In silico design of a novel nucleotide antiviral agent by free energy perturbation

• Type of Material: Article
• Authors: Dharmeshkumar Patel, Emory University; Bryan Cox, Emory University; Mahesh Kasthuri, Emory University; Seema Mengshetti, Emory University; Leda Bassit, Emory University; Kiran Verma, Emory University; Olivia Ollinger-Russell, Emory University; Franck Amblard, Emory University; Raymond Schinazi, Emory University
• Language: English
• Date: 2022-04-07
• Publisher: WILEY
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2022 John Wiley & Sons A/S.
• Final Published Version (URL): http://dx.doi.org/10.1111/cbdd.14042
• Title of Journal or Parent Work: CHEMICAL BIOLOGY & DRUG DESIGN
• Volume: 99
• Issue: 6
• Start Page: 801
• End Page: 815
• Grant/Funding Information: This work was supported in part by NIH grant 1R21-AI-129607 and 5P30-AI-50409 (CFAR).
• Keywords: Biochemistry & Molecular Biology; Science & Technology; DRUG DISCOVERY; INHIBITION; PRODRUGS; Chemistry, Medicinal; NUCLEOSIDE ANALOGS; INTERFERON; BETA-D-2'-DEOXY-2'-FLUORO-2'-C-METHYLCYTIDINE; SUBSTRATE-SPECIFICITY; REPLICATION; viral polymerase; KINASE; Life Sciences & Biomedicine; Pharmacology & Pharmacy; alchemical free energy perturbation; flavivirus; structure-based drug design; PRONUCLEOTIDES; RNA-dependent RNA polymerase; nucleoside antiviral agents

Abstract

Nucleoside analogs are the backbone of antiviral therapies. Drugs from this class undergo processing by host or viral kinases to form the active nucleoside triphosphate species that selectively inhibits the viral polymerase. It is the central hypothesis that the nucleoside triphosphate analog must be a favorable substrate for the viral polymerase and the nucleoside precursor must be a satisfactory substrate for the host kinases to inhibit viral replication. Herein, free energy perturbation (FEP) was used to predict substrate affinity for both host and viral enzymes. Several uridine 5’-monophosphate prodrug analogs known to inhibit hepatitis C virus (HCV) were utilized in this study to validate the use of FEP. Binding free energies to the host monophosphate kinase and viral RNA-dependent RNA polymerase (RdRp) were calculated for methyl-substituted uridine analogs. The 2’-C-methyl-uridine and 4’-C-methyl-uridine scaffolds delivered favorable substrate binding to the host kinase and HCV RdRp that were consistent with results from cellular antiviral activity in support of our new approach. In a prospective evaluation, FEP results suggest that 2’-C-dimethyl-uridine scaffold delivered favorable monophosphate and triphosphate substrates for both host kinase and HCV RdRp, respectively. Novel 2’-C-dimethyl-uridine monophosphate prodrug was synthesized and exhibited sub-micromolar inhibition of HCV replication. Using this novel approach, we demonstrated for the first time that nucleoside analogs can be rationally designed that meet the multi-target requirements for antiviral activity.