Modelling and docking of Indian SARS-CoV-2 spike protein 1 with ACE2: implications for co-morbidity and therapeutic intervention

Presently, India bears amongst the highest burden of non-communicable diseases such as diabetes mellitus (DM), hypertension (HT), and cardio vascular disease (CVD) and thus represents a vulnerable target to the SARS-CoV-2/COVID-19 pandemic. Involvement of the angiotensin converting enzyme 2 (ACE2) in susceptibility to infection and pathogenesis by SARS-CoV-2 is currently an actively pursued research area. An increased susceptibility to infection in individuals with DM, HT and CVD together with higher levels of circulating ACE2 in these settings presents a scenario where interaction with soluble ACE2 may result in disseminated virus-receptor complexes that could enhance virus acquisition and pathogenesis. Thus, understanding the SARS-CoV-2 receptor binding domain-ACE2 interaction, both membrane bound and in the cell free context may contribute to elucidating the role of co-morbidities in increased susceptibility to infection and pathogenesis. Both Azithromycin and Hydroxychloroquine (HCQ) have shown efficacy in mitigating viral carriage in infected individuals. Furthermore, each of these compounds generate active metabolites which in turn may also modulate virus-receptor interaction and thus influence clinical outcomes. In this study, we model the structural interaction of S1 with both full-length and soluble ACE2. Additionally, therapeutic drugs and their active metabolites were docked with soluble ACE2 protein. Our results show that S1 from either of the reported Indian sequences can bind both full-length and soluble ACE2, albeit with varying affinity that can be attributed to a reported substitution in the RBD. Furthermore, both Azythromycin and HCQ together with their active metabolites can allosterically affect, to a range of extents, binding of S1 to ACE2.