Diabetes mellitus remains a significant global health problem, and targeting glucokinase regulatory protein (GKRP) offers a promising strategy to regulate glucokinase (GK) activity more safely without increasing the risk of hypoglycemia. Coffee, which is rich in bioactive phenolic compounds, has the potential to provide a natural product-based antidiabetic candidate. This study aims to identify Coffea arabica compounds as potential GKRP inhibitors and to characterize the complexes' dynamics. Initially, Coffea arabica compounds were screened using a blind docking approach against GKRP and ADME filtering. Out of 134 compounds, 12 compounds, particularly Fontanesine B (Fon), Formononetin (For), and Hesperetin (Hes), exhibited high binding scores (−8.1 to −10.6 kcal/mol) while adhering to Lipinski's rule and showing high gastrointestinal absorption. The 12 potential compounds were further characterized using density functional theory (DFT), simulated with GKRP-F1P complex in triplicate 200 ns molecular dynamics (MD) simulations, and calculated for their binding free energy using MM/GBSA. Principal component analysis (PCA) showed that some coffee ligands restrict the collective motion of GKRP, while the dynamic cross-correlation matrix (DCCM) revealed a strengthening of the motion correlation around the F1P binding site and the GK binding interface. Most of the ligands are strong electrophiles that interact with the key nucleophilic residue Glu153, stabilizing the bound configuration of F1P and lowering its binding energy. Overall, these results highlight coffee-derived polyphenols as promising GKRP inhibitors that can potentially maintain glucokinase activity and provide a basis for the development of coffee-based antidiabetic candidates.
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