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].

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5267

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

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5268

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

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5269

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

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5270

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).

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5271

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

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5272

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

KCal/mol

H-B

Caspase-3

Vanillin acid

36.9 4

Caspase-9 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.

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5273

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.

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5274

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.

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5275

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, K. (2015). Molecular docking studies of

resveratrol against the human oral cancer cell line proteins (KB cells). Int. J. Curr. Adv. Res.,

4: 2319-2325.

13. Manimekalai, I., Sivakumari, K., Ashok, K. and Rajesh, S. (2016a). Phytochemical

profiling of mangosteen fruit, Garcinia mangostana. World. J. Pharm. Sci., 5(2): 221-252.

14. Manimekalai, I., Sivakumari, K., Ashok, K. and Rajesh, S. (2016b). Antioxiodant and

anticancer potential of mangosteen fruit, Garcinia mangostana against hepatocellular

carcinoma (HepG-2) cell line. World. J. Pharm. Sci., 5(2): 253-293.

15. Saranya, A., Sivakumari, K., Ashok, K. and Rajesh, S. (2017). Phytochemical profiling

and anticancer study of lyophilized pure fruit juice of Citrus limon (L.) Osbeck against

human breast cancer (MCF-7) cell line. J Adv. Mol. Bio., 1(2): 91-103.

16. Manimaran, M., Sivakumari, K., Ashok, K. and Rajesh, S. (2017). Evaluation of the in

vitro antimicrobial effect of resveratrol on human pathogens. Int. J. Zoological Studies. 2(5):

123-127.

17. Ashok, K., Sivakumari, K. and Rajesh, S. (2018). Achyranthes aspera mediated green

synthesis of silver nanoparticles. AJPS., 5(1): 64-73.

18. Jayameena, P., Sivakumari, K., Ashok, K. and Rajesh, S. (2018). 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). J.

Cancer Research and Treatment. 6(2): 28-33.

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5276

19. Karthika, S., Sivakumari, K., Rajesh S., Ashok, K. and Shyamala Devi K. (2018). In

silico molecular prediction of ascorbic acid, betalain and gallic acid from Hylocereus undatus

against apoptotic proteins (caspase-3, caspase-9 and β -actin). J. Pharm. Sci. Innov., 7(6):

215-220.

20. Rajini Selvaraj, Sivakumari, K., Flora Priyadarshini, J., Ashok, K. Jayaprakash, P. and

Rajesh, S. (2018). Phytochemical profiling and antibacterial activity of propolis. Int. J. Sci.

Res., 7(6):373-376.

21. Flora Priyadarshini, J., Sivakumari, K., Rajini Selvaraj, Ashok, K. Jayaprakash, P. and

Rajesh, S. (2018). Phytochemical profiling of crude propolis collected from beehives. Int. J.

Sci. Res., 7(6):370-372.

22. Jayameena, P., Sivakumari, K., Ashok, K. and Rajesh, S. (2018). In vitro anti-

inflammatory (membrane stabilization) and antioxidant potential of Rutin. Res. J. Lifesci.

Bioinfo. Pharma. ChemSci., 4(3): 265-274.

23. Flora Priyadarshini, J., Sivakumari, K., Ashok, K. Jayaprakash, P. and Rajesh, S. (2018).

GC-MS analysis for identification of active compounds in propolis and molecular docking

studies of selected compounds against apoptoic proteins (Caspase-3, Caspase-9 and β-Actin).

J. Biol. Chem. Research. 35(2): 349-358.

24. Flora Priyadarshini, J., Sivakumari, K., Ashok, K. Jayaprakash, P. and Rajesh, S. (2018).

GC-MS analysis for identification of active compounds in propolis and molecular docking

studies of selected compounds against chronic hepatitis B protein (Large envelop protein). J.

Biol. Chem. Research. 35(2): 409-417.

25. Jayaprakash, P., Sivakumari, K., Ashok, K. and Rajesh, S. (2018). In Silico Molecular

Docking of Alginic acid and Fucoidan compound present in S. wightii against Apoptotic

Proteins (Caspase-3, Caspase-9 and β-Actin). IJBPAS., 7(8): 1551-1565.

26. Karthika, S., Sivakumari, K., Rajesh S., Ashok K. and Shyamala Devi, K. (2018). In

Silico Molecular Prediction of Ascorbic acid, Betalain and Gallic acid from Hylocerus

undatus against apoptotic proteins (Caspase-3, Caspase-9 and β-Actin). J. Pharma. Sci.

Innov., 7(6): 215-220.

27. Sivakumar, P., Manimekalai, I., Sivakumari, K. and Ashok, K. (2019). Phytochemical

profiling of Fig fruit (Ficus Racemosa) extracts. IJRAR. 6(1): 784-822.

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5277

28. Sivakumar, P., Manimekalai, I., Sivakumari, K. and Ashok, K. (2019). Anticancer effect

of Fig fruit (Ficus Racemosa) extract against Human Hepatocellular Carcinoma (HepG-2)

cell line. IJRAR. 6(1): 767-783.

29. Rajini Selvaraj., Sivakumari, K., Rajesh, S. and Ashok, K. (2020). Molecular Docking

interaction of Propolis with Caspase-3, Caspase-9, BAX, BCL-2 AND BCL-XL. IJRAR.,

7(2): 33-38.

30. Banerjee S, Ranganathan V, Patti A, Arora A (2018) Valorisation of pineapple wastes for

food and therapeutic applications. Trends Food Sci Technol 82:60–70.

31. Xu, Y.; Shi, C.; Wu, Q.; Zheng, Z.; Liu, P.; Li, G.; Peng, X.; Xia, X. Antimicrobial

activity of punicalagin against Staphylococcus aureus and its effect on biofilm formation.

Foodborne Pathog. Dis. 2017, 14, 282.

32. Choi, H.A.; Cheong, D.E.; Lim, H.D.; Kim, W.H.; Ham, M.H.; Oh, M.H.; Wu, Y.; Shin,

H.J.; Kim, G.J.Antimicrobial and anti-biofilm activities of the methanol extracts of medicinal

plants against dental pathogens Streptococcus mutans and Candida albicans. J. Microbiol.

Biotechnol. 2017, 27, 1242–1248.

33. Lu, L.; Hu, W.; Tian, Z.R.; Yuan, D.D.; Yi, G.J.; Zhou, Y.Y.; Cheng, Q.; Zhu, J.; Li,

M.X. Developing natural products as potential anti-biofilm agents. Chin. Med. 2019, 14, 11.

34. Raja B, Deepa Mol S. The protective role of vanillic acid against acetaminophen induced

hepatotoxicity in rats. J Pharm Res 2010;3:1480–4.

35. Getz GS, Reardon CA. Nutrition and cardiovascular disease. Arterioscler Thromb Vasc

Biol 2007;27:2499–506.

36. Szwajgier D, Borowiec K, Pustelniak K (2017) The neuroprotective effects of phenolic

acids: molecular mechanism of action. Nutrients 9:477

Mukt Shabd Journal

Volume IX, Issue V, MAY/2020

ISSN NO : 2347-3150

Page No : 5278