Deciphering the interactions of phytochemicals with alcohol dehydrogenase 1 (ADH1) in <i>Saccharomyces cerevisiae</i> : a molecular simulations study

The present study has investigated the interactions of the phytochemicals present in sugarcane bagasse (SCB) with alcohol dehydrogenase (ADH1) enzyme in <i>Saccharomyces cerevisiae</i> using molecular simulations. ADH1 catalyzes the reduction of acetaldehyde to ethanol. The metabolic hindrance induced by phytochemicals can adversely affect kinetics and yield of ethanol fermentation. The phytochemicals in SCB biomass were detected using LC-ESI-MS/QTOF analysis after dilute acid/alkali pretreatment and extraction using methanol and acetonitrile. Molecular docking simulation revealed high binding affinity of four phytochemicals for ADH1 enzyme due to low binding energies and inhibition constants: chlorogenic acid (-8.64 kcal/mol, 0.464 μM), apigenin (-7.72 kcal/mol, 2.2 μM), diosmetin (-7.47 kcal/mol, 3.37 μM), and caffeic acid (-7.03 kcal/mol, 7.07 μM). The molecular dynamics simulations showed that root mean square deviation (RMSD) values of the complexes of chlorogenic acid (0.22 nm) and apigenin (0.27 nm) were significantly smaller than apoprotein (0.37 nm), which indicates their stability. The root mean square fluctuation (RMSF) value of active site residues of the phytochemical complexes (chlorogenic acid = 0.15 nm, apigenin = 0.13 nm) was also smaller than that of apoprotein (0.17 nm). These results clearly indicate that phytochemicals can hinder metabolic pathway of <i>S. cerevisiae</i> due to preferential binding to ADH1.