Molecular docking studies of anti-apoptotic BCL-2, BCL-XL, and MCL-1 proteins with ginsenosides from Panax ginseng

Journal of Enzyme Inhibition and Medicinal Chemistry

Volumn 27, Issue 5, 2012, Pages 685-692

  Sathishkumar, Natarajan ^a   Sathiyamoorthy, Subramaniyam ^a   Ramya, Mathiyalagan ^a   Yang, Dong Uk ^a   Lee, Hee Nyeong ^a   Yang, Deok Chun ^a  

^a Kyung Hee University   (South Korea)

Author keywords

BCL 2 family proteins; Cancer; Ginsenosides; Molecular docking; Panax ginseng

Indexed keywords

APOPTOSIS INHIBITOR; GINSENOSIDE; GINSENOSIDE RF; GINSENOSIDE RG 1; GINSENOSIDE RG 2; GINSENOSIDE RH 2; HYDROGEN; PROTEIN BCL 2; PROTEIN BCL XL; PROTEIN MCL 1;

AMINO ACID SEQUENCE; ANTINEOPLASTIC ACTIVITY; APOPTOSIS; ARTICLE; CANCER INHIBITION; GINSENG; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN STABILITY; PROTEIN STRUCTURE; X RAY DIFFRACTION;

AMINO ACID SEQUENCE; BCL-X PROTEIN; GINSENOSIDES; HUMANS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MOLECULAR SEQUENCE DATA; PANAX; PROTO-ONCOGENE PROTEINS C-BCL-2; SEQUENCE HOMOLOGY, AMINO ACID;

ARALIACEAE; PANAX GINSENG;

EID: 84866078172     PISSN: 14756366     EISSN: 14756374     Source Type: Journal    
DOI: 10.3109/14756366.2011.608663     Document Type: Article

References (42)

