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Research Article

Natural polyphenolic inhibitors against the antiapoptotic BCL-2

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Pages 391-400 | Received 02 Jun 2016, Accepted 15 Feb 2017, Published online: 06 Mar 2017

References

  • Igney FH, Krammer PH. Death and anti-death: tumour resistance to apoptosis. Nat Rev Cancer 2002;2:277–88.
  • Reed JC. Apoptosis-based therapies. Nat Rev Drug Discov 2002;1:111–21.
  • Pinto M, Perez JJ, Rubio-Martinez J. Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xL and Bcl-2 proteins. J Comput-Aided Mol Des 2004;18:13–22.
  • Adams JM, Cory S. Life-or-death decisions by the Bcl-2 protein family. Trends Biochem Sci 2001;26:61–6.
  • Cao X, Yap JL, Newell-Rogers MK, et al. The novel BH3 alpha-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer 2013;12:42.
  • Czabotar PE, Lessene G, Strasser A, Adams JM. Control of apoptosis by the BCL-2 protein family: implications for physiology and therapy. Nat Rev Mol Cell Biol 2014;15:49–63.
  • Hosseini A, Espona-Fiedler M, Soto-Cerrato V, et al. Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members. PLoS One 2013;8:e57562.
  • Opferman JT, Korsmeyer SJ. Apoptosis in the development and maintenance of the immune system. Nat Immunol 2003;4:410–15.
  • Kim H, Rafiuddin-Shah M, Tu H-C, et al. Hierarchical regulation of mitochondrion-dependent apoptosis by BCL-2 subfamilies. Nat Cell Biol 2006;8:1348–58.
  • Willis SN, Fletcher JI, Kaufmann T, et al. Apoptosis initiated when BH3 ligands engage multiple Bcl-2 homologs, not Bax or Bak. Science 2007;315:856–9.
  • Antignani A, Youle RJ. How do Bax and Bak lead to permeabilization of the outer mitochondrial membrane? Curr Opin Cell Biol 2006;18:685–9.
  • Green DR, Kroemer G. The pathophysiology of mitochondrial cell death. Science 2004;305:626–9.
  • Ku B, Liang C, Jung JU, Oh B-H. Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX. Cell Res 2011;21:627–41.
  • Liu X, Dai S, Zhu Y, et al. The structure of a Bcl-xL/Bim fragment complex: implications for Bim function. Immunity 2003;19:341–52.
  • Maity A, Yadav S, Verma CS, Dastidar SG. Dynamics of Bcl-xL in water and membrane: molecular simulations. PLoS One 2013;8:e76837.
  • Petros AM, Nettesheim DG, Wang Y, et al. Rationale for Bcl‐XL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies. Protein Sci 2000;9:2528–34.
  • Sattler M, Liang H, Nettesheim D, et al. Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis. Science 1997;275:983–6.
  • Dlugosz PJ, Billen LP, Annis MG, et al. Bcl-2 changes conformation to inhibit Bax oligomerization. EMBO J 2006;25:2287–96.
  • Lin B, Kolluri SK, Lin F, et al. Conversion of Bcl-2 from protector to killer by interaction with nuclear orphan receptor Nur77/TR3. Cell 2004;116:527–40.
  • Wang K, Gross A, Waksman G, Korsmeyer SJ. Mutagenesis of the BH3 domain of BAX identifies residues critical for dimerization and killing. Mol Cell Biol 1998;18:6083–9.
  • Yin X-M, Oltvai ZN, Korsmeyer SJ. BH1 and BH2 domains of Bcl-2 are required for inhibition of apoptosis and heterodimerization with Bax. Nature 1994;369:321–3.
  • Zha H, Aimé-Sempé C, Sato T, Reed JC. Proapoptotic protein Bax heterodimerizes with Bcl-2 and homodimerizes with Bax via a novel domain (BH3) distinct from BH1 and BH2. J Biol Chem 1996;271:7440–4.
  • Ding J, Zhang Z, Roberts GJ, et al. Bcl-2 and Bax interact via the BH1–3 groove-BH3 motif interface and a novel interface involving the BH4 motif. J Biol Chem 2010;285:28749–63.
  • Suzuki M, Youle RJ, Tjandra N. Structure of Bax: coregulation of dimer formation and intracellular localization. Cell 2000;103:645–54.
  • Petros AM, Olejniczak ET, Fesik SW. Structural biology of the Bcl-2 family of proteins. Biochimica Et Biophysica Acta (BBA)-Mol Cell Res 2004;1644:83–94.
  • Day CL, Chen L, Richardson SJ, et al. Solution structure of prosurvival Mcl-1 and characterization of its binding by proapoptotic BH3-only ligands. J Biol Chem 2005;280:4738–44.
  • Acoca S, Cui Q, Shore GC, Purisima EO. Molecular dynamics study of small molecule inhibitors of the Bcl-2 family. Proteins Struct Funct Bioinf 2011;79:2624–36.
