Myocardial infarction (MI) and stroke are examples of ischaemic diseases that continue to pose serious health risks since few specific treatments address the underlying molecular causes of these conditions, which include pathological thrombosis and mitochondrial dysfunction. In order to close this gap, we used an integrated in-silico method to find strong inhibitors for Protease-Activated Receptor-1 (PAR-1) and Cyclophilin D (CypD) from the structurally diverse CMNPD marine natural product library. To account for protein flexibility, our method combines High Throughput Virtual Screening (HTVS), Standard Precision (SP), and Extra Precision (XP) docking with meticulous Induced Fit Docking (IFD). After undergoing 500 ns Molecular Dynamics (MD) simulations, the best candidate compounds showed remarkable structural stability with RMSD values between 0.6 and 1.7 Å. Strong binding affinities were found by thermal MM-GBSA calculations, with CMNPD29955 showing a ΔG of -63.146 kcal/mol towards CypD and CMNPD3572 and CMNPD22037 showing ΔG values of -96.24 and -98.092 kcal/mol against PAR-1, respectively. Lead molecules of each target were found to have important hydrophobic and hydrogen bonding interactions with crucial active site residues in MD modelling. The dynamic stability and energetic favorability of these chemicals were further confirmed by complementary techniques, including WaterMap, Principal Component Analysis (PCA), and Free Energy Landscape (FEL). In addition to CMNPD3572 and CMNPD22037 as potential PAR-1 antagonists, this work emphasises CMNPD29955 as a new lead inhibitor that targets mitochondrial dysfunction via CypD. To transform computational insights into effective and complementary therapeutic alternatives, lead optimisation, experimental validation, and preclinical assessment of these special marine-derived molecules will be crucial in the future.
