Comparative analysis of pharmacophore features and quantitative structure-activity relationships for CD38 covalent and non-covalent inhibitors

Chemical Biology and Drug Design

Volumn 86, Issue 6, 2015, Pages 1411-1424

  Zhang, Shuang ^a   Xue, Xiwen ^a   Zhang, Liangren ^a   Zhang, Lihe ^a   Liu, Zhenming ^a  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

Author keywords

3D QSAR; CD38; comparative analysis; covalent and non covalent inhibitors; pharmacophore characteristics

Indexed keywords

HYDROGEN; PROTEIN INHIBITOR; CD38 ANTIGEN; CD38 PROTEIN, HUMAN; MEMBRANE PROTEIN;

ARTICLE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; COVALENT BOND; CRYSTAL STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; PHARMACOPHORE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATIC ELECTRICITY; ALGORITHM; ANTAGONISTS AND INHIBITORS; BINDING SITE; CHEMICAL PHENOMENA; CHEMISTRY; CLUSTER ANALYSIS; COMPARATIVE STUDY; DRUG DESIGN; HUMAN; MOLECULAR DOCKING;

ALGORITHMS; ANTIGENS, CD38; BINDING SITES; CLUSTER ANALYSIS; DRUG DESIGN; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MEMBRANE GLYCOPROTEINS; MOLECULAR DOCKING SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; STATIC ELECTRICITY;

EID: 84956794944     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12606     Document Type: Article

References (44)

