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In Silico Molecular Docking of Vanillic Acid Against Apoptotic Proteins

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In Silico Molecular Docking of Vanillic Acid Against Apoptotic Proteins Mukt Shabd Journal ISSN NO : 2347-3150 IN SILICO MOLECULAR DOCKING OF VANILLIC ACID AGAINST APOPTOTIC PROTEINS Senthil. J, Janaki Devi. V1, Padma Priya. V1 Ashok. K* and Babu. M*, *1Department of Microbiology and Biotechnology, Faculty of Arts and Science, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India ABSTRACT The present molecular docking study can be useful for the design and development of novel compound having better inhibitory activity against apoptotic proteins (Caspase-3 and Caspase-9). The docking scores were highest for Caspase-9 with 36.471 kcal/mol with the stronger interaction followed by Caspase-3 (36.9 kcal/mol) and the LogP, lower hydrogen bond counts, confirming the capability of the vanillic acid for binding at the active site of the receptor. The results clearly show that the molecular docking mechanism used to detect the novel anticancer inhibitor has been successfully obtained from a natural polyphenolic compound. Keywords: Vanillic acid, Discovery Studio, Caspase-3 and Caspase-9 INTRODUCTION Vanillic acid (4-hydroxy-3-methoxybenzoic acid) (VA) is a polyphenolic dihydroxybenzoic acid compound produced by secondary metabolism in plants and is widely used in the food industry as a flavoring, food additive and preservative and in pharmaceutical industries as analeptic drug (etamivan) (Fig. 1A and B). The pleasant vanilla scent is due to the molecular structure corresponding to the oxidative form of vanillin aldehyde (vanilla). VA can be found in many foods, including rice, wheat, mango, strawberries, sugar cane, herbs and spices, beer, wine, tea and juices [1-30]. Volume IX, Issue V, MAY/2020 Page No : 5267 Mukt Shabd Journal ISSN NO : 2347-3150 Fig. 1: Vanillic acid A- 2D structure and B-3D structure Taking together, these findings suggest that vanillic acid has beneficial properties such as antimicrobial, hepatotoxicity, antioxidant, cardiovascular disease, hemorheological effects, neuroprotective effects and antihypertensive [31-36]. The objective of the study is to identify that apoptotic proteins fit to the domain and active sites, to assess the chemical and physical properties of the protein, to analyze the potentiality of the therapeutic agents in terms of their properties, to perform Docking of the proteins with a compound vanillin acid and to evaluate the compound docking and active site binding. MATERIALS AND METHODS Preparation of protein structure Apoptotic protein structures of Caspase-3 (Fig. 2 and 3) and Caspase-9 (Fig. 4 and 5) were obtained from RCSB Protein Data Bank (http: //www. pdb. org). All water molecules were removed and on the final stage hydrogen atoms were added to the target protein molecule. Caspase-3 (PDB ID 2DKO.A) Gene: CASP3 Organism: Homo sapiens (Human) BLAST sequence >sp|P42574|10-28 Volume IX, Issue V, MAY/2020 Page No : 5268 Mukt Shabd Journal ISSN NO : 2347-3150 SKSIKNLEPKIIHGSESMD FASTA sequence >3KJF:B|PDBID|CHAIN|SEQUENCE SGVDDDMACHKIPVDADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKL EFMHILTRVNRKVATEFESFSFDAT FHAKKQIPCIVSMLTKELYFYHHHHHHHH Fig. 2: 3D structure of Caspase-3 Fig. 3: Caspase-3 protein sequence chain view Volume IX, Issue V, MAY/2020 Page No : 5269 Mukt Shabd Journal ISSN NO : 2347-3150 Caspase-9 (PDB ID 2AR9) Gene: CASP9 Organism: Homo sapiens (Human) BLAST sequence >sp|P55211|1-92 MDEADRRLLRRCRLRLVEELQVDQLWDALLSRELFRPHMIEDIQRAGSGSRRDQAR QLII DLETRGSQALPLFISCLEDTGQDMLASFLRTN FASTA sequence >2AR9:A|PDBID|CHAIN|SEQUENCE MGALESLRGNADLAYILSMEPCGHCLIINNVNFCRESGLRTRTGSNIDCEKLRRRFSS LHFMVEVKGDLTAKKMVLALLE LARQDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSVEKIVNIFNGTSCPSL GGKPKLFFIQASGGEQKDHGFEV ASTSPEDESPGSNPEPDATPFQEGLRTFDQLDAISSLPTPSDIFVSYSTFPGFVSWRDPK SGSWYVETLDDIFEQWAHSE DLQSLLLRVANAVSVKGIYKQMPCIVSMLRKKLFFKTS Fig. 4: 3D structure of Caspase-9 Volume IX, Issue V, MAY/2020 Page No : 5270 Mukt Shabd Journal ISSN NO : 2347-3150 Fig. 5: Caspase-9 protein sequence chain view Preparation of ligand structure ChemSketch, chemically intelligent drawing interface freeware developed by Advanced Chemistry Development, Inc., (http: //www. acdlabs. com). Volume IX, Issue V, MAY/2020 Page No : 5271 Mukt Shabd Journal ISSN NO : 2347-3150 Physical and chemical properties of ligand were retrieved from https://pubchem.ncbi.nlm.nih.gov/compound/8468. The key results in a (Discovery Studio) docking log are the docked structures found at the end of each run, the energies of these docked structures and their similarities to each other. RESULTS AND DISCUSSION Fig. 6: Pharmacore model of vanillin acid against apoptotic proteins Volume IX, Issue V, MAY/2020 Page No : 5272 Mukt Shabd Journal ISSN NO : 2347-3150 Fig. 7: Docked complex of vanillin