kinase in signal transduction through the T cell antigen receptor. Cell 1992, 70, 585-593.
4. Weiss, A.; Littman, D. R. Signal transduction by lymphocyte antigen receptors. Cell 1994, 76, 263-274.
5. Straus, D. B.; Chan, A. C.; Patai, B.; Weiss, A. SH2 domain function is essential for the role of the Lck tyrosine kinase in T cell receptor signal transduction. J. Biol. Chem. 1996, 271, 9976-9981.
6. Pawson, T.; Gish, G. D. SH2 and SH3 domains: from structure to function. Cell 1992, 71, 359-362.
7. Cody, W. L.; Lin, Z.-W.; Panek, R. L.; Rose, D. W.; Rubin, J. R. Progress in the development of inhibitors of SH2 domains. Curr. Pharm. Des. 2000, 6, 59-98.
8. Cousins-Wasti, R.; Ingraham, R. H.; Morelock, M. M.; Grygon, C. A. Determination of affinities for lck SH2 binding peptides using a sensitive fluorescence assay: comparison between the pYEEIP and pYQPQP consensus sequences reveals context-dependent binding specificity. Biochemistry 1996, 35, 16746-16752.
9. Sawyer, T. K. Src homology-2 domains: structure, mechanisms, and drug discovery. Biopolymers 1998, 47, 243-261.
10. Beaulieu, P. I.; Cameron, D. R.; Ferland, J. M.; Gauthier, J.; Ghiro, E.; et al. Ligands for the tyrosine kinase p56lck SH2 domain: discovery of potent dipeptide derivatives with mono-charged, nonhydrolyzable phosphate replacements. J. Med. Chem. 1999, 42, 1757-1766.
11. Lee, T. R.; Lawrence, D. S. SH2-directed ligands of the Lck tyrosine kinase. J. Med. Chem. 2000, 43, 1173-1179.
12. Kuriyan, J.; Cowburn, D. Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 259-288.
13. Songyang, Z.; Cantley, L. C. Recognition and specificity in protein tyrosine kinase-mediated signalling. Trends Biochem. Sci. 1995, 20, 470-475.
14. Marengere, L.; Songyang, Z.; Gish, G. D.; Schaller, M. D.; Parsons, J. T.; et al. SH2 domain specificity and activity modified by a single residue. Nature 1994, 369, 502-505.
15. Songyang, Z.; Gish, G.; Mbamalu, G.; Pawson, T.; Cantley, L. C. A single point mutation switches the specificity of group III Src homology (SH2) domains to that of group I SH2 domains. J. Biol. Chem. 1995, 270, 26029-26032.
16. Brennan, M. B. Drug Discovery Filtering Out Failures Early in the Game. Chem. Eng. News 2000, 78, 63-73.
17. Estrada, E.; Uriarte, E.; Montero, A.; Teijeira, M.; Santana, L. D.; et al. A novel approach for the virtual screening and rational design of anticancer compounds. J. Med. Chem. 2000, 43, 1975-1985.
18. Baxter, C. A.; Murray, C. W.; Waszkowycz, B.; Li, J.; Sykes, R. A.; et al. New approach to molecular docking and its application to virtual screening of chemical databases. J. Chem. Inf. Comput. Sci. 2000, 40, 254-262.
19. Walters, W. P.; Stahl, M. T.; Murcko, M. A. Virtual screening - an overview. Drug Discovery Today 1998, 3, 160-178.
20. Massova, I.; Martin, P.; Bulychev, A.; Kocz, R.; Doyle, M.; et al. Templates for design of inhibitors for serine proteases: application of the program DOCK to the discovery of novel inhibitors for thrombin. Bioorg. Med. Chem. Lett. 1998, 8, 2463-2466.
21. Li, S.; Gao, J.; Satoh, T.; Friedman, T. M.; Edling, A. E.; et al. A computer screening approach to immunoglobulin superfamily structures and interactions: discovery of small non-peptidic CD4 inhibitors as novel immunotherapeutics. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 73-78.
