1. Multi-stage structure-based virtual screening approach towards identification of potential SARS-CoV-2 NSP13 helicase inhibitors
- Author
-
Mahmoud A. El Hassab, Wagdy M. Eldehna, Sara T. Al-Rashood, Amal Alharbi, Razan O. Eskandrani, Hamad M. Alkahtani, Eslam B. Elkaeed, and Sahar M. Abou-Seri
- Subjects
Pharmacology ,sars cov-2 nsp13 helicase ,SARS-CoV-2 ,protein-ligand interaction fingerprint ,COVID-19 ,Quantitative Structure-Activity Relationship ,structure-based pharmacophore ,General Medicine ,molecular dynamics simulations ,RM1-950 ,Molecular Dynamics Simulation ,Viral Nonstructural Proteins ,Ligands ,High-Throughput Screening Assays ,COVID-19 Drug Treatment ,Molecular Docking Simulation ,Catalytic Domain ,Exoribonucleases ,Drug Discovery ,docking ,Humans ,Therapeutics. Pharmacology ,Research Article ,Research Paper - Abstract
On account of its crucial role in the virus life cycle, SARS-COV-2 NSP13 helicase enzyme was exploited as a promising target to identify a novel potential inhibitor using multi-stage structure-based drug discovery approaches. Firstly, a 3D pharmacophore was generated based on the collected data from a protein-ligand interaction fingerprint (PLIF) study using key interactions between co-crystallised fragments and the NSP13 helicase active site. The ZINC database was screened through the generated 3D-pharmacophore retrieving 13 potential hits. All the retrieved hits exceeded the benchmark score of the co-crystallised fragments at the molecular docking step and the best five-hit compounds were selected for further analysis. Finally, a combination between molecular dynamics simulations and MM-PBSA based binding free energy calculations was conducted on the best hit (compound FWM-1) bound to NSP13 helicase enzyme, which identified FWM-1 as a potential potent NSP13 helicase inhibitor with binding free energy equals −328.6 ± 9.2 kcal/mol., Graphical Abstract
- Published
- 2022