SARS-CoV-2 is an enveloped non-segmented positively stranded RNA infectious virus that mainly affects enteric and respiratory systems (Graham et al., 2013). Its infection and amelioration in the host are majorly governed by several structural proteins (Joshi et al., 2020; Prajapat et al., 2020). Amidst numerous structural proteins, spike protein and main protease of SARS-CoV-2 are stated to show essential impacts on viral replication through proteolytic machinery and involvement in transcription, translation, and amplification of viral proteins (Paules et al., 2020). Spike protein plays a critical role in binding to host cell receptor and is thought to represent a key determinant of the host range restriction (de Wilde, 2017). Main protease on the other hand exclusively cleaves polypeptide sequences after the glutamine residue and to the best of our knowledge is known as an ideal drug target due to the absence of human host cell protease showing this substrate specificity (Ullrich & Nitsche, 2020). The 3 D structures of spike protein and main protease were preprocessed, optimized and minimized to obtain the refined structures for drug repurposing.