22. Chen, I.-J.; Neamati, N.; Nicklaus, M. C.; Orr, A.; Anderson, L.; et al. Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets. Bioorg. Med. Chem. 2000, 8, 2385-2398.
23. Deborah, A. L.; Willian, V. M.; Linda, K. J. Application of virtual screening tools to a protein-protein interaction: database mining studies on the growth hormone. Med. Chem. Res. 1999, 9, 579-591.
24. Pan, Y.; Huang, N.; Cho, S.; MacKerell, A. D., Jr. Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening. J. Chem. Inf. Comput. Sci. 2003, 43, 267-272.
25. SYBYL, version 6.7; Tripos Associates: St. Louis, MO, 2002.
26. Gasteiger, J.; Rudolph, C.; Sadowski, J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comput. Methodol. 1990, 3, 537.
27. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; et al. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
28. Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.
29. Leach, A. R.; Kuntz, I. D. Conformational analysis of flexible ligands in macromolecular receptor sites. J. Comput. Chem. 1992, 13, 730-748.
30. Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983, 221, 709-713.
31. Ferrin, T. E.; Huang, C. C.; Jarvis, L. E.; Langridge, R. The MIDAS display system. J. Mol. Graphics 1988, 6, 13-27.
32. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1984, 28, 849-857.
33. Ewing, T. J. A.; Kuntz, I. D. Critical evaluation of search algorithms used in automated molecular docking. J. Comput. Chem. 1997, 18, 1175-1189.
34. Oprea, T. I. Property distribution of drug-related chemical databases. J. Comput.-Aided Mol. Des. 2000, 14, 251-264.
35. Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. Is There a Difference between Leads and Drugs? A Historical Perspective. J. Chem. Inf. Comput. Sci. 2001, 41, 1308-1315.
36. Teague, S. J.; Davis, A. M.; Leeson, P. D.; Oprea, T. I. The design of leadlike combinatorial libraries. Angew. Chem., Int. Ed. 1999, 38, 3743-3748.
37. Godden, J. W.; Xue, L.; Bajorath, J. Combinatorial preferences affect molecular similarity/diversity calculations using binary fingerprints and Tanimoto coefficients. J. Chem. Inf. Comput. Sci. 2000, 40, 163-166.
38. MOE; Chemical Computing Group Inc.: Montreal, Quebec, Canada, 2002.
39. Marshall, A. G. Biophysical Chemistry: Principles, Techniques, and Applications; John Wiley & Sons: New York, 1978.
40. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery development settings. Adv. Drug Delivery Res. 1997, 23, 3-25.
41. Su, A.-I.; Lorber, D. M.; Weston, G. S.; Baase, W. A.; Matthew, B. W.; et al. Docking molecules by families to increase the diversity of hits in database screening: computational strategy and experimental evaluation. Proteins 2001, 42, 279-293.
42. Kubinyi, H. Structure-based design of enzyme inhibitors and receptor ligands. Curr. Opin. Drug Discovery Dev. 1998, 1, 4-15.
43. Shoichet, B. K.; Leach, A. R.; Kuntz, I. D. Ligand solvation in molecular docking. Proteins: Struct., Funct., Genet. 1999, 34, 4-16.
44. Payne, G.; Stolz, L. A.; Pei, D.; Band, H.; Shoelson, S. E.; et al. The phosphopeptide-binding specificity of Src family SH2 domains. Chem. Biol. 1994, 1, 99-105.
45. Songyang, Z.; Shoelson, S. E.; Chaudhuri, M.; Gish, G.; Pawson, T.; et al. SH2 domains recognize specific phosphopeptide sequences. Cell 1993, 72, 767-778.
46. Liu, X.; Brodeur, S. R.; Gish, G.; Songyang, Z.; Cantley, L. C.; et al. Regulation of c-Src tyrosine kinase activity by the Src SH2 domain. Oncogene 1993, 8, 1119-1126.
47. Humphrey, W.; Dalke, A.; Schulten, K. VMD-visual molecular dynamics. J. Mol. Graphics 1996, 14, 33-38.