Cavities tell more than sequences: Exploring functional relationships of proteases via binding pockets

Journal of Chemical Information and Modeling

Volumn 53, Issue 8, 2013, Pages 2082-2092

  Glinca, Serghei ^a   Klebe, Gerhard ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CLASSIFICATION (OF INFORMATION); LIGANDS; PHYSICOCHEMICAL PROPERTIES; PROTEINS;

CLUSTERING PROCEDURE; COMPUTATIONAL APPROACH; FUNCTIONAL RELATIONSHIP; LIGAND RECOGNITION; NUMBER OF CLUSTERS; SEQUENCE INFORMATIONS; SMALL-MOLECULE DRUGS; STRUCTURAL LEVELS;

BINDING SITES;

PEPTIDE HYDROLASE; PROTEIN BINDING;

ALGORITHM; ANIMAL; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; DRUG DESIGN; HUMAN; METABOLISM; MOUSE; PROTEIN CONFORMATION; REPRODUCIBILITY; ARTICLE; PROTEIN BINDING;

ALGORITHMS; ANIMALS; BINDING SITES; CLUSTER ANALYSIS; DRUG DESIGN; HUMANS; MICE; MODELS, MOLECULAR; PEPTIDE HYDROLASES; PROTEIN BINDING; PROTEIN CONFORMATION; REPRODUCIBILITY OF RESULTS;

EID: 84883220985     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300550a     Document Type: Article

References (55)