  • Birt D, Mitchell D, Gold B, et al. Inhibition of ultraviolet light induced skin carcinogenesis in SKH-1 mice by apigenin, a plant flavonoid. Anticancer Res 1996;17:85–91.
  • Kimira M, Arai Y, Shimoi K, Watanabe S. Japanese intake of flavonoids and isoflavonoids from foods. J Epidemiol 1998;8:168–75.
  • Miyajima Y, Kikuzaki H, Hisamoto M, Nakatani N. Antioxidative polyphenols from berries of Pimenta dioica. Biofactors 2004;22:301–3.
  • Seelinger G, Merfort I, Wölfle U, Schempp CM. Anti-carcinogenic effects of the flavonoid luteolin. Molecules 2008;13:2628–51.
  • Lin Y, Shi R, Wang X, Shen HM. Luteolin, a flavonoid with potential for cancer prevention and therapy. Curr Cancer Drug Targets 2008;8:634.
  • Verma S, Singh A, Mishra A. Complex disruption effect of natural polyphenols on Bcl-2-Bax: molecular dynamics simulation and essential dynamics study. J Biomol Struct Dynamics 2015;33:1094–106.
  • Dhanjal JK, Grover S, Sharma S, et al. Structural insights into mode of actions of novel natural Mycobacterium protein tyrosine phosphatase B inhibitors. BMC Genom 2014;15:S3.
  • Goyal M, Dhanjal JK, Goyal S, et al. Development of dual inhibitors against Alzheimer’s disease using fragment-based QSAR and molecular docking. BioMed Res Int 2014;2014:979606.
  • Maindola P, Jamal S, Grover A. Cheminformatics based machine learning models for AMA1-RON2 abrogators for inhibiting plasmodium falciparum erythrocyte invasion. Mol Inform 2015;34:655–64.
  • Patel K, Tyagi C, Goyal S, et al. Curcumin-based IKKβ inhibiting anticancer lead design using novel fragment-based group QSAR modelling. Med Chem Res 24:2022–32.
  • Patel K, Tyagi C, Goyal S, et al. Identification of chebulinic acid as potent natural inhibitor of M. tuberculosis DNA gyrase and molecular insights into its binding mode of action. Comput Biol Chem 2015;59:37–47.
  • Sinha S, Tyagi C, Goyal S, et al. Fragment based G-QSAR and molecular dynamics based mechanistic simulations into hydroxamic-based HDAC inhibitors against spinocerebellar ataxia. J Biomol Struct Dyn 2015;34:1–39.
  • Tyagi C, Bathke J, Goyal S, et al. Targeting the intersubunit cavity of Plasmodium falciparum glutathione reductase by a novel natural inhibitor: Computational and experimental evidence. Int J Biochem Cell Biol 2015;61:72–80.
  • Tyagi C, Gupta A, Goyal S, et al. Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the α-β interfacial site of human tubulin. BMC Genomics 2014;15:S3.
  • Vats C, Dhanjal JK, Goyal S, et al. Computational design of novel flavonoid analogues as potential AChE inhibitors: analysis using group-based QSAR, molecular docking and molecular dynamics simulations. Struct Chem 2015;26:467–76.
  • Oltersdorf T, Elmore SW, Shoemaker AR, et al. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 2005;435:677–81.
  • Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639–62.
  • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 2009;30:2785–91.
  • Berendsen HJ, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 1995;91:43–56.
  • Lindahl E, Hess B, Van Der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001;7:306–17.
  • SchuÈttelkopf AW, Van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr Sect D Biol Crystallogr 2004;60:1355–63.
  • van Gunsteren WF, Billeter S, Eising A, et al. 1996. Biomolecular simulation: The {GROMOS96} manual and user guide.
  • van Gunsteren WF, Daura X, Mark AE. GROMOS force field. Encyclopedia of computational chemistry. 1998;2:1211–16.
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605–12.
  • Kollman PA, Massova I, Reyes C, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889–97.
  • Kumari R, Kumar R, Lynn A. g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inform Model 2014;54:1951–62.
  • Homeyer N, Gohlke H. Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method. Mol Informat 2012;31:114–22.
  • Van Aalten D, Findlay J, Amadei A, Berendsen H. Essential dynamics of the cellular retinol-binding protein-evidence for ligand-induced conformational changes. Protein Eng 1995;8:1129–35.
  • DeLano WL. 2002. The PyMOL molecular graphics system.
  • Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127–34.

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