tetano
Editor, Senior Moderator
ChemMedChem
. 2024 Mar 8:e202400095.
doi: 10.1002/cmdc.202400095. Online ahead of print. Identification of Potential inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations
Giorgio Di Paco[SUP] 1 [/SUP], Marina Macchiagodena[SUP] 2 [/SUP], Piero Procacci[SUP] 3 [/SUP]
Affiliations
We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing by ATP hydrolysis the unwinding of double or single-stranded RNA in the viral replication process inside the host cell. The druggable sites for broad-spectrum inhibitors are represented by the RNA binding sites at the 5' entrance and 3' exit of the central channel, a structural motif that is highly conserved across coronaviruses. Potential binders were first generated using structure-based ligand techniques. Their potency was assessed by using four popular docking scoring functions. Common docking hits for NSP13 were finally tested using advanced nonequilibrium alchemical techniques for binding free energy calculations on a high-performing parallel cluster. Four potential NSP13 inhibitors with potency from submicrimolar to nanomolar were finally identified.
Keywords: Drug discovery; NSP13 Helicase inhibitors; Nonequilibrium Alchemical simulations; SARS-CoV-2; molecular dynamics.
. 2024 Mar 8:e202400095.
doi: 10.1002/cmdc.202400095. Online ahead of print. Identification of Potential inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations
Giorgio Di Paco[SUP] 1 [/SUP], Marina Macchiagodena[SUP] 2 [/SUP], Piero Procacci[SUP] 3 [/SUP]
Affiliations
- PMID: 38456332
- DOI: 10.1002/cmdc.202400095
We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing by ATP hydrolysis the unwinding of double or single-stranded RNA in the viral replication process inside the host cell. The druggable sites for broad-spectrum inhibitors are represented by the RNA binding sites at the 5' entrance and 3' exit of the central channel, a structural motif that is highly conserved across coronaviruses. Potential binders were first generated using structure-based ligand techniques. Their potency was assessed by using four popular docking scoring functions. Common docking hits for NSP13 were finally tested using advanced nonequilibrium alchemical techniques for binding free energy calculations on a high-performing parallel cluster. Four potential NSP13 inhibitors with potency from submicrimolar to nanomolar were finally identified.
Keywords: Drug discovery; NSP13 Helicase inhibitors; Nonequilibrium Alchemical simulations; SARS-CoV-2; molecular dynamics.