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Viroinformatics-Based Analysis of SARS-CoV-2 Core Proteins for Potential Therapeutic Targets

Authors
  • Agrawal, Lokesh1, 2
  • Poullikkas, Thanasis3, 4
  • Eisenhower, Scott3, 5
  • Monsanto, Carlo
  • Bakku, Ranjith Kumar6
  • Chen, Min-Hua
  • Kalra, Rajkumar Singh7
  • 1 Universidad Integral del Caribe y América Latina, Kaminda Cas Grandi #79, Willemstad, Curacao
  • 2 Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
  • 3 (S.E.)
  • 4 Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, 2-1-1 Tennodai, Tsukuba 305-8576, Japan
  • 5 Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
  • 6 Tsukuba Life Science Innovation Program (TLSI), University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
  • 7 AIST-INDIA DAILAB, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
Type
Published Article
Journal
Antibodies
Publisher
MDPI
Publication Date
Jan 11, 2021
Volume
10
Issue
1
Identifiers
DOI: 10.3390/antib10010003
PMID: 33440681
PMCID: PMC7839017
Source
PubMed Central
Keywords
License
Green

Abstract

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus for which no known effective antiviral drugs are available. In the present study, to accelerate the discovery of potential drug candidates, bioinformatics-based in silico drug discovery approaches are utilized. We performed multiple sequence alignments of the Spike (S) protein with 75 sequences of different viruses from the Orthocoronavirinae subfamily. This provided us with insights into the evolutionarily conserved domains that can be targeted using drugs or specific antibodies. Further, we analyzed the mechanism of SARS-CoV-2 core proteins, i.e., S and RdRp (RNA-dependent RNA polymerase), to elucidate how the virus infection can utilize hemoglobin to decrease the blood oxygen level. Moreover, after a comprehensive literature survey, more than 60 antiviral drugs were chosen. The candidate drugs were then ranked based on their potential to interact with the Spike and RdRp proteins of SARS-CoV-2. The present multidimensional study further advances our understanding of the novel viral molecular targets and potential of computational approaches for therapeutic assessments. The present study can be a steppingstone in the selection of potential drug candidates to be used either as a treatment or as a reference point when designing a new drug/antibody/inhibitory peptide/vaccine against SARS-CoV-2.

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