Exploring putative enteric methanogenesis inhibitors using molecular simulations and a graph neural network

Authors: ARYEE, RANDY - Iowa State University; MOHAMMED, NOOR - Iowa State University; DEY, SUPANTHA - Iowa State University; B, ARUNRAJ - Iowa State University; NADENDLA, SWATHI - Iowa State University; SAJEEVAN, KARUNA ANNA - Iowa State University; Beck, Matthew; Frazier, Anthony - Nathan; Koziel, Jacek; MANSELL, THOMAS - Iowa State University; CHOWDHURY, RATUL - Iowa State University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 9/16/2024
Publication Date: 9/16/2024
Citation: Aryee, R., Mohammed, N.S., Dey, S., B, A., Nadendla, S., Sajeevan, K., Beck, M.R., Frazier, A.N., Koziel, J.A., Mansell, T.J., Chowdhury, R. 2024. Exploring putative enteric methanogenesis inhibitors using molecular simulations and a graph neural network. BioRxiv. Available: https://doi.org/10.1101/2024.09.16.613350.
DOI: https://doi.org/10.1101/2024.09.16.613350

Interpretive Summary: Enteric methane (CH4) from cattle represents a significant source of greenhouse gas emission in the U.S. and globally. It further represents a significant energy loss to livestock production. Accordingly, mitigation strategies have been developed to mitigate enteric CH4 emissions from beef and dairy. The mitigation strategies with the largest mitigation potential are direct methanogenesis inhibitors, including 3-nitrooxypropanol (3-NOP) and bromoform. These compounds inhibit the final step of CH4 production by methanogenic archaea. To date there is a lack of understanding on how CH4 inhibitors inhibit methyl coenzyme M reductase (MCR), which is involved in the final step of methanogenesis. There is a lack of knowledge on the number of molecules that can interact with the active binding site of MCR and the binding affinity. As such, researchers from ARS (Bushland, TX) and Iowa State University employed modeling approaches to determine the molecular “flooding” effects and binding affinities of known CH4 inhibitors. It was determined that bromoform has a lower binding affinity than 3-NOP, but bromoform has a greater “flooding” effect, with three molecules binding the active site of MCR compared with two molecules of the 3-NOP. These results provide important insights into the underlying modes-of-action of enteric CH4 inhibitors and may explain differences in the compounds’ mitigation potentials.

Technical Abstract: When released into the atmosphere, methane (CH4) acts as a key contributor to global warming. As CH4 is a short-lived cli-mate forcer (atmospheric lifespan of 12 years), its mitigation represents the most promising means to address climate change in the short-term. Enteric CH4, the biosynthesized CH4 from the rumen of ruminants, represents 5.1% of total global greenhouse gas (GHG) emissions, 23% of emissions from agriculture, and 27.2% of global CH4 emissions. Furthermore, enteric CH4 represents a significant energy loss to the animal, as 2-12% of gross energy intake is lost as CH4 depending on the diet. Therefore, it is imperative to investigate methanogenesis inhibitors and their underlying modes-of-action. We hereby elucidate the detailed biophysical and thermodynamic interplay of anti-methanogenic molecules and the tetrapyrrole cofactor F430 of methyl coenzyme M reductase (MCR) and interpret the stoichiometric ratios and binding affinities of fifteen selected inhibitor molecules. We leverage this prior knowledge in a graph neural network to first functionally cluster these fifteen known inhibitors among ~54,000 bovine metabolites. This work also identifies precursors of putative inhibitors and lays foundation for computational and de novo design of inhibitor molecules that retain/reject one or more biochemical properties of known inhibitors discussed in this study.