Role of cofactors/co-enzymes in stabilizing protein-ligand complexes

Abstract

Flavin adenine dinucleotide (FAD) is a ubiquitous redox cofactor that plays a fundamental role in various metabolic and enzymatic reactions. It is involved in electron transfer processes essential for cellular respiration, energy production, and redox homeostasis. Beyond its classical biochemical functions, recent research has suggested that FAD may serve as a promising drug target, particularly in the context of neurological diseases, where alterations in flavoproteins and redox imbalances contribute to disease progression. Despite its well-established role in enzymatic catalysis, the contribution of FAD to the overall stability of protein-ligand complexes remains an open question. Investigating how FAD influences ligand binding and protein conformational dynamics is crucial for understanding its potential as a therapeutic target. In this study, we employed molecular dynamics (MD) simulations in an explicit solvent environment to analyze the interaction energy of protein-ligand complexes containing FAD. A set of diverse protein systems with FAD-dependent interactions was selected, and each complex was subjected to long-timescale MD simulations to capture its structural and energetic properties. By applying energy decomposition analysis, we calculated the interaction energies of all residues within the system, with a particular focus on FAD and the ligand. This allowed us to quantify the contribution of FAD to the stability of the complex and assess its role in modulating ligand interactions. To further understand the structural consequences of FAD removal, volumetric analysis was performed to compare the binding pocket volumes in the presence and absence of FAD. This analysis provided insights into whether the cofactor-induced conformational changes in the binding site, potentially affecting ligand binding and protein function. The comparison of pocket volumes aimed to reveal possible allosteric effects exerted by FAD, shedding light on its stabilizing role within the protein-ligand system. Our findings highlight the importance of FAD in modulating protein-ligand interactions, both from an energetic and structural perspective. The study provides a detailed understanding of how FAD contributes to the stability of protein-ligand complexes and underscores its potential as a target in drug discovery efforts for neurological diseases. By elucidating the molecular mechanisms through which FAD influences binding interactions, this work lays the foundation for future studies exploring FAD-targeted therapeutic strategies. These insights could be particularly valuable in the design of small-molecule inhibitors or modulators that exploit FAD’s structural and energetic role in protein function.