Informatics and Computational Approaches for the Discovery and Optimization of Natural Product-Inspired Inhibitors of the SARS-CoV-2 2′-O-Methyltransferase

Abstract

The urgent need for new classes of orally available, safe, and effective antivirals�covering a breadth of emerging viruses�is evidenced by the loss of life and economic challenges created by the HIV-1 and SARS-CoV-2 pandemics. As frontline interventions, small-molecule antivirals can be deployed prophylactically or postinfection to control the initial spread of outbreaks by reducing transmissibility and symptom severity. Natural products have an impressive track record of success as prototypic antivirals and continue to provide new drugs through synthesis, medicinal chemistry, and optimization decades after discovery. Here, we demonstrate an approach using computational analysis typically used for rational drug design to identify and develop natural product-inspired antivirals. This was done with the goal of identifying natural product prototypes to aid the effort of progressing toward safe, effective, and affordable broad-spectrum inhibitors of Betacoronavirus replication by targeting the highly conserved RNA 2′-O-methyltransferase (2′-O-MTase). Machaeriols RS-1 (7) and RS-2 (8) were identified using a previously outlined informatics approach to first screen for natural product prototypes, followed by in silico-guided synthesis. Both molecules are based on a rare natural product group. The machaeriols (3−6), isolated from the genus Machaerium, endemic to Amazonia, inhibited the SARS-CoV-2 2′-O-MTase more potently than the positive control, Sinefungin (2), and in silico modeling suggests distinct molecular interactions. This report highlights the potential of computationally driven screening to leverage natural product libraries and improve the efficiency of isolation or synthetic analog development.

Cheminformatics approach to identify andrographolide derivatives as dual inhibitors of methyltransferases (nsp14 and nsp16) of SARS-CoV-2

“…Amongst all the andrographolide derivatives investigated, compounds 2734589 and 138968421 showed the potential as effective natural drug candidate against both nsp14 and nsp16 proteins due to their strong interaction primarily via hydrophobic and hydrogen bonding. A much lower binding energy and thereby greater affinity was observed for both the compounds compared to other reported natural compounds like amentoflavone (− 9.3 kcal/mol), baicalin (− 8.7 kcal/mol), daidzin (− 8.3 kcal/mol), luteoloside (− 8.3 kcal/mol), machaeriols (− 8.9 kcal/mol) 17 , 18 . Further, these reported lead compounds are majorly stabilized by hydrogen bonds which are in good resonance with both the compounds identified in our study.…”