1. Screening of Severe Acute Respiratory Syndrome Coronavirus 2 RNA-Dependent RNA Polymerase Inhibitors Using Computational Approach
- Author
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Vikram Dalal, Viney Kumar, and Poonam Dhankhar
- Subjects
Drug ,Protein Conformation ,viruses ,media_common.quotation_subject ,Amino Acid Motifs ,Drug Evaluation, Preclinical ,RNA-dependent RNA polymerase ,Molecular Dynamics Simulation ,Molecular mechanics ,Antiviral Agents ,Small Molecule Libraries ,chemistry.chemical_compound ,Computational Chemistry ,RNA polymerase ,Catalytic Domain ,Drug Discovery ,Genetics ,Amino Acid Sequence ,Molecular Biology ,Pandemics ,Research Articles ,media_common ,Coronavirus RNA-Dependent RNA Polymerase ,biology ,Molecular Structure ,Sequence Homology, Amino Acid ,Chemistry ,SARS-CoV-2 ,Active site ,Small molecule ,Virology ,In vitro ,COVID-19 Drug Treatment ,Molecular Docking Simulation ,Computational Mathematics ,Computational Theory and Mathematics ,Drug development ,Modeling and Simulation ,biology.protein ,Sequence Alignment ,Databases, Chemical ,Protein Binding - Abstract
The detrimental effect of coronavirus disease 2019 (COVID-19) pandemic has manifested itself as a global crisis. Currently, no specific treatment options are available for COVID-19, so therapeutic interventions to tackle the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection must be urgently established. Therefore, cohesive and multidimensional efforts are required to identify new therapies or investigate the efficacy of small molecules and existing drugs against SARS-CoV-2. Since the RNA-dependent RNA Polymerase (RdRP) of SARS-CoV-2 is a promising therapeutic target, this study addresses the identification of antiviral molecules that can specifically target SARS-CoV-2 RdRP. The computational approach of drug development was used to screen the antiviral molecules from two antiviral libraries (Life Chemicals [LC] and ASINEX) against RdRP. Here, we report six antiviral molecules (F3407-4105, F6523-2250, F6559-0746 from LC and BDG 33693278, BDG 33693315, LAS 34156196 from ASINEX), which show substantial interactions with key amino acid residues of the active site of SARS-CoV-2 RdRP and exhibit higher binding affinity (>7.5 kcalmol(−1)) than Galidesivir, an Food and Drug Administration-approved inhibitor of the same. Further, molecular dynamics simulation and Molecular Mechanics Poisson-Boltzmann Surface Area results confirmed that identified molecules with RdRP formed higher stable RdRP-inhibitor(s) complex than RdRP-Galidesvir complex. Our findings suggest that these molecules could be potential inhibitors of SARS-CoV-2 RdRP. However, further in vitro and preclinical experiments would be required to validate these potential inhibitors of SARS-CoV-2 protein.
- Published
- 2021