In Silico Molecular Docking Studies of Rutin Compound against Apoptotic Proteins (Tumor Necrosis Factor, Caspase-3, NF-Kappa-B, P53, Collagenase, Nitric Oxide Synthase and Cytochrome C)

Jayameena P.¹, Sivakumari K.^1, , Ashok K.¹ and Rajesh S.¹

¹Department of Zoology, Presidency College, Chennai – 600 005, Tamil Nadu, India

Cite this paper:
Jayameena P., Sivakumari K., Ashok K. and Rajesh S.. In Silico Molecular Docking Studies of Rutin Compound against Apoptotic Proteins (Tumor Necrosis Factor, Caspase-3, NF-Kappa-B, P53, Collagenase, Nitric Oxide Synthase and Cytochrome C). Journal of Cancer Research and Treatment. 2018; 6(2):28-33. doi: 10.12691/jcrt-6-2-1

Abstract

Rutin as a flavonoid compound contains many flavonoids having antitumor properties. Therefore, the present study was aimed to dock rutin compound with apoptotic proteins like TNF, Caspase-3, NF-Kappa-B, P53, Collagenase, Nitric Oxide Synthase and Cytohrome C by AutoDock software. The docking scores were highest in Nitric oxide synthase (-3.68 kcal/mol) followed by Tumor Necrosis Factor (-3.22 kcal/mol), Caspase-3 (-2.95 kcal/mol), Collagenase (-2.47 kcal/mol), Cytochrome C (-2.31 kcal/mol), NF-kappa-B (-1.8 kcal/mol) and P53 (-0.32 kcal/mol). The Log P value and lower hydrogen bond counts, confirming the ability of rutin compound for binding at the active sites of the receptor was determined by the in silico method. The potential drug candidate can further be validated by wet lab studies for its proper function.

Keywords:
Rutin AutoDock and Apoptotic proteins

This work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

References:

