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J Chem Theory Comput ; 16(11): 7160-7172, 2020 Nov 10.
Article in English | MEDLINE | ID: covidwho-889116


In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CLpro) of SARS-CoV-2. The core structures of 3CLpro ligands were previously identified using a multimodal structure-based ligand design in combination with docking techniques. The calculated binding free energies for four additional ligands with known activity (either for SARS-CoV or SARS-CoV-2 main protease) are also reported. The nature of binding in the 3CLpro active site and the involved residues besides the CYS-HYS catalytic dyad have been thoroughly characterized by enhanced sampling simulations of the bound state. We have identified several noncongeneric compounds with predicted low micromolar activity for 3CLpro inhibition, which may constitute possible lead compounds for the development of antiviral agents in Covid-19 treatment.

Betacoronavirus/enzymology , Cysteine Endopeptidases/metabolism , Viral Nonstructural Proteins/metabolism , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19 , Coronavirus 3C Proteases , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Humans , Ligands , Molecular Docking Simulation , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protease Inhibitors/pharmacology , Protease Inhibitors/therapeutic use , Protein Binding , SARS-CoV-2 , User-Computer Interface , Viral Nonstructural Proteins/antagonists & inhibitors
Chem Commun (Camb) ; 56(62): 8854-8856, 2020 Aug 04.
Article in English | MEDLINE | ID: covidwho-635466


Using a combination of enhanced sampling molecular dynamics techniques and non-equilibrium alchemical transformations with full atomistic details, we have shown that hydroxychloroquine (HCQ) may act as a mild inhibitor of important functional proteins for SARS-CoV2 replication, with potency increasing in the series PLpro, 3CLpro, RdRp. By analyzing the bound state configurations, we were able to improve the potency for the 3CLpro target, designing a novel HCQ-inspired compound, named PMP329, with predicted nanomolar activity. If confirmed in vitro, our results provide a molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19.

Cysteine Endopeptidases/metabolism , Hydroxychloroquine/metabolism , Molecular Dynamics Simulation , Papain/metabolism , RNA-Dependent RNA Polymerase/metabolism , Viral Nonstructural Proteins/metabolism , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Binding Sites , COVID-19 , Catalytic Domain , Coronavirus 3C Proteases , Coronavirus Infections/drug therapy , Coronavirus Infections/pathology , Coronavirus Papain-Like Proteases , Cysteine Endopeptidases/chemistry , Humans , Hydroxychloroquine/chemistry , Hydroxychloroquine/therapeutic use , Pandemics , Papain/chemistry , Pneumonia, Viral/drug therapy , Pneumonia, Viral/pathology , RNA-Dependent RNA Polymerase/chemistry , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry