In December 2019, the Coronavirus disease-2019 (COVID-19) virus emerged in Wuhan, China. The first resolved COVID-19 crystal structure (main protease) has been developed and various repurposing activities are in process. In this study, a knowledge gap in relation to COVID-19, with the previously known fatal Coronavirus (CoV) epidemics, Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) CoVs, is covered by the investigation of sequence statistics, molecular modelling, virtual screening, docking, and sequence comparison statistics of the COVID-19 main protease. COVID-19 main protease Mpro formed a sequence similarity group with SARS CoV that was distant from MERS CoV. The identity % was 96 and 51 for COVID-19/SARS and COVID-19/MERS CoV sequence comparisons, respectively. We used molecular docking and a molecular interaction approach to identify small-molecules that bind to the isolated Viral S-protein at its host receptor region. These molecules have good solubility and pharmacodynamics properties. They also obey Lipinski’s rule, which makes them promising compounds to pursue further biochemical and cell-based assays to explore their potential for use against COVID-19. We hypothesize that the top score identified molecules that may be used to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of selected compounds is given that can be tested experimentally.
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