[1]	Bailey K, Cook HW, McMaster CR. The phospholipid scramblase PLSCR1 increases UV induced apoptosis primarily through the augmentation of the intrinsic apoptotic pathway and independent of direct phosphorylation by protein kinase C δ. Biochim.Biophys Acta 2005;1733:199-209.
[2]	Alam JJ. Apoptosis: target for novel drugs. Trends Biotechnol 2003; 21:479-83.
[3]	Carnat AP, Carnat A, Fraisse D, Lamaison JL, Heitz A, Wylde R. Violarvensin, a new flavone di-C-glycoside from viola arvensis. J Nat Prod 1998; 61: 272–274.
[4]	Goncalves AFK, Friedrich RB, Boligon AA, Piana M, Beck RCR, Athayde ML. Antioxidant capacity, total phenolic contents, and HPLC determination of rutin in Viola tricolor (L) flowers. Free Radicals Antioxid 2012; 2: 32–37.
[5]	Buszewski B, Kawka S, Suprynowicz Z, Wolski T. Simultaneous isolation of rutin and esculin from plant material and drugs using solid-phase extraction. J Pharm Biomed Anal 1993; 11: 211-215.
[6]	Tang DQ, Wei YQ, Gao YY, Yin XX. Protective effects of rutin on rat glomerular mesangial cells cultured in high glucose conditions. Phytother Res 2011; 25: 1640–1647.
[7]	Wu CH, Lin MC, Wang HC, Yang MY, Jou MJ, Wang CJ. Rutin inhibits oleic acid induced lipid accumulation via reducing lipogenesis and oxidative stress in hepatocarcinoma cells. J Food Sci 2011; 76: 65-72.
[8]	Chen S, Gong J, Liu F, Mohammed U. Naturally occurring polyphenolic antioxidants modulate IgE-mediated mast cell activation. Immunology 2000; 100: 471-480.
[9]	Lee S, Suh S, Kim S. Protective effects of the green tea polyphenol (-)-epigallocatechin gallate against hippocampal neuronal damage after transient global ischemia in gerbils. Neurosci Lett 2000; 287: 191-194.
[10]	Novakovic A, Gojkovic-Bukarica L, Peric M, Nezic D, Djukanovic B, Markovic-Lipkovski J. The mechanism of endothelium-independent relaxation induced by the wine polyphenol resveratrol in the human internal mammary artery. J Pharmacol Sci 2006; 101: 85–90.
[11]	Kittal RR, McKinnon RA, Sorich MJ. Comparison data stes for benchmarking QSAR methodologies in lead optimization. J Chem Inf Model 2009:49:1810-20.
[12]	Ashok K, Sivakumari K. In silico docking of fucoidan compound against the selective proteins of HepG-2 cell line. IJCPS 2015 6(4): 13-16.
[13]	Manimaran M, Sivakumari K, Ashok K. Molecular docking studies of 16.Reseveratrol against the human oral cancer cell line proteins (KB cells). Int J Curr Adv Res 2015 4(10): 275-280.
[14]	Muthukala B, Sivakumari K, Ashok K. In silico docking of Qucertin compound against the HeLa cell line proteins. Int J Curr Pharma Res 2015: 13-16.
[15]	Rajesh S, Sivakumari K, Ashok K. In silico docking of selected compound from Cardiospermum halicacabum Linn. leaf against human hepatocellular carcinoma (HepG-2) cell line. Int. J. Comp. Bioin. In Silico Model, 2016; 5(2): 780-786.
[16]	Sanghani HV, Ganatra SH, Pande R. Molecular docking studies of potent anticancer agent. J Comput Sci Syst Biol 2015: 5: 012-015.
[17]	Bleicher, KH., Bohm, HJ., Muller, K, Alanine, AI. Hit and lead generation: Beyond high-throughput screening. Nat. Rev. Drug Discov., 2003: 2(5): 369-378.
[18]	DiMasi, JA. Trends in drug development costs. Drug Inform., 1995: 29: 375-380.
[19]	DiMasi, JA., Hansen, RW, Grabowski, HG. The price of innovation: New estimates of drug development costs. J. Health Econ., 2003: 22(2): 151-185.
[20]	Irwin, J., Lorber, DM., McGovern, SL., Wei, B, Shoichet, BK. Molecular docking and drug discovery. Comp. Nanosci. Nanotech., 2002: 2: 50-51.
[21]	Taft, CA., Silva, VB, Silva, CHT. Current topics in computer-aided drug design. J. Pharm Sci., 2008: 97(3):1089-1098.
[22]	Manimaran, M, Sivakumari, S, Ashok, K, Rajesh, S. Evaluation of the in vitro antimicrobial effect of resveratrol on human pathogens. Int. J. Zoology Studies, 2017: 2(5): 123-127.
[23]	Ishizaki, Y., Cheng, L., Mudge, AW, Raff, MC. Programmed cell death by default in embryonic cells, fibroblasts and cancer cells. Mol. Biol. Cell., 1995: 6(11): 1443-1458.
[24]	Weil, M., Jacobson, MD., Coles, HS., Davies, TJ., Gardner, RL., Raff, KD, Raff, MC. Constitutive expression of the machinery for programmed cell death. J. Cell Biol., 1996: 133(5): 1053-1059.
[25]	Minn, AJ., Kettlun, CS., Liang, H., Kelekar, A., Vander Heiden, MG., Chang, BS., Fesik, SW., Fill, M, Thompson, CB. BCL-XL regulates apoptosis by heterodimerization-dependent and -independent mechanisms. EMBOJ., 1999: 18: 632-643.
[26]	Krammer, PH. CD95’s deadly mission in the immune system. Nature, 2000: 407(6805): 789-795.
[27]	Boatright, KM., Renatus, M., Scott, FL., Sperandio, S., Shin, H., Pedersen, IM., Ricci, JE., Edris, WA., Sutherlin, DP, Green, DR. A unified model for apical caspase activation. Mol. Cell., 2003: 11(2): 529-541.
[28]	Kroemer, G., Galluzzi, L, Brenner, C. Mitochondrial membrane permeabilization in cell death. Physiol. Rev., 2007: 87(1): 99-163.
[29]	Di Stasi, A., Tey, SK., Dotti, G., Fujita, Y., Kennedy-Nasser, A., Martinez, C., Straathof, K., Liu, E., Durett, AG, Grilley, B. Inducible apoptosis as a safety switch for adoptive cell therapy. N. Eng. J. Med., 2011: 365(18):1673-1683.
[30]	Singh, AK, McGuirk, JP. Allogeneic stem cell transplantation: A historical and scientific overview. Cancer Res., 2016: 76(22): 6445-6451.
[31]	Falcon, C. AL-Obaidi, M, Di Stasi, A. Exploiting cell death pathways for inducible cell elimination to modulate graft-versus-host-disease. Biomed., 2017: 5(30): 1-15.
[32]	Yang, HL., Chen, CS., Chang, WH., Lu, FJ., Lai, YC, Chen, CC. Growth inhibition and induction of apoptosis in MCF-7 breast cancer cells by Antrodia camphorata. Can. Lett., 2006: 231(2): 215-227.
[33]	Kamesaki, H. Mechanisms involved in chemotherapy-induced apoptosis and their implications in cancer chemotherapy. Int. J. Hematol., 1998: 68(1): 29-43.
[34]	Mittal, RR., McKinnon, RA, Sorich, MJ. Comparison data sets for benchmarking QSAR methodologies in lead optimization. J. Chem. Inf. Model, 2009: 49(7): 1810-1820.
[35]	Sliwoski, G., Kothiwale, S., Meiler, J, Lowe, EW. Jr. Computational methods in drug discovery. Pharmacol. Rev., 2014: 66(1): 334-395.
[36]	Jazayeri, A., Dias, JM, Marshall, FH. From G protein-coupled receptor structure resolution to rational drug design. J. Biol. Chem., 2015: 290(32): 19489-19495.
[37]	Alvarez Dorta D, Sivignon A, Chalopin, T. The antiadhesive strategy in crohn’s disease: Orally active mannosides to decolonize pathogenic E. coli from the gut. Chem. Biochem., 2016: 17(10): 936-952.
[38]	Singh, R., Singh, S, Nath Pandey, P. In silico analysis of Sirt2 from Schistosoma monsoni: Structures, conformations and interactions with inhibitors. J. Biomol. Stru. Dyn., 2016: 34(5): 1042-1051.
[39]	Thangaraj, K., Karthiga A., Shanmugam, KR., Ravi, C., Sanjeev, K, Manju V. In silico molecular docking analysis of orientin, a potent glycoside of luteolin against BCL-2 family proteins. J. Chem. Pharma. Res., 2017: 9(5): 65-72.
[40]	Singh, P, Bast, F. In silico molecular docking study of natural compounds on wild and mutated epidermal growth factor receptor. Med. Chem. Res., 2014: 23(12): 5074-5085.