1. Kawasaki, Y.; Freire, E. Finding a better path to drug selectivity Drug Discov. Today 2011, 16, 985-990
2. Huggins, D. J.; Sherman, W.; Tidor, B. Rational approaches to improving selectivity in drug design J. Med. Chem. 2012, 55, 1424-1444
3. Keiser, M. J.; Roth, B. L.; Armbruster, B. N.; Ernsberger, P.; Irwin, J. J.; Shoichet, B. K. Relating protein pharmacology by ligand chemistry Nat. Biotechnol. 2007, 25, 197-206
4. Gregori-Puigjané, E.; Mestres, J. SHED: Shannon entropy descriptors from topological feature distributions J. Chem. Inf. Model. 2006, 46, 1615-1622
5. Pérot, S.; Sperandio, O.; Miteva, M. A.; Camproux, A.-C.; Villoutreix, B. O. Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery Drug Discov. Today 2010, 15, 656-667
6. Kuhn, D.; Weskamp, N.; Hüllermeier, E.; Klebe, G. Functional classification of protein kinase binding sites using Cavbase ChemMedChem 2007, 2, 1432-1447
7. Kinnings, S. L.; Jackson, R. M. Binding site similarity analysis for the functional classification of the protein kinase family J. Chem. Inf. Model. 2009, 49, 318-329
8. Feldman, H. J.; Labute, P. Pocket similarity: are alpha carbons enough? J. Chem. Inf. Model. 2010, 50, 1466-1475
9. Spitzer, R.; Cleves, A. E.; Jain, A. N. Surface-based protein binding pocket similarity Proteins 2011, 79, 2746-2763
10. Weber, A.; Casini, A.; Heine, A.; Kuhn, D.; Supuran, C. T.; Scozzafava, A.; Klebe, G. Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition J. Med. Chem. 2004, 47, 550-557
11. An, J.; Totrov, M.; Abagyan, R. Pocketome via comprehensive identification and classification of ligand binding envelopes Mol. Cell. Proteomics 2005, 4, 752-761
12. Milletti, F.; Vulpetti, A. Predicting polypharmacology by binding site similarity: from kinases to the protein universe J. Chem. Inf. Model. 2010, 50, 1418-1431
13. Defranchi, E.; Schalon, C.; Messa, M.; Onofri, F.; Benfenati, F.; Rognan, D. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements PLoS ONE 2010, 5, e12214
14. Ren, J.; Xie, L.; Li, W. W.; Bourne, P. E. SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison Nucleic Acids Res. 2010, 38, W441-W444
15. Mestres, J.; Gregori-Puigjané, E.; Valverde, S.; Solé, R. V. The topology of drug-target interaction networks: implicit dependence on drug properties and target families Mol. Biosyst. 2009, 5, 1051-1057
16. Schmitt, S.; Kuhn, D.; Klebe, G. A new method to detect related function among proteins independent of sequence and fold homology J. Mol. Biol. 2002, 323, 387-406
17. Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins J. Mol. Graphics Modell. 1997, 15, 359-363
18. Kuhn, D.; Weskamp, N.; Schmitt, S.; Hüllermeier, E.; Klebe, G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase J. Mol. Biol. 2006, 359, 1023-1044
19. Zhao, Y.; Karypis, G. Data Clustering in Life Sciences Molec. Biotechnol. 2005, 31, 55-80
20. Bairoch, A. The ENZYME database in 2000 Nucleic Acids Res. 2000, 28, 304-305
21. Rawlings, N. D.; Barrett, A. J.; Bateman, A. MEROPS: the peptidase database Nucleic Acids Res. 2010, 38, D227-D233
22. ChEMBL. http://www.ebi.ac.uk/chembl/ (accessed July 2011).
23. Pearson, W. R.; Lipman, D. J. Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. 1988, 85, 2444-2448
24. Landrum, G. RDKit: Open-source cheminformatics. http://www.rdkit.org (accessed June 2011).
25. Xu, R.; Wunsch, D. C. Clustering; Wiley-IEEE Press: New Jersey, 2009.
26. Kaufman, L.; Rousseeuw, P. J. Finding Groups in Data An Introduction to Cluster Analysis; John Wiley and Sons: New York, 1990.
27. Rost, B. Twilight zone of protein sequence alignments Prot. Eng. Des. Sel. 1999, 12, 85-94
28. Rousseeuw, P. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis J. Comput. Appl. Math. 1987, 20, 53-65
29. Pollard, K. S.; van der Laan, M. J. New methods for identifying significant clusters in gene expression data. Proceedings of the American Statistical Association, Biometrics Section [CD-ROM]; American Stastistical Association: Alexandria, VA, 2002.
30. Halkidi, M.; Batistakis, Y.; Vazirgiannis, M. On Clustering Validation Techniques J. Intell. Inf. Syst. 2001, 17, 107-145
31. Hubert, L.; Arabie, P. Comparing partitions J. Classif. 1985, 2, 193-218
32. Meila, M. Comparing clusterings-an information based distance J. Multivar. Anal. 2007, 98, 873-895
33. Schrödinger, LLC. The PyMOL Molecular Graphics System, version 1.3r1; 2010.
34. Nanao, M. H.; Tcherniuk, S. O.; Chroboczek, J.; Dideberg, O.; Dessen, A.; Balakirev, M. Y. Crystal structure of human otubain 2 EMBO Rep. 2004, 5, 783-788