against Caspase-3 Fig. 8: Docked complex of vanillin against Caspase-9 Table 1: Docking score of vanillin acid against apoptotic proteins Name of the protein Ligand Lib docking score H-B KCal/mol Caspase-3 36.9 4 Caspase-9 Vanillin acid 36.471 3 To study the binding mode of Vanillin acid interaction with apoptotic protein, intermolecular flexible docking simulations were performed and. Energy values were calculated from the docked conformations of the protein‐inhibitor complexes. Docking studies yielded crucial information concerning the orientation of the inhibitors in the binding pocket of the target protein. Several potential inhibitors have been identified through the docking simulation. The binding affinity of the apoptotic proteins with the Vanillin acid was measured by kcal/mol. The docking scores were highest for Caspase-9 with 36.471 kcal/mol with the stronger interaction followed by Caspase-3 (36.9 kcal/mol.) as showed in the table 1 and Fig. 6, 7 and 8 Analysis of ligand binding interaction with the protein can be useful for new preventive and therapeutic drug for cancer. The results obtained from this study would be useful in both understanding the inhibitory mode as well as in rapidly and accurately predicting the activities of new inhibitors on the basis of docking scores. Volume IX, Issue V, MAY/2020 Page No : 5273 Mukt Shabd Journal ISSN NO : 2347-3150 Moreover, the apoptosis induced by the vanillin acid is mitochondrial mediated pathway as shown in the figure 9. Fig. 9: Apoptosis was mediated by mitochondrial pathway For the first time, natural polyphenolic compound (Vanillin acid) is docked with apoptotic proteins, which can bind to the active site of the protein and interfere with its activity, thereby ensuring the anticancer activity of the vanillic acid. The docking study of the results showed that the vanillin acid tested could be bound to the apoptotic proteins. The results clearly show that the molecular docking mechanism used to detect the novel anticancer inhibitor has been successfully obtained from a natural polyphenolic compound. Volume IX, Issue V, MAY/2020 Page No : 5274 Mukt Shabd Journal ISSN NO : 2347-3150 CONCLUSSION In this study, the molecular docking was applied to explore the binding mechanism and to correlate its docking score with the activity of Vanillin acid. The results of our present study can be useful for the design and development of novel compound having better inhibitory activity against several type of cancer. These potential drug candidates can further be validated in wet lab studies for its proper function. REFERENCES 1. Kim SJ, Kim MC, Um JY and Hong SH (2010). The beneficial effect of vanillic acid on ulcerative colitis. Molecules 15: 7208-7217. 2. Kroymann J (2011). Natural diversity and adaptation in plant secondary metabolism. Curr. Opin. Plant Biol. 14: 246-251. 3. Kumar S, Prahalathan P and Raja B (2011). Antihypertensive and antioxidant potential of vanillic acid, a phenolic compound in L-NAME-induced hypertensive rats: a dose- dependence study. Redox Rep. 16: 208-215. 4. Navarro SD, Mauro MO, Pesarini JR, Ogo FM, et al. (2015). Resistant starch: a functional food that prevents DNA damage and chemical carcinogenesis. Genet. Mol. Res. 14: 1679- 1691. 5. Taner G, Özkan Vardar D, Aydin S, Aytaç Z, et al. (2016). Use of in vitro assays to assess the potential cytotoxic, genotoxic and antigenotoxic effects of vanillic and cinnamic acid. Drug Chem. Toxicol. 16: 1-8. 6. Akomolafe SF, Oboh G, Oyeleye SI, Molehin OR, Ogunsuyi OB. Phenolic composition and inhibitory ability of methanolic extract from pumpkin (Cucurbita pepo L.) seeds on Fe- induced thiobarbituric acid reactive species in albino rat’s testicular tissue in-vitro. J Appl Pharm Sci. 2016;6:115-20. 7. Almeida IV, Cavalcante FML, Vicentini VEP. Different responses of vanillic acid, a phenolic compound, in HTC cells: cytotoxicity, antiproliferative activity, and protection from DNA-induced damage. Genet Mol Res. 2016;15:1-12. 8. Muthukala, B., Sivakumari, K. and Ashok, K. (2015). In silico docking of Qucertin compound against the HeLa cell line proteins. Int. J. Curr. Pharm. Res., 7(1):13-16. Volume IX, Issue V, MAY/2020 Page No : 5275 Mukt Shabd Journal ISSN NO : 2347-3150 9. Nethaji, R., Thooyavan, G., Mullai Nilla, K. and Ashok, K. (2015). Phytochemical profiling, antioxidant and antimicrobial activity of methanolic extract in Rambutan fruit (Nephelium lappacium) epicarp against the human pathogens. Int. J Curr. Innovation Res., 1(9): 201-206. 10. Muthukala, B., Sivakumari, K. and Ashok, K. (2015). Antioxidant and anti-inflammatory potential of Qucertin. Int. J. Curr. Pharm. Res., 7(3):1-2. 11. Ashok, K. and Sivakumari, K. (2015). In silico docking of fucoidan compound against the selective proteins of HepG-2 cell line. Int. J. Chem. Pharm. Sci., 6(4): 976-979. 12. Manimaran, M., Sivakumari, K. and Ashok,
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