The Role of Molecular Modeling and Bioinformatics in Treating a Pandemic Disease: The Case of COVID-19
Abdallah S. Abdelsattar1, 2, Zahraa M. El-Awadly3, Mai Abdelgawad4, Fayrouz Mahmoud3, Sahar A. Allam5, Mohamed A. Helal3, 6, *
Identifiers and Pagination:Year: 2021
First Page: 216
Last Page: 234
Publisher Id: TOCOVIDJ-1-216
Article History:Received Date: 09/3/2021
Revision Received Date: 28/7/2021
Acceptance Date: 25/8/2021
Electronic publication date: 23/12/2021
Collection year: 2021
open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The COVID-19 pandemic first appeared in Wuhan, China, in December 2019 in a cluster of pneumonia patients. The causative agent was found to be SARS-CoV-2. Here, we are summarizing current treatment strategies and highlighting the role of bioinformatics, molecular modeling, and structural biology during the COVID-19 pandemic. There are different pharmacological treatments, mostly repurposed drugs, employed for the treatment of COVID-19, including antiviral drugs, corticosteroids, biologic drugs, antibiotics, antifungal agents, and anticoagulants. Some immune-based therapies are also under evaluation, including convalescent plasma, IL-1, IL-6 inhibitors, and interferons. Different bioinformatics networks are established to provide information about the structure, transcriptome, and pathogenicity of the virus. The genotyping analysis for SARS-CoV-2 is also useful in identifying different mutations, SNPs, and conservative domains along the viral genome. Cryo-EM and X-ray diffraction had a crucial role in determining the structure of viral proteins such as spike (S) protein, main protease, and RdRp. NMR had a minor role and determining the structure of nucleocapsid (N) protein only. Several docking studies were performed to predict the interaction of certain FDA-approved drugs with known efficacy and toxicity, while others used natural products. Among different study types, in silico drug prediction and repurposing have the lowest risk with less off-target results. Therefore, bioinformatics and in silico studies have an important role during pandemics in providing information about viral structure and function and predicting potential treatments.