Bioinformatic Analysis of Phenylalanine Ammonia-Lyase Gene: Implications in Oligomeric Procyanidin Biosynthesis in Peach and Interaction with Cardiac Myosin Genes (MYBPC3) in Hypertrophic Cardiomyopathy

Abstract

Background: Phenylalanine ammonia-lyase (PAL) is a key enzyme in the biosynthetic pathway of phenolic compounds, including oligomeric procyanidins (OPCs), in peach (Prunus persica), playing a crucial role in antioxidant activity and cardioprotective effects. Objectives: In this study, the PAL protein sequence was retrieved and analyzed using bioinformatic approaches to characterize its physicochemical properties, secondary structure, and three-dimensional conformation. Methods: To investigate the potential effects of OPCs on hypertrophic cardiomyopathy (HCM), molecular docking was performed between three major ligands — procyanidin B1, procyanidin B2, and procyanidin C1 — and the human myosin binding protein C (MYBPC3). Results: The results revealed that all three ligands exhibited significant negative binding energies and stable interactions with key regions of MYBPC3. Among them, procyanidin B1 showed the highest binding affinity with a binding energy of -7.39 kcal/mol and an inhibition constant (Ki) of 3.78 µM. Cleft, pore, and tunnel analyses using MOLE 2.0 identified multiple structural pathways for ligand accommodation. Conclusions: These findings suggest that OPCs derived from peach may interact with MYBPC3, potentially influencing molecular pathways associated with HCM and contributing to the development of natural therapeutic compounds.