1. Raff M. Cell suicide for beginners. Nature 1998;396:119-122. (Pubitemid 28523602)
2. Reed JC. Mechanisms of apoptosis. Am J Pathol 2000;157:1415-1430.
3. Wang D, Liao W, Arora PS. Enhanced metabolic stability and protein-binding properties of artificial alpha helices derived from a hydrogen-bond surrogate: Application to Bcl-xL. Angew Chem Int Ed Engl 2005;44:6525-6529. (Pubitemid 41502788)
4. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100:57-70. (Pubitemid 30046295)
5. Adams JM, Cory S. The Bcl-2 protein family: Arbiters of cell survival. Science 1998;281:1322-1326. (Pubitemid 28406819)
6. Chittenden T, Flemington C, Houghton AB, Ebb RG, Gallo GJ, Elangovan B et al. A conserved domain in Bak, distinct from BH1 and BH2, mediates cell death and protein binding functions. Embo J 1995;14:5589-5596.
7. Zhai D, Ke N, Zhang H, Ladror U, Joseph M, Eichinger A et al. Characterization of the anti-apoptotic mechanism of Bcl-B. Biochem j 2003;376:229-236. (Pubitemid 37487218)
8. Michels J, Johnson PW, Packham G. Mcl-1. Int J Biochem Cell Biol 2005;37:267-271. (Pubitemid 39330187)
9. Petros AM, Olejniczak ET, Fesik SW. Structural biology of the Bcl-2 family of proteins. Biochim Biophys Acta 2004;1644:83-94. (Pubitemid 38281265)
10. Fernández Y, Gu B, Martínez A, Torregrosa A, Sierra A. Inhibition of apoptosis in human breast cancer cells: Role in tumor progression to the metastatic state. Int J Cancer 2002;101:317-326. (Pubitemid 34983186)
11. Lebedeva I, Rando R, Ojwang J, Cossum P, Stein CA. Bcl-xL in prostate cancer cells: Effects of overexpression and down-regulation on chemosensitivity. Cancer Res 2000;60: 6052-6060.
12. Kakizoe T. Asian studies of cancer chemoprevention: Latest clinical results. Eur J Cancer 2000;36:1303-1309.
13. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H et al. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242. (Pubitemid 30047768)
14. Leung KW, Wong AS. Pharmacology of ginsenosides: A literature review. Chin Med 2010;5:20.
15. Attele AS, Wu JA, Yuan CS. Ginseng pharmacology: multiple constituents and multiple actions. Biochem Pharmacol 1999;58:1685-1693. (Pubitemid 29505408)
16. Sathiyamoorthy S, In JG, Gayathri S, Kim YJ, Yang DC. Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. Mol Biol Rep 2010;37:3465-3472.
17. Choi KT. Botanical characteristics, pharmacological effects and medicinal components of Korean Panax ginseng C A Meyer. Acta Pharmacol Sin 2008;29:1109-1118.
18. Briskin DP. Medicinal plants and phytomedicines. Linking plant biochemistry and physiology to human health. Plant Physiol 2000;124:507-514.
19. Vogler BK, Pittler MH, Ernst E. The efficacy of ginseng. A systematic review of randomised clinical trials. Eur J Clin Pharmacol 1999;55:567-575. (Pubitemid 29489202)
20. Park J, Rhee D and Lee Y. Biological Activities and Chemistry of Saponins from Panax ginseng C. A. Meyer. Phytochemistry Reviews. 2005; 4: 159-75. (Pubitemid 41752174)
21. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q et al. The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 2005;33:D233-D237. (Pubitemid 40207868)
22. Porter J, Payne A, de Candole B, Ford D, Hutchinson B, Trevitt G et al. Tetrahydroisoquinoline amide substituted phenyl pyrazoles as selective Bcl-2 inhibitors. Bioorg Med Chem Lett 2009;19:230-233.
23. Lee EF, Czabotar PE, Smith BJ, Deshayes K, Zobel K, Colman PM et al. Crystal structure of ABT-737 complexed with Bcl-xL: Implications for selectivity of antagonists of the Bcl-2 family. Cell Death Differ 2007;14:1711-1713. (Pubitemid 47278856)
24. Dutta S, Gullá S, Chen TS, Fire E, Grant RA, Keating AE. Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol 2010;398:747-762.
25. Goodsell DS, Morris GM, Olson AJ. Automated docking of flexible ligands: Applications of AutoDock. J Mol Recognit 1996;9:1-5. (Pubitemid 126565462)
26. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748. (Pubitemid 27170693)
27. Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489. (Pubitemid 26335901)
28. Laurie AT, Jackson RM. Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005;21:1908-1916. (Pubitemid 40668026)
29. Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: A public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 2009;37:W623-W633.
30. Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO et al. An overview of the PubChem BioAssay resource. Nucleic Acids Res 2010;38:D255-D266.
31. Geldenhuys WJ, Gaasch KE, Watson M, Allen DD, Van der Schyf CJ. Optimizing the use of open-source software applications in drug discovery. Drug Discov Today 2006;11:127-132. (Pubitemid 43375963)
32. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680. (Pubitemid 24354800)
33. Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry. 1998; 19: 1639-62. (Pubitemid 128590223)
34. Manavalan B, Basith S, Choi YM, Lee G, Choi S. Structure-function relationship of cytoplasmic and nuclear I?B proteins: An in silico analysis. Plos one 2010;5:e15782.
35. Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G. Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins 2004;57:678-683. (Pubitemid 39626989)
36. Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem 2003;66:27-85. (Pubitemid 37392314)
37. Accelrys. Accelrys Discovery Studio 2.5, San Diego, CA. 2009.
38. Yun TK, Choi SY. Non-organ specific cancer prevention of ginseng: A prospective study in Korea. Int J Epidemiol 1998;27:359-364.
39. Kim HS, Lee EH, Ko SR, Choi KJ, Park JH, Im DS. Effects of ginsenosides Rg3 and Rh2 on the proliferation of prostate cancer cells. Arch Pharm Res 2004;27:429-435.
40. Min JK, Kim JH, Cho YL, Maeng YS, Lee SJ, Pyun BJ et al. 20(S)-Ginsenoside Rg3 prevents endothelial cell apoptosis via inhibition of a mitochondrial caspase pathway. Biochem Biophys Res Commun 2006;349:987-994.
41. Kim YS, Jin SH, Lee YH, Kim SI, Park JD. Ginsenoside Rh2 induces apoptosis independently of Bcl-2, Bcl-xL, or Bax in C6Bu-1 cells. Arch Pharm Res 1999;22:448-453.
42. Nakata H, Kikuchi Y, Tode T, Hirata J, Kita T, Ishii K et al. Inhibitory effects of ginsenoside Rh2 on tumor growth in nude mice bearing human ovarian cancer cells. Jpn J Cancer Res 1998;89:733-740. (Pubitemid 28401159)