Evidence-Based Disruption of the HSPA8–Spike Protein Complex: In-Depth Molecular Dynamics Characterisation of Selected Small Molecules

COVID-19 pandemic significantly disrupted global economies, health systems, and people’s social lives. To this day, some countries still report new cases of COVID-19 infections supporting the need for therapeutic strategies to combat this disease, tar-geting conserved regions within the viral proteins and key host proteins involved in viral entry and replication. This study is built on a previous publication that virtually screened for small molecules strongly binding to the HSPA8–spike protein complex through molecular docking simulations. The current study aimed to provide in-depth insights into the ligand-mediated disruptions of the HSPA8–spike protein complex, focusing on NSC36398 and NSC281245 small molecules. An all-atom molecular dy-namics simulation was performed using GROMACS v2018.6 to determine the dynamic behaviour of the HSPA8–spike protein complex in ligand-free and ligand-bound sys-tems. Post-MD analysis was performed using various tools and software, focusing mainly on structural analysis, conformational dynamics analysis, interaction analysis, and binding free energy calculations. The post-MD analysis validated the previous docking results, highlighting NSC36398 and NSC281245 as promising HSPA8–spike protein complex inhibitors. NSC36398 displayed a modest and stable binding interac-tion characterised by multiple hydrogen bonds and allosterically destabilising the HSPA8–spike protein interaction surface. NSC281245 displayed strong binding to the protein complex with minimal allosteric disruption. These findings suggest that NSC36398 is a promising allosteric inhibitor for HSPA8–spike protein complex, and NSC281245 is also a promising candidate, providing a framework for designing next-generation small-molecule compounds with inhibitory properties towards the host-viral interaction.