An in-silico approach for finding inhibitor against Oxidoreductase enzyme from methanogeneic bacteria: A new way for inhibiting methanogenesis

Sarra Akermi, Sagar Barage, Ritushree Biswas, Subrata Sinha, Surabhi Johari, Anshul Nigam, Sunil Jayant

Abstract


Methane play crucial role in global warming in which methane emissions contribution of ruminant is substantial (~ 15%) due to presence of methanogens in their digestive system. Methanogens release large amount of methane into the environment via methanogenesis where, F420:NADP oxidoreductase catalyzes key step of electron transfer between NADP+ and F420 in methanogenesis. Thus, F420:NADP oxidoreductase is crucual enzyme to regulate methane production in cattle. However, the structural detail of F420:NADP oxidoreductase is not available till date. Hence , we predicted 3D structure of F420:NADP oxidoreductase of M. barkeri and M. smithii using homology modeling technique. Subsequently, we screened herbal plant metabolities against predicted models of F420:NADP oxidoreductase from M. barkeri and M. smithii followed by MD simulation. Molecular docking and MD simulation studies revealed that, saponin efficiently accommodate in NADP binding cavity of enzyme and shows lowest binding free energy than other metabolites. Furthermore, F420:NADP oxidoreductase enzyme residues T90, R92, M119, K121, R160, R163, K223, K228 and V117 involvedin hydrogen bonding and hydrophobic interaction with saponin. Overall, saponin could be used as potential inhibitor for Oxidoreductase enzyme to control methanogenesis.

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Akermi 2020

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