Sugarcane polyphenol oxidase: Structural elucidation using molecular modeling and docking analyses

Polyphenol oxidase (PPO) enzymes induce undesirable browning in fruits, vegetables, and juices like sugarcane and apple. Inactivation of PPO is crucial to mitigate this issue, achieved through methods like heat, radiation, ultrasound, pH adjustment, adsorbent addition, and inhibitors. Inhibitor selection is traditionally a time-consuming trial-and-error process. This study aimed to develop a homology model of sugarcane PPO and to streamline inhibitor selection using a rational approach, relying on knowledge of PPO's structure and active site. The research utilized homology modeling through SWISS-MODELER to predict the 3D structures of two types of sugarcane copper-based PPOs: met-PPO (Cu-Cu active site) and oxy-PPO (Cu-O-Cu active site), both composed of 235 amino acids. Model quality was assessed using Global Model Quality Estimation (GMQE) and Qualitative Model Energy Analysis (QMEAN), yielding favorable scores of 0.17 (GMQE), 0.44 ± 0.05 (QMEAN Co-Global) and z-score of –4.03. Ramachandran analysis indicated 78.8 % and 17.5 % of amino acid residues fell within the most favored and additional allowed regions, respectively. Docking analysis revealed strong affinities between m-hydroxybenzoic acid and p-hydroxybenzoic acid with binding energies of –4.40 Kcal/mol and –4.38 Kcal/mol, respectively, for met-PPO and oxy-PPO. Identified active site residues are ARG369, HIS325, GLU321, ALA361, and TRP313. This study enhances comprehension of sugarcane PPO and its active site, aiding rational inhibitor design to counteract undesired browning reactions.