REPOSITORY > RESULTS

Abstract

The emergence of SARS-CoV-2 variants underscores the need for antiviral strategies targeting conserved viral components. The SARS-CoV-2 envelope protein (Epro), a viroporin essential for viral assembly and release, represents a promising yet underexplored target. This doctoral research integrates computational modelling and experimental characterisation to identify novel Epro inhibitors and explore the antiviral potential of natural products.
A structure-based drug discovery platform was employed, including high-throughput virtual screening (HTVS) of nearly one billion compounds from the ZINC15 database, followed by molecular dynamics simulations, and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis. Among the prioritised candidates, two of the eight candidates blocked the SARS-CoV-2 Epro ion channel for extended periods by forming hydrogen bonds with the amino acid residues GLU8, THR9, THR11, LEU12, and ASN15 within the N-terminal vestibule. However, in vitro testing of six structurally related, commercially available analogues showed no antiviral activity against a coronavirus surrogate, murine hepatitis virus (MHV), highlighting the importance of experimental validation.
Subsequently, a novel lead candidate (LC), (S)-N-(2-((1S,3S,5S,7S)-adamantan-2-yl)ethyl)-2-(butylamino)-3-(1H-indol-3-yl)propenamide, was identified from the Faculty of Chemistry and Chemical Technology (FKKT) compound library. It showed the highest predicted binding affinity and stable interactions within the N-terminal vestibule of Epro, forming hydrogen bonds with amino acid residues GLU8, THR11, ASN15, and LEU18. In vitro assays, including plaque reduction assays, qPCR, light microscopy, and transmission electron microscopy, confirmed potent antiviral activity against MHV by reducing viral infectivity, delaying RNA replication, and impairing virion egress, consistent with disruption of Epro function. These findings validate Epro as a viable antiviral target and support LC as a promising lead candidate.
In parallel, investigations into the antiviral activity of Helichrysum italicum revealed that the ethanolic extract exhibited strong selective activity against enveloped viruses, while no effect was observed against a non-enveloped virus. Chemical analysis by HPLC-MS/MS showed a phenolic-rich composition, and in vitro experiments confirmed that quercetin contributes to antiviral activity by acting at the entry stages of the viral life cycle. However, the overall effect most likely results from synergistic interactions between multiple constituents.
In conclusion, this doctoral thesis demonstrates the importance of integrating computational and experimental approaches in antiviral research and highlights the complementary potential of synthetic compounds and natural products. These findings contribute to the development of new antiviral strategies targeting conserved viral targets.