COMPUTATIONAL STUDIES ON DIFFERENT TYPES OF APOPTOTIC PROTEINS DOCKED WITH A DIETARY FLAVONOID ERIODICTYOL IN COLON CANCER
DOI:
https://doi.org/10.22159/ajpcr.2017.v10i1.14982Abstract
Objective: In this study, to evaluate the computational studies of eriodictyol docked with apoptotic proteins.
Methods: AutoDock Vina and Molecular Graphics Laboratory tools were used to determine the interaction between proteins and eriodictyol. Discovery studio visualizer and PyMOL were used to determine the interaction of amino acid residues between apoptotic proteins and eriodictyol.
Results: The obtained results revealed more binding affinities of p53, caspase 8, B-cell lymphoma (Bcl)-2, Bcl-2 - associated X protein (BAX), and adenomatous polyposis coli (APC) of −10.6, −10.9, −9.0, −9.5, and 7.2 kcal/mol, respectively. Interaction of hydrophobic polar contacts of amino acid residues of p53 (CYS-277 and ALA-276), caspase 8 [THR-467, THR-337 (2), and GLU-396 (2)], Bcl-2 [ARG-103 (3), ALA-104 (2), and PHE-105, TYR-
101], BAX [GLY-108, TRY-107, ASN-106, and GLN-155 (2)], and APC [GLU-40 (2) and LEU-37 (2)] were notified between macromolecules and small molecules. The calculation of root-mean-square deviation of proteins and eriodictyol showed the lower binding energies to be 11.6, 12.5, 15.9, 19.6, and 15.8 and the upper binding energies to be 12.4, 15.3, 16.9, 20.7, and 18, respectively. The homology of binding energies was determined below 2Ã… which is computationally less expensive and easily determined the hydrophobic polar contacts.
Conclusions: The homology of binding energies was determined below 2Å which is computationally less expensive  and easily determined the hydrophobic polar contacts. The results were proved that the eriodictyol highly interacted with apoptotic proteins. It might be a strong anti-inflammatory activity of colon cancer. In future, computational molecular docking studies should aid further in vitro and in vivo studies.
Keywords: AutoDock Vina, p53, Eriodictyol, Caspase 8, B-cell lymphoma-2, Bcl-2 - associated X protein, Adenomatous polyposis coli.
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Karthi N, Manju V. Synergistic effects of selected anticancer drugs with vitamin-E against HT-29 human adenocarcinoma cell lines. Indian J Res Pharm Biotechnol 2014;2(1):1246-53.
Cancer Facts and Figures. The American Cancer Society, 2016. Available from: http://www.cancer.org.
Coker-Gurkan A, Arisan ED, Obakan P, Guvenir E, Unsal NP. Inhibition of autophagy by 3-MA potentiates purvalanol-induced apoptosis in Bax deficient HCT 116 colon cancer cells. Exp Cell Res 2014;328(1):87-98.
Bucolo C, Leggio GM, Drago F, Salomone S. Eriodictyol prevents early retinal and plasma abnormalities in streptozotocin-induced diabetic rats. Biochem Pharmacol 2012;84(1):88-92.
Hu Q, Zhang DD, Wang L, Lou H, Ren D. Eriodictyol-7-O-glucoside, a novel Nrf2 activator, confers protection against cisplatin-induced toxicity. Food Chem Toxicol 2012;50(6):1927-32.
Huang TC, Tseng KY, Tsai SS, Liu HJ, Ho CH, Lin HY, et al. Eriodictyol decreases very late antigen-4 (VLA-4) expression, cellular adhesion, and migration through an NF kB-dependent pathway in monocytes. J Funct Foods 2012;2:263-70.
Imen MB, Chaabane F, Nadia M, Soumaya KJ, Kamel G, Leila CG. Anti-melanogenesis and antigenotoxic activities of eriodictyol in murine melanoma (B16-F10) and primary human keratinocyte cells. Life Sci 2015;135:173-8.
Lou H, Jing X, Ren D, Wei X, Zhang X. Eriodictyol protects against H(2)O(2)-induced neuron-like PC12 cell death through activation of Nrf2/ARE signaling pathway. Neurochem Int 2012;61(2):251-7.
