Small molecule affinity fingerprinting: A tool for enzyme family subclassification, target identification, and inhibitor design

Chemistry and Biology

Volumn 9, Issue 10, 2002, Pages 1085-1094

  Greenbaum, Doron C ^a   Arnold, William D ^a   Lu, Felice ^a   Hayrapetian, Linda ^b   Baruch, Amos ^b   Krumrine, Jennifer ^a   Toba, Samuel ^a   Chehade, Kareem ^b   Brömme, Dieter ^c   Kuntz, Irwin D ^a   Bogyo, Matthew ^b  

^a Department of Pharmaceutical Chemistry ^*  (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE PROTEINASE INHIBITOR; EPOXIDE; PAPAIN;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; DRUG ANTAGONISM; DRUG DESIGN; DRUG SCREENING; ENZYME SPECIFICITY; KINETICS; METABOLISM; METHODOLOGY; PROTEIN BINDING; RAT; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; ANIMALS; BINDING SITES; CLUSTER ANALYSIS; CYSTEINE PROTEINASE INHIBITORS; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; EPOXY COMPOUNDS; KINETICS; MODELS, MOLECULAR; PAPAIN; PROTEIN BINDING; RATS; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

ANIMALIA;

EID: 0036775883     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(02)00238-7     Document Type: Article

References (31)

1. Eisenberg D., Marcotte E.M., Xenarios I., Yeates T.O. Protein function in the post-genomic era. Nature. 405:2000;823-826.
2. Fetrow J.S., Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281:1998;949-968.
3. Hull R.D., Singh S.B., Nachbar R.B., Sheridan R.P., Kearsley S.K., Fluder E.M. Latent semantic structure indexing (LaSSI) for defining chemical similarity. J. Med. Chem. 44:2001;1177-1184.
4. Kick E.K., Roe D.C., Skillman A.G., Liu G., Ewing T.J., Sun Y., Kuntz I.D., Ellman J.A. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. Chem. Biol. 4:1997;297-307.
5. Hopkins S.C., Vale R.D., Kuntz I.D. Inhibitors of kinesin activity from structure-based computer screening. Biochemistry. 39:2000;2805-2814.
6. Huo S., Wang J., Cieplak P., Kollman P.A., Kuntz I.D. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions. insight into structure-based ligand design J. Med. Chem. 45:2002;1412-1419.
7. Kauvar L.M. Affinity fingerprinting. Biotechnology (N Y). 13:1995;965-966.
8. Kauvar L.M., Higgins D.L., Villar H.O., Sportsman J.R., Engqvist-Goldstein A., Bukar R., Bauer K.E., Dilley H., Rocke D.M. Predicting ligand binding to proteins by affinity fingerprinting. Chem. Biol. 2:1995;107-118.
9. Frye S.V. Structure-activity relationship homology (SARAH). a conceptual framework for drug discovery in the genomic era Chem. Biol. 6:1999;R3-R7.
10. Greenbaum D., Medzihradszky K.F., Burlingame A., Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem. Biol. 7:2000;569-581.
11. Greenbaum D., Baruch A., Hayrapetian L., Darula Z., Burlingame A., Medzihradszky K., Bogyo M. Chemical approaches for functionally probing the proteome. Mol. Cell Proteomics. 1:2002;60-68.
12. Barrett A.J., Kembhavi A.A., Brown M.A., Kirschke H., Knight C.G., Tamai M., Hanada K. L-trans-Epoxysuccinyl-leucylamido(4-guanidino)butane (E-64) and its analogues as inhibitors of cysteine proteinases including cathepsins B, H and L. Biochem. J. 201:1982;189-198.
13. Turk D., Guncar G., Podobnik M., Turk B. Revised definition of substrate binding sites of papain-like cysteine proteases. Biol. Chem. 379:1998;137-147.
14. Meara J.P., Rich D.H. Mechanistic studies on the inactivation of papain by epoxysuccinyl inhibitors. J. Med. Chem. 39:1996;3357-3366.
15. Nazif T., Bogyo M. Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. Proc. Natl. Acad. Sci. USA. 98:2001;2967-2972.
16. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868.
17. Schaschke N., Assfalg-Machleidt I., Machleidt W., Turk D., Moroder L. E-64 analogues as inhibitors of cathepsin B. On the role of the absolute configuration of the epoxysuccinyl group. Bioorg. Med. Chem. 5:1997;1789-1797.
18. Lamb M.L., Burdick K.W., Toba S., Young M.M., Skillman A.G., Zou X., Arnold J.R., Kuntz I.D. Design, docking, and evaluation of multiple libraries against multiple targets. Proteins. 42:2001;296-318.
19. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W.et al. Calculating structures and free energies of complex molecules. combining molecular mechanics and continuum models Acc. Chem. Res. 33:2000;889-897.
20. Ewing T.J., Makino S., Skillman A.G., Kuntz I.D. Dock 4.0. search strategies for automated molecular docking of flexible molecule databases J. Comput. Aided Mol. Des. 15:2001;411-428.
21. Pearlman D.A., Case D.A., Caldwell J.W., Ross W.S., Cheatham T.E. III, DeBolt S., Ferguson D., Seibel G., Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energenic properties of molecules. Comp. Phys. Commun. 91:1995;1-41.
22. Zhao B., Janson C.A., Amegadzie B.Y., D'Alessio K., Griffin C., Hanning C.R., Jones C., Kurdyla J., McQueney M., Qiu X.et al. Crystal structure of human osteoclast cathepsin K complex with E-64. Nat. Struct. Biol. 4:1997;109-111.
23. Turk D., Podobnik M., Popovic T., Katunuma N., Bode W., Huber R., Turk V. Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution. A basis for the design of specific epoxysuccinyl inhibitors Biochemistry. 34:1995;4791-4797.
24. Somoza J.R., Zhan H., Bowman K.K., Yu L., Mortara K.D., Palmer J.T., Clark J.M., McGrath M.E. Crystal structure of human cathepsin V. Biochemistry. 39:2000;12543-12551.
25. Guncar G., Pungercic G., Klemencic I., Turk V., Turk D. Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. EMBO J. 18:1999;793-803.
26. Brinen L.S., Hansell E., Cheng J., Roush W.R., McKerrow J.H., Fletterick R.J. A target within the target. probing cruzain's P1' site to define structural determinants for the Chagas' disease protease Struct. Fold. Des. 8:2000;831-840.
27. McGrath M.E., Palmer J.T., Bromme D., Somoza J.R. Crystal structure of human cathepsin S. Protein Sci. 7:1998;1294-1302.
28. Bogyo M., Verhelst S., Bellingard-Dubouchaud V., Toba S., Greenbaum D. Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. Chem. Biol. 7:2000;27-38.
29. Bogyo M., Shin S., McMaster J.S., Ploegh H.L. Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes. Chem. Biol. 5:1998;307-320.
30. 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. 28:2000;235-242.
31. Jorgensen W.L., Chandrasekhar J., Madura J., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:1983;926-935.