3D-QSAR and Molecular Docking Studies of Antiarrhythmic Activity of Cardiac Sodium Channel (PDB: 8F6P) with Simulation Dynamic on a Series of Phenytoin Derivatives

Background: Cardiac arrhythmias are life-threatening disorders associated with abnormal electrical conduction in the heart, primarily regulated by ion channels such as the cardiac sodium channel (Nav1.5). In the present study, a series of phenytoin derivatives (MB-1 to MB-8) were designed and evaluated for their antiarrhythmic potential targeting the cardiac sodium channel 8F6P using integrated computational approaches, including 3D-QSAR, molecular docking, ADMET prediction, toxicity assessment, and molecular interaction analysis. Materials and Methods: Physicochemical evaluation revealed that all compounds complied with Lipinski’s rule of five and Veber criteria, indicating good oral drug-likeness and bioavailability. ADMET profiling demonstrated high gastrointestinal absorption, non-permeability across the blood-brain barrier, and minimal inhibition of key cytochrome P450 enzymes for most derivatