Jerine Peter S, Nagesh Kishan Panchal, Mary Thomas, Gayathri Ashok, Megha Treesa Saju, Padma Thiagarajan, Evan Prince Sabina
Jerine Peter S, Nagesh Kishan Panchal, Mary Thomas, Gayathri Ashok, Megha Treesa Saju, Padma Thiagarajan, Evan Prince Sabina*
School of Biosciences and Technology, Vellore Institute of Technology, Vellore-632014, India.
Volume - 13,
Issue - 12,
Year - 2020
A large percentage of people in the modern society is vastly affected by the damage in gastrointestinal tract by many non-steroidal anti-inflammatory drugs and by the unfortunate lifestyle. The stomach is mainly affected over here by the local effect and the systemic interactions with the secretion in prostaglandin. In comparing with other organs a very few progress has been brought on human related prediction for intestinal toxicity. Single nucleotide polymorphism or SNP modelling is the main aim of the work to remodel the genes that get mutated in gastrotoxicity so that remodelling those genes can help for better binding of those proteins to the ligands and also for generating information about the proteins function. Computer visualization technique is chiefly used for the modelling purpose by taking the 3D structure of the proteins and by looking the SNP database we changes the mutated nucleotide to another nucleotide and checks the binding affinity. Here the nucleotide changed protein sequence is submitted to I-TASSER they will remodel the protein 3D structure so that the new protein model quality is checked through RAM- PAGE. By these a research new protein model for SNP varients was structured. The docking analysis was carried out with the ligands of Madhuca longifolia and structured protein. Among the 29 ligands MI Saponina, MI Saponin B and quercitin 3 glucoside have shown their maximum interaction in most of the receptors. In future, in-vitro and in-vivo studies can be held to make an effective medicine for gastrotoxicity
Cite this article:
Jerine Peter S, Nagesh Kishan Panchal, Mary Thomas, Gayathri Ashok, Megha Treesa Saju, Padma Thiagarajan, Evan Prince Sabina. Gastrotoxicity gene modelling and its binding affinity of docked complex with the ligands of Madhuca longifolia. Research J. Pharm. and Tech. 2020; 13(12):5799-5805. doi: 10.5958/0974-360X.2020.01011.2
1. Karlebach G, Shamir R. Modelling and analysis of gene regulatory networks. Nature Reviews Molecular Cell Biology. 2008; 9(10): 770-780.
2. Ivanov IV, Qian X, Pal R. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks. IGI Global; 2001. https:// www.igi-global.com/book/emerging-research-analysis-modeling-gene/145652. Accessed October 21, 2019.
3. Wu B, Song H-P, Zhou X, et al. Screening of minor bioactive compounds from herbal medicines by in silico docking and the trace peak exposure methods. Journal of Chromatography. A. 2016;1436: 91-99.
4. Anbarasu K, Mahjabeen A, Mahendran R. Insights on Impact of Missense SNPs of Human USH2A associated with Usher Syndrome II. Research Journal of Pharmacy and Technology. 2017;10(10):3365.
5. Yao S, Sucheston LE, Zhao H, et al. Germline genetic variants in ABCB1, ABCC1 and ALDH1A1, and risk of hematological and gastrointestinal toxicities in a SWOG Phase III trial S0221 for breast cancer. The Pharmacogenomics Journal. 2014;14(3):241-247.
6. Ranjan S, Sharma PK. Association of Brain-Derived Neurotrophic factor (BDNF) gene SNP G196A with Type 2 Diabetes and Obesity: A Meta-Analysis. Research Journal of Pharmacy and Technology. 2017;10(12):4297.
7. Mani A, Ravi L, Krishnan K. Antibacterial and antifungal potential of marine Streptomyces sp. VITAK1 derived novel compound Pyrrolidinyl-Hexadeca-Heptaenone by in Silico docking analysis. Research Journal of Pharmacy and Technology. 2018;11(5):1901.
8. Grupe A, Germer S, Usuka J, et al. In silico mapping of complex disease-related traits in mice. Science (New York, N.Y.). 2001;292(5523):1915-1918.
9. Kumar RS, Kaavya G. Binding Efficiency of Molecules from Medicinal Plants with Fidgetin Like Protein 2-A Novel Target for Diabetic Foot Ulcer. Research Journal of Pharmacy and Technology. 2017;10(11):3757.
10. Sheng T, Lu Y, Yang K, et al. Association Between Single Nucleotide Polymorphisms (SNPs) in the Promoter of Adiponectin Gene, Hypoadiponectinemia, and Diabetes. Research Journal of Science and Technology. 2016;8(1):34.
11. Rainsford KD, Whitehouse MW. Paracetamol [acetaminophen]-induced gastrotoxicity: revealed by induced hyperacidity in combination with acute or chronic inflammation. Inflammopharmacology. 2006;14(3-4):150-154.
12. Rainsford KD. Gastrointestinal and other side-effects from the use of aspirin and related drugs; biochemical studies on the mechanisms of gastrotoxicity. Agents and Actions. Supplements. 1977;(1):59-70.
13. Patil MP, Singh RD, Koli PB, et al. Antibacterial potential of silver nanoparticles synthesized using Madhucalongifolia flower extract as a green resource. Microbial Pathogenesis. 2018; 121:184-189.
14. Singh A, Singh S, Anbarasu A. In silico Evaluation of Non-Synonymous SNPs in IRS-1 gene associated with type II diabetes mellitus. Research Journal of Pharmacy and Technology. 2018;11(5):1957.
15. Annalakshmi R, Mahalakshmi S, Charles A, Sahayam CS. GC–MS and HPTLC analysis of leaf extract of Madhuca longifolia (Koenig) Linn. Drug Invention Today. 2013;5(2):76-80.
16. Govindammal M, Prasath M, Sathya B, Selvapandiyan M. Investigation on the Binding Interaction Between Clomipramine and Doxepin with LeuT by Molecular Docking Analysis. Asian Journal of Research in Chemistry. 2017;10(4):486-490.
17. Sikarwar RLS. Mahua (Madhuca longifolia (Koen.) Macbride) - A paradise tree for the tribals of Madhya Pradesh. In: 2002.
18. Simon JP, Parthasarathy M, Nithyanandham S, Katturaja R, Namachivayam A, Prince SE. Protective effect of the ethanolic and methanolic leaf extracts of Madhuca longifolia against diclofenac-induced toxicity in female Wistar albino rats. Pharmacological Reports. May 2019.
19. Chen Y-C. Beware of docking! Trends in Pharmacological Sciences. 2015;36(2):78-95.
20. Al-Koofee DAF, Mobarak SMH. Primer1: A Network Service for Tetra-Arms PCR Primer Design Based on Well-Known dbSNP. Research Journal of Pharmacy and Technology. 2018;11(8):3633.
21. Mahendran R, Jeyabasker S, Francis A, Manoharan S. Homology Modeling and in silico docking analysis of BDNF in the treatment of Alzheimer’s disease. Research Journal of Pharmacy and Technology. 2017;10(9):2899.
22. Anbarasu K, Jagadeeswari P, Mahendran R. In-silico Screening of Deleterious NF1 SNPs Associated with Neurofibromatosis Type I. Research Journal of Pharmacy and Technology. 2017;10(9):3247.
23. Sudha R, Devi PB, Nithya G. Docking Analysis of various synthesised Benzilic acid derivatives towards Sirutin protein and toxicity studies. Research Journal of Pharmacy and Technology. 2019;12(7):3277.