In silico drug designing for COVID-19: an approach of highthroughput virtual screening, molecular and essential dynamics simulations

Rakesh KumarPranay Tanwar


SARS-CoV2, a new coronavirus has emerged in Wuhan city of China, December last year causing pneumonia named COVID-19 which has now spread to entire world. By April 2020, number of confirmed cumulative cases crossed ~2.4 million worldwide, according to WHO. Till date, no effective treatment or drug is available for this virus. Availability of X-ray structures of SARS-CoV2 main protease (Mpro) provided the potential opportunity for structure based drug designing. Here, we have made an attempt to do computational drug design by targeting main protease of SARS-CoV2. Highthroughput virtual screening of million molecules and natural compounds databases was performed followed by docking. Six ligands showed better binding affinities which were further optimized by MD simulation and rescoring of binding energy was calculated through MM/PBSA method. In addition, conformational effect of various ligands on protein was examined through essential dynamics simulation. Three compounds namely ZINC14732869, ZINC19774413 and ZINC19774479 were finally filtered that displayed high binding free energies than N3 inhibitor and form conformationally stable complex. Hence, current study features the discovery of novel inhibitors for main protease of Co...Continue Reading

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