Thymoquinone as a potential anti-SARS-CoV-2 agent: In-vitro antiviral profiling and multi-scale in-silico analysis
Abstract
The persistent global threat of SARS-CoV-2 underscores the necessity for identifying potent and biocompatible antiviral agents. This study employs an integrated multi-layered framework—combining in-silico quantum calculations, molecular docking, coarse-grained dynamics analyses (iMODS-NMA and CABS-flex), and in-vitro assays to evaluate thymoquinone (TQ), the primary bioactive constituent of Nigella sativa , as a potential inhibitor of the SARS-CoV-2 replication machinery. Density functional theory (DFT) calculations revealed a narrow HOMO–LUMO energy gap (3.8637 eV) and a favorable molecular electrostatic potential (MEP), indicating TQ's high chemical reactivity and propensity for targeted biological interactions. Docking simulations suggested a favorable binding pose and moderate affinity of TQ toward both the catalytic RNA-dependent RNA polymerase (RdRp, nsp12) and the essential nsp7–nsp8 cofactor complex. Quantum-level analyses (QTAIM, NBO, and NCI) using model cyclodipeptides (cycloAsn-Asn and cycloSer-Ser) confirmed stabilizing non-covalent interactions, providing chemically interpretable insights into protein–ligand recognition. Normal Mode Analysis (NMA) via the iMODS server and RMSF calculations through CABS-flex revealed that TQ binding is associated with low-energy collective motions and localized flexibility changes within RdRp, supporting a plausible allosteric modulation hypothesis rather than definitive target-specific inhibition. Structurally characterized via…
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