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Open AccessArticle

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

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
Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-0006, Japan
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
Research Workgroup, Ronin Institute, 127 Haddon Place, Montclair, NJ 07043-2314, USA
7
Department of Computer Science, Faculty of Engineering Information and Systems, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
8
Tsukuba Life Science Innovation Program (TLSI), University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
9
Department of Biomedical Engineering, Chung Yuan Christian University, 200, Chung Pei Road, Taoyuan City 32023, Taiwan
10
AIST-INDIA DAILAB, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Antibodies 2021, 10(1), 3; https://doi.org/10.3390/antib10010003
Received: 10 November 2020 / Revised: 28 November 2020 / Accepted: 6 January 2021 / Published: 11 January 2021
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. View Full-Text
Keywords: COVID-19/SARS-CoV-2/coronavirus 2; lower respiratory tract diseases; Spike protein; RdRp; hypoxia COVID-19/SARS-CoV-2/coronavirus 2; lower respiratory tract diseases; Spike protein; RdRp; hypoxia
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MDPI and ACS Style

Agrawal, L.; Poullikkas, T.; Eisenhower, S.; Monsanto, C.; Bakku, R.K.; Chen, M.-H.; Kalra, R.S. Viroinformatics-Based Analysis of SARS-CoV-2 Core Proteins for Potential Therapeutic Targets. Antibodies 2021, 10, 3. https://doi.org/10.3390/antib10010003

AMA Style

Agrawal L, Poullikkas T, Eisenhower S, Monsanto C, Bakku RK, Chen M-H, Kalra RS. Viroinformatics-Based Analysis of SARS-CoV-2 Core Proteins for Potential Therapeutic Targets. Antibodies. 2021; 10(1):3. https://doi.org/10.3390/antib10010003

Chicago/Turabian Style

Agrawal, Lokesh; Poullikkas, Thanasis; Eisenhower, Scott; Monsanto, Carlo; Bakku, Ranjith K.; Chen, Min-Hua; Kalra, Rajkumar S. 2021. "Viroinformatics-Based Analysis of SARS-CoV-2 Core Proteins for Potential Therapeutic Targets" Antibodies 10, no. 1: 3. https://doi.org/10.3390/antib10010003

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