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

References

• Raff M. Cell suicide for beginners. Nature 1998;396:119–122.
   PubMed Web of Science ®Google Scholar
• Reed JC. Mechanisms of apoptosis. Am J Pathol 2000;157:1415–1430.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100:57–70.
   PubMed Web of Science ®Google Scholar
• Adams JM, Cory S. The Bcl-2 protein family: arbiters of cell survival. Science 1998;281:1322–1326.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Michels J, Johnson PW, Packham G. Mcl-1. Int J Biochem Cell Biol 2005;37:267–271.
   PubMed Web of Science ®Google Scholar
• Petros AM, Olejniczak ET, Fesik SW. Structural biology of the Bcl-2 family of proteins. Biochim Biophys Acta 2004;1644:83–94.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Kakizoe T. Asian studies of cancer chemoprevention: latest clinical results. Eur J Cancer 2000;36:1303–1309.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Leung KW, Wong AS. Pharmacology of ginsenosides: a literature review. Chin Med 2010;5:20.
   PubMedGoogle Scholar
• Attele AS, Wu JA, Yuan CS. Ginseng pharmacology: multiple constituents and multiple actions. Biochem Pharmacol 1999;58:1685–1693.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Choi KT. Botanical characteristics, pharmacological effects and medicinal components of Korean Panax ginseng C A Meyer. Acta Pharmacol Sin 2008;29:1109–1118.
   PubMed Web of Science ®Google Scholar
• Briskin DP. Medicinal plants and phytomedicines. Linking plant biochemistry and physiology to human health. Plant Physiol 2000;124:507–514.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Goodsell DS, Morris GM, Olson AJ. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 1996;9:1–5.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Laurie AT, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005;21:1908–1916.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem 2003;66:27–85.
   PubMedGoogle Scholar
• Accelrys. Accelrys Discovery Studio 2.5, San Diego, CA. 2009.
   Google Scholar
• Yun TK, Choi SY. Non-organ specific cancer prevention of ginseng: a prospective study in Korea. Int J Epidemiol 1998;27:359–364.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar