Indian journal of Medical Biochemistry

Register      Login

VOLUME 24 , ISSUE 3 ( September-December, 2020 ) > List of Articles

SHORT COMMUNICATION

Ligand-based Drug Design Approach in Designing New Leads from Existing Pharmacophores; Binding Pocket Estimation and Binding Pocket-directed Screening of Antiviral Drugs for Treatment of Novel Corona COVID-19 and Topoisomerase Inhibitors

Dushyanth R Vennapu, Mahesh S Palled

Keywords : Docking, Hits and leads, Homology

Citation Information : Vennapu DR, Palled MS. Ligand-based Drug Design Approach in Designing New Leads from Existing Pharmacophores; Binding Pocket Estimation and Binding Pocket-directed Screening of Antiviral Drugs for Treatment of Novel Corona COVID-19 and Topoisomerase Inhibitors. Indian J Med Biochem 2020; 24 (3):143-148.

DOI: 10.5005/jp-journals-10054-0160

License: CC BY-NC 4.0

Published Online: 00-12-2020

Copyright Statement:  Copyright © 2020; Jaypee Brothers Medical Publishers (P) Ltd.


Abstract

Using the homology modeling-derived protein structure, and literature-reported cases of the treatment of coronavirus by chloroquine and remdesivir. ICMR guidelines for the usage of a low toxic metabolite of chloroquine hydroxychloroquine as prophylactic medication for healthcare professionals as preventive measures for those who treat corona patients. Further, Japanese flu drug favipiravir in treatment is efficient in the treatment of corona. The protein model suggested by I-TASSER was used in docking; the active site of the protein was predicted using similarity search and the potential leads are screened for their efficiency in combating corona outbreak from epidemic to pandemic.


PDF Share
  1. Paraskevis D, Kostaki EG, Magiorkinis G, et al. Full-genome evolutionary analysis of the novel corona virus (2019-NCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infect Genet Evol 2020;79:104212. DOI: 10.1016/j.meegid.2020.104212.
  2. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin | bioRxiv https://www.biorxiv.org/content/10.1101/2020.01.22.914952v2 (accessed Apr 20, 2021).
  3. Zhou N, Pan T, Zhang J, et al. Glycopeptide antibiotics potently inhibit Cathepsin L in the late endosome/lysosome and block the entry of Ebola virus, middle east respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus (SARS-CoV). J Biolog Chem 2016. 9218–9232. DOI: 10.1074/jbc.M116.716100.
  4. Gordon CJ, Tchesnokov EP, Feng JY, et al. The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from MERS corona virus. J Biolog Chem 2020;295(15):4773–4779. DOI: 10.1074/jbc.AC120.013056.
  5. Wang M, Cao R, Zhang L, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res 2020;30:269–271. DOI: 10.1038/s41422-020-0282-0.
  6. Cheng VCC, Lau SKP, Woo PCY, et al. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Yuen Clin Microbiol Rev 2007;20(4):660–694.
  7. Wu C, Liu Y, Yang Y, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B 2020;10(5):766–788. DOI: 10.1016/j.apsb.2020.02.008.
  8. Joshi G, Amrutkar SM, Baviskar AT, et al. Synthesis and biological evaluation of new 2, 5 dimethylthiophene/furan based N-acetyl pyrazolines as selective topoisomerase II inhibitors Darpan. RSC Adv. 2016;6:14880–14892.
  9. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Proto 2010;5:725–738. DOI: 10.1038/nprot.2010.5.
  10. Yang J, Yan R, Roy A, et al. The I-TASSER suite: protein structure and function prediction. Nat Metho 2015;12:7–8. DOI: 10.1038/nmeth.3213.
  11. Yang J, Zhang Y. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 2015;43:W174–W181.
  12. Lagorce D, Sperandio O, Galons H, et al. FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinformatics 2008;9:396. DOI: 10.1186/1471-2105-9-396.
  13. Katariya KD, Shah SR, Reddy D. Anticancer, antimicrobial activities of quinoline based hydrazone analogues: synthesis, characterization and molecular docking. Bioorga Chem 2020;94:103406. DOI: 10.1016/j.bioorg.2019.103406ISSN 0045-2068.
PDF Share

© Jaypee Brothers Medical Publishers (P) LTD.