1. Zhao Y.J., Lam C.M.C., Lee H.C., (2012) The membrane-bound enzyme CD38 exists in two opposing orientations. Sci Signal; 5: ra67.
2. Takasawa S., Tohgo A., Noguchi N., Koguma T., Nata K., Sugimoto T., Yonekura H., Okamoto H., (1993) Synthesis and hydrolysis of cyclic ADP-ribose by human leukocyte antigen CD38 and inhibition of the hydrolysis by ATP. J Biol Chem; 268: 26052-26054.
3. Tohgo A., Takasawa S., Noguchi N., Koguma T., Nata K., Sugimoto T., Furuya Y., Yonekura H., Okamoto H., (1994) Essential cysteine residues for cyclic ADP-ribose synthesis and hydrolysis by CD38. J Biol Chem; 269: 28555-28557.
4. Lund F.E., Yu N., Kim K.M., Reth M., Howard M.C., (1996) Signaling through CD38 augments B cell antigen receptor (BCR) responses and is dependent on BCR expression. J Immunol; 157: 1455-1467.
5. Howard M., Grimaldi J., Bazan J., Lund F., Santos-Argumedo L., Parkhouse R., Walseth T., Lee H.C., (1993) Formation and hydrolysis of cyclic ADP-ribose catalyzed by lymphocyte antigen CD38. Science; 262: 1056-1059.
6. +. J Biol Chem; 270: 30327-30333.
7. Ausiello C.M., la Sala A., Ramoni C., Urbani F., Funaro A., Malavasi F., (1996) Secretion of IFN-γ, IL-6, granulocyte-macrophage colony-stimulating factor and IL-10 cytokines after activation of human purified T lymphocytes upon CD38 ligation. Cell Immunol; 173: 192-197.
8. Ausiello C.M., Urbani F., la Sala A., Funaro A., Malavasi F., (1995) CD38 ligation induces discrete cytokine mRNA expression in human cultured lymphocytes. Eur J Immunol; 25: 1477-1480.
9. Dianzani U., Funaro A., DiFranco D., Garbarino G., Bragardo M., Redoglia V., Buonfiglio D., De Monte L.B., Pileri A., Malavasi F., (1994) Interaction between endothelium and CD4+ CD45RA+ lymphocytes. Role of the human CD38 molecule. J Immunol; 153: 952-959.
10. Deaglio S., Aydin S., Vaisitti T., Bergui L., Malavasi F., (2008) CD38 at the junction between prognostic marker and therapeutic target. Trends Mol Med; 14: 210-218.
11. Guse A.H., (2005) Second messenger function and the structure-activity relationship of cyclic adenosine diphosphoribose (cADPR). FEBS J; 272: 4590-4597.
12. Zhang H., Graeff R., Lee H.C., Hao Q., (2013) Crystal structures of human CD38 in complex with NAADP and ADPRP. Messenger; 2: 44-53.
13. Lee H., (2011) Cyclic ADP-ribose and NAADP: fraternal twin messengers for calcium signaling. Sci China Life Sci; 54: 699-711.
14. Lin H., (2007) Nicotinamide adenine dinucleotide: beyond a redox coenzyme. Org Biomol Chem; 5: 2541-2554.
15. Liu Q., Kriksunov I.A., Jiang H., Graeff R., Lin H., Lee H.C., Hao Q., (2008) Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38. Chem Biol; 15: 1068-1078.
16. Liu Q., Kriksunov I.A., Graeff R., Munshi C., Lee H.C., Hao Q., (2006) Structural basis for the mechanistic understanding of human CD38-controlled multiple catalysis. J Biol Chem; 281: 32861-32869.
17. Sauve A.A., Schramm V.L., (2002) Mechanism-based inhibitors of CD38: a mammalian cyclic ADP-ribose synthetase. Biochemistry; 41: 8455-8463.
18. + glycohydrolase by arabino analogues of beta-NAD. J Biol Chem; 267: 9606-9611.
19. Sauve A.A., Deng H., Angeletti R.H., Schramm V.L., (2000) A covalent intermediate in CD38 is responsible for ADP-ribosylation and cyclization reactions. J Am Chem Soc; 122: 7855-7859.
20. Chen Z., Kwong A.K.Y., Yang Z., (2011) Studies of the synthesis of nicotinamide nucleoside and nucleotide analogues and their inhibitions towards CD38 NADase. Heterocycles; 83: 2837-2850.
21. Kwong A.K., Chen Z., Zhang H., Leung F.P., Lam C.M., Ting K.Y., Zhang L.R., Hao Q., Zhang L.H., Lee H.C., (2012) Catalysis-based inhibitors of the calcium signaling function of CD38. Biochemistry; 51: 555-564.
22. Wang S., Zhu W., Wang X., Li J., Zhang K., Zhang L.R., Zhao Y.J., Lee H.C., Zhang L.H., (2014) Design, synthesis and SAR studies of NAD analogues as potent inhibitors towards CD38 NADase. Molecules; 19: 15754-15767.
23. Zhou Y., Ting K.Y., Lam C.M.C., Kwong A.K.Y., Xia J., Jin H., Liu Z., Zhang L.R., Lee H.C., Zhang L.H., (2012) Design, synthesis and biological evaluation of noncovalent inhibitors of human CD38 NADase. ChemMedChem; 7: 223-228.
24. Wu D., Ting K., Duan Y., Li N., Li J., Zhang L.R., Lee H.C., Zhang L.H., (2013) Synthesis and activity of novel indole derivatives as inhibitors of CD38. Acta Pharm Sin B; 3: 245-253.
25. + metabolism, protein acetylation, and treatment of metabolic syndrome. Diabetes; 62: 1084-1093.
26. Kellenberger E., Kuhn I., Schuber F., Muller-Steffner H., (2011) Flavonoids as inhibitors of human CD38. Bioorg Med Chem Lett; 21: 3939-3942.
27. Kellenberger E., Kuhn I., Schuber F., Muller-Steffner H., (2014) Inhibition of glioma progression by a newly discovered CD38 inhibitor. Int J Cancer; 136: 1422-1433.
28. Liu Q., Kriksunov I.A., Graeff R., Munshi C., Lee H.C., Hao Q., (2005) Crystal structure of human CD38 extracellular domain. Structure; 13: 1331-1339.
29. 2+ signaling. Messenger; 2: 19-32.
30. Dong M., Si Y.Q., Sun S.Y., Pu X.P., Yang Z.J., Zhang L.R., Zhang L.H., et al,. (2011) Design, synthesis and biological characterization of novel inhibitors of CD38. Org Biomol Chem; 9: 3246-3257.
31. Moreau C., Liu Q., Graeff R., Wagner G.K., Thomas M.P., Swarbrick J.M., Shuto S., Lee H.C., Hao Q., Potter B.V.L., (2013) CD38 structure-based inhibitor design using the N1-cyclic inosine 5′-diphosphate ribose template. PLoS ONE; 8: e66247.
32. Clark M., Cramer R.D., Van Opdenbosch N., (1989) Validation of the general purpose tripos 5.2 force field. J Comput Chem; 10: 982-1012.
33. Gasteiger J., Marsili M., (1980) Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron; 36: 3219-3228.
34. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E., (2000) The protein data bank. Nucleic Acids Res; 28: 235-242.
35. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., Weiner P., (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc; 106: 765-784.
36. Sanner M.F., (1999) Python: a programming language for software integration and development. J Mol Graph Model; 17: 57-61.
37. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J., (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem; 19: 1639-1662.
38. Wolber G., Langer T., (2004) LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model; 45: 160-169.
39. Ståhle L., Wold S., (1987) Partial least squares analysis with cross-validation for the two-class problem: A Monte Carlo study. J Chemometr; 1: 185-196.
40. Wold S., Albano C., Dunn W.J. III, Edlund U., Esbensen K., Geladi P., Hellberg S., Johansson E., Lindberg W., Sjöström M., (1984) Multivariate Data Analysis in Chemistry. In:, Kowalski B., editor. Chemometrics: Mathematics and Statistics in Chemistry: Springer Netherlands; p. 17-95.
41. Wold S., (1978) Cross-validatory estimation of the number of components in factor and principal components models. Technometrics; 20: 397-405.
42. Cramer R.D., Patterson D.E., Bunce J.D., (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc; 110: 5959-5967.
43. Liu Q., Kriksunov I.A., Moreau C., Graeff R., Potter B.V.L., Lee H.C., Hao Q., (2007) Catalysis-associated conformational changes revealed by human CD38 complexed with a non-hydrolyzable substrate analog. J Bioll Chem; 282: 24825-24832.
44. Liu Q., Kriksunov I.A., Graeff R., Lee H.C., Hao Q., (2007) Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38. J Biol Chem; 282: 5853-5861.