35. Das, C.; Hoang, Q. Q.; Kreinbring, C. A.; Luchansky, S. J.; Meray, R. K.; Ray, S. S.; Lansbury, P. T.; Ringe, D.; Petsko, G. A. Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1 Proc. Natl. Acad. Sci. 2006, 103, 4675-4680
36. Liu, Y.; Lashuel, H.; Choi, S.; Xing, X.; Case, A.; Ni, J.; Yeh, L. A.; Cuny, G. D.; Stein, R. L.; Lansbury, P. J. Discovery of Inhibitors that Elucidate the Role of UCH-L1 Activity in the H1299 Lung Cancer Cell Line Chem. Biol. 2003, 10, 837-846
37. Lai, L.; Xu, Z.; Zhou, J.; Lee, K.-D.; Amidon, G. L. Molecular basis of prodrug activation by human valacyclovirase, an alpha-amino acid ester hydrolase J. Biol. Chem. 2008, 283, 9318-9327
38. Xing, Y.; Li, Z.; Chen, Y.; Stock, J. B.; Jeffrey, P. D.; Shi, Y. Structural mechanism of demethylation and inactivation of protein phosphatase 2A Cell 2008, 133, 154-163
39. O'Farrell, P. A.; Gonzalez, F.; Zheng, W.; Johnston, S. A.; Joshua-Tor, L. Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease Structure 1999, 7, 619-627
40. Davis, T. L.; Walker, J. R.; Finerty, P. J.; Mackenzie, F.; Newman, E. M.; Dhe-Paganon, S. The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition J. Mol. Biol. 2007, 366, 216-229
41. Donkor, I. O. Calpain inhibitors: a survey of compounds reported in the patent and scientific literature Expert. Opin. Ther. Pat. 2011, 21, 601-636
42. Choe, Y.; Leonetti, F.; Greenbaum, D. C.; Lecaille, F.; Bogyo, M.; Brömme, D.; Ellman, J. A.; Craik, C. S. Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities J. Biol. Chem. 2006, 281, 12824-12832
43. Cuerrier, D.; Moldoveanu, T.; Campbell, R. L.; Kelly, J.; Yoruk, B.; Verhelst, S. H. L.; Greenbaum, D.; Bogyo, M.; Davies, P. L. Development of calpain-specific inactivators by screening of positional scanning epoxide libraries J. Biol. Chem. 2007, 282, 9600-9611
44. Weskamp, N.; Hüllermeier, E.; Klebe, G. Merging chemical and biological space: Structural mapping of enzyme binding pocket space Proteins 2009, 76, 317-330
45. Stegemann, B.; Klebe, G. Cofactor-binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space Proteins 2011, 626-648
46. Hilpert, K.; Ackermann, J.; Banner, D. W.; Gast, A.; Gubernator, K.; Hadvary, P.; Labler, L.; Mueller, K.; Schmid, G. Design and synthesis of potent and highly selective thrombin inhibitors J. Med. Chem. 1994, 37, 3889-3901
47. Sanderson, P. E. J. Small, noncovalent serine protease inhibitors Med. Res. Rev. 1999, 19, 179-197
48. Nar, H.; Bauer, M.; Schmid, A.; Stassen, J.-M.; Wienen, W.; Priepke, H. W.; Kauffmann, I. K.; Ries, U. J.; Hauel, N. H. Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors Structure 2001, 9, 29-37
49. McGrath, M. E.; Mirzadegan, T.; Schmidt, B. F. Crystal structure of phenylmethanesulfonyl fluoride-treated human chymase at 1.9 Å Biochemistry 1997, 36, 14318-14324
50. Molinari, J. F.; Scuri, M.; Moore, W. R.; Clark, J.; Tanaka, R.; Abraham, W. M. Inhaled tryptase causes bronchoconstriction in sheep via histamine release Am. J. Respir. Crit. Care Med. 1996, 154, 649-653
51. Combrink, K. D.; Gülgeze, H. B.; Meanwell, N. A.; Pearce, B. C.; Zulan, P.; Bisacchi, G. S.; Roberts, D. G.; Stanley, P.; Seiler, S. M. 1,2-Benzisothiazol-3-one 1,1-dioxide inhibitors of human mast cell tryptase J. Med. Chem. 1998, 41, 4854-4860
52. Hopkins, C. R.; Czekaj, M.; Kaye, S. S.; Gao, Z.; Pribish, J.; Pauls, H.; Liang, G.; Sides, K.; Cramer, D.; Cairns, J.; Luo, Y.; Lim, H.-K.; Vaz, R.; Rebello, S.; Maignan, S.; Dupuy, A.; Mathieu, M.; Levell, J. Design, synthesis, and biological activity of potent and selective inhibitors of mast cell tryptase Bioorg. Med. Chem. Lett. 2005, 15, 2734-2737
53. Lee, C.-S.; Liu, W.; Sprengeler, P. A.; Somoza, J. R.; Janc, J. W.; Sperandio, D.; Spencer, J. R.; Green, M. J.; McGrath, M. E. Design of novel, potent, and selective human beta-tryptase inhibitors based on alpha-keto-[1,2,4]-oxadiazoles Bioorg. Med. Chem. Lett. 2006, 16, 4036-4040
54. Olivero, A. G.; Eigenbrot, C.; Goldsmith, R.; Robarge, K.; Artis, D. R.; Flygare, J.; Rawson, T.; Sutherlin, D. P.; Kadkhodayan, S.; Beresini, M.; Elliott, L. O.; DeGuzman, G. G.; Banner, D. W.; Ultsch, M.; Marzec, U.; Hanson, S. R.; Refino, C.; Bunting, S.; Kirchhofer, D. A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo J. Biol. Chem. 2005, 280, 9160-9169
55. Young, W. B.; Mordenti, J.; Torkelson, S.; Shrader, W. D.; Kolesnikov, A.; Rai, R.; Liu, L.; Hu, H.; Leahy, E. M.; Green, M. J.; Sprengeler, P. A.; Katz, B. A.; Yu, C.; Janc, J. W.; Elrod, K. C.; Marzec, U. M.; Hanson, S. R. Factor VIIa inhibitors: chemical optimization, preclinical pharmacokinetics, pharmacodynamics, and efficacy in an arterial baboon thrombosis model Bioorg. Med. Chem. Lett. 2006, 16, 2037-2041