Kim MJ, Yun HS, Hong EH, Lee SJ, Baek JH, Lee CW, et al. Depletion of end-binding protein 1 (EB1) promotes apoptosis of human non-small-cell lung cancer cells via reactive oxygen species and Bax-mediated mitochondrial dysfunction. Cancer
Lett 2013;339(1):15-24.
Harms KL, Chen X. The C terminus of p53 family proteins is a cell fate determinant. Mol Cell Biol 2005;25(5):2014-30.
De Grandis V, Bizzarri AR, Cannistraro S. Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin. J Mol Recognit 2007;20(4):215-26.
Janouskova H, Ray AM, Noulet F, Lelong-Rebel I, Choulier L, Schaffner F, et al. Activation of p53 pathway by Nutlin-3a inhibits the expression of the therapeutic target a5 integrin in colon cancer cells. Cancer Lett 2013;336(2):307-18.
Jourdan M, Reme T, Goldschmidt H, Fiol G, Pantesco V, De Vos J, et al. Gene expression of anti - And pro-apoptotic proteins in malignant and normal plasma cells. Br J Haematol 2009;145(1):45-58.
Shipra G, Gauri M, Chandra PM, Kishore SP. Identification of novel potent inhibitors against Bcl-xL anti-apoptotic protein using docking studies. Protein Pept Lett 2012;19(12):1302-17.
Li SZ, Zhang HH, Zhang JN, Zhang ZY, Zhang XF, Zhang XD, et al. ALLN hinders HCT116 tumor growth through Bax-dependent apoptosis. Biochem Biophys Res Commun 2013;437(2):325-30.
Hu T, Wang L, Zhang L, Lu L, Shen J, Chan RL, et al. Sensitivity of apoptosis-resistant colon cancer cells to tanshinones is mediated by autophagic cell death and p53-independent cytotoxicity. Phytomedicine
;22(5):536-44.
Dong GZ, Lee SY, Zhao HY, Lee YI, Jeong JH, Jeon R, et al. Diarylheptanoids from lesser galangal suppress human colon cancer cell growth through modulating Wnt/β-catenin pathway. J Funct Foods 2015;18:47-57.
Cristofaro M, Contursi A, D’Amore S, Martelli N, Spaziante AF, Moschetta A, et al. Adenomatous polyposis coli (APC)-induced apoptosis of HT29 colorectal cancer cells depends on mitochondrial oxidative metabolism. Biochim Biophys Acta 2015;1852(9):1719-28.
Kim JH, Kim YH, Song GY, Kim DE, Jeong YJ, Liu KH, et al. Ursolic acid and its natural derivative corosolic acid suppress the proliferation of APC-mutated colon cancer cells through promotion of β-catenin degradation. Food Chem Toxicol 2014;67:87-95.
Dow LE, O’Rourke KP, Simon J, Tschaharganeh DF, van Es JH, Clevers H, et al. Apc restoration promotes cellular differentiation and reestablishes crypt homeostasis in colorectal cancer. Cell 2015;161(7):1539-52.
Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struct Biol 1996;6(3):402-6.
Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31(2):455-61.
Jung IP, Cho JH, Koo BS, Yoon MY. Functional evaluation of residues in the herbicide-binding site of Mycobacterium tuberculosis acetohydroxyacid synthase by site-directed mutagenesis. Enzyme Microb Technol 2015;78:18-26.
Ren W, Truong TM, Ai HW. Study of the binding energies between unnatural amino acids and engineered orthogonal tyrosyl-tRNA synthetases. Sci Rep 2015;5:12632.
Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat Rev Drug Discov 2004;3(11):935-49.
Ranjan S, Dasgupta N, Chinnappan S, Ramalingam C, Kumar A. A novel approach to evaluate titanium dioxidenanoparticle–protein interaction through docking: An insight into mechanism of action. Proc Natl Acad Sci India B Biol Sci 2015;1-7. DOI: 10.1007/s40011-015-0673-z.
Jha AN, Vishveshwara S, Banavar JR. Amino acid interaction preferences in proteins. Protein Sci 2010;19(3):603-16.
Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157(1):105-32.
Feinstein WP, Brylinski M. Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 2015;7:18.
Alhossary A, Handoko SD, Mu Y, Kwoh CK. Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinformatics 2015;31(13):2214-6.
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