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COVID-19 is a newly-emerged respiratory disease that is caused by the SARS-CoV-2, the seventh known Coronaviruses strain that has struck a global pandemic. The sharp increase in the number of positive cases worldwide necessitates highly-sensitive diagnostics kits and effective antiviral drugs to be developed for the populations. One of the antigens that is targeted for antibody neutralisation is the coronavirus Spike protein that consists of the S1 and S2 subunits, which mediated the entry pathway into the host’s cell. Thus, the Spike protein has been suggested as a potential target for Covid-19 diagnostics and drug design. This study aims to evaluate the interactions between the SARS-CoV-2 Spike protein and the known monoclonal antibodies from Coronaviruses and to screen for potential Spike protein inhibitors. Virtual screening was conducted based on two compounds, N‐acetyl‐D‐glucosamine (NAG) and Hesperetin, which is a small molecule that binds to the SARS-CoV-2 Spike protein structure and a natural compound that has prophylactic agents against SARS-CoV-2 infection as it binds to Spike protein, respectively. Protein-protein interaction studies were conducted by using the STRING webserver, prior to performing rigid docking using SWISSDOCK and visualised using USCF Chimera. Meanwhile, ligand-based screening was conducted through Ultrafast Shape Recognition Virtual Screening Database (USR-VS), and structure-based screening was performed  via  AutoDock4 software. The toxicity of the compounds was predicted using ProTox-II database. Possible interactions have been observed between the known monoclonal antibodies with the SARS-CoV-2 Spike protein, where M396 monoclonal antibody has shown the strongest interaction with a binding energy of -8.50 kcal/mol. Meanwhile, virtual screening has yielded several compounds that indicate the possibility to inhibit the SARS-CoV-2 Spike protein, where Tamarixetin has shown the strongest binding energy of -7.93 kcal/mol. These findings have potentials to be further evaluated in the future for the development of improved diagnostic kits and potential therapeutic drugs that specifically target the Spike protein of SARS-CoV-2.

iop conference series. materials science and engineering

Virtual Screening and In Silico Interactions Studies for Potential Antivirals and Diagnostics against the Spike protein from the Novel Coronavirus SARS-Cov-2