Computational Identification of Marine-Derived Inhibitors of Cyclophilin D and Protease-Activated Receptor-1 for the Treatment of Ischemic Disease

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. • By focusing on thrombosis (Protease-Activated Receptor-1 (PAR-1)) and mitochondrial dysfunction (Cyclophilin D (CypD)), an integrated multi-stage in-silico workflow was used to find new treatments for ischemic diseases. • Lead compounds demonstrated excellent dynamic stability during 500 ns molecular dynamics simulations, with RMSD values consistently between 0.6 and 1.7 Å. • MM-GBSA binding free energy calculations revealed strong affinities, including CMNPD3572 and CMNPD22037 for PAR-1 (ΔG ≈ -96 to -98 kcal/mol) and CMNPD29955 for CypD (ΔG ≈ −63 kcal/mol). • Further advanced analyses, such as WaterMap, PCA and Free Energy Landscape studies, confirmed favorable hydration thermodynamics along with stable conformational dynamics and energetically preferred binding states. • CMNPD29955 emerged as a novel marine-derived CypD inhibitor. CMNPD3572 and CMNPD22037 are as PAR-1 inhibitors highlighting a promising strategy to mitigate mitochondrial dysfunction alongside PAR-1–mediated thrombosis in ischemic disorders.