Atomistic Interplay of Remdesivir Bound SARS-CoV-2 Replicase and Thermodynamic Evaluation of Site-Directed Water Molecules: An Approach to Brownian Dynamics Simulation

Abstract

Aim/Background: The replication-transcription complex (RTC) of SARS-CoV-2 plays a critical role in viral RNA synthesis and replication, primarily through the RNA-dependent RNA polymerase (RdRp). Remdesivir (RDV), a nucleotide analogue, inhibits RTC by disrupting nucleotide incorporation. However, understanding the detailed thermodynamic behaviour and conformational dynamics of the RdRp-RDV complex, including the role of catalytic site water molecules, remains crucial for guiding new antiviral development. Materials and Methods: We performed 100 ns of classical unbiased molecular dynamics (MD) simulation using the Desmond module of Schrödinger Suite (OPLS4 force field) on the SARS-CoV-2 RdRp-Remdesivir complex (PDB ID: 7bv2). Protein-ligand interaction analyses, metastable state clustering, and molecular mechanics/generalized Born surface area (MM/GBSA) calculations were conducted. The role of water molecules at the RdRp catalytic site was evaluated through solvent accessibility, water-bridge formation, and resolvation energy assessments. Results: The RdRp-RDV complex displayed minimal conformational fluctuations with stable ligand RMSD (~1.07 Å). Three metastable clusters were identified, with cluster 3 contributing 95% of the population and demonstrating the highest ligand binding stability. Key residues-Arg553, Arg555, Asp623, and Asp760-showed significant interaction sustainability via hydrogen bonds, ionic contacts, and water bridges. Water-mediated interactions notably contributed to binding stability, influencing ligand pose orientation. The average binding free energy (ΔG) was -28.99 kcal/mol, with key residues contributing strongly to system enthalpy. Water molecules at the active site provided additional stability, confirmed by free energy contributions ranging from 10.66 to 12.05 kcal/ mol. Conclusion: This study elucidates the atomistic dynamics and thermodynamic profiling of the RdRp-RDV complex, highlighting the critical role of water molecules and specific amino acid residues in sustaining ligand binding. These insights offer strategic guidance for the rational design of next-generation RdRp inhibitors with enhanced pharmacodynamic profiles targeting SARS-CoV-2.