Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations

PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files

We present PDBrestore, a free web interface for repairing protein PDB chains extracted from either a local PDB file or a PDB file downloaded from the Protein Data Bank. PDBrestore performs several key tasks: It adds hydrogen atoms, completes missing atoms in side chains, fills gaps in the sequence, derives the itp parameter file for a ligand according to the GAFF2 force field for GROMACS applications, and generates a reasonably pre-equilibrated solvated simulation box. The interface is designed to streamline the cumbersome preparatory work required to set up an initial protein-ligand coordinates PDB file for use in drug design projects, such as free energy perturbation or thermodynamic integration calculations of ligand binding affinities. Additionally, PDBrestore is available as a command-line application within the open-source ORAC distribution, which can be freely downloaded from the website: www1.chim.unifi.it/orac.

Analogs of NIH Molecular Probe ML283 Are Potent SARS-CoV-2 Helicase Inhibitors

The National Institutes of Health molecular probe ML283 was synthesized as a potent, selective inhibitor of the helicase encoded by the hepatitis C virus. Because modeling with AutoDock Vina predicted that ML283 might bind the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nonstructural protein 13 (nsp13) helicase, the effects of a collection of ML283 analogs and other hepatitis C virus (HCV) helicase inhibitors on the SARS-CoV-2 helicase were analyzed. Only modest impacts on nsp13-catalyzed ATP hydrolyses were observed with some compounds, most of which were analogs of the drug ebselen, not ML283. In contrast, a new molecular-beacon-based helicase assay revealed that ML283 and many ML283 analogs are potent SARS-CoV-2 helicase inhibitors. Analog potencies correlate with the binding energies predicted by modeling, which suggests that a pocket surrounded by the carboxy-terminal nsp13 RecA-like helicase motor domain might be exploitable for antiviral drug development.

Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations

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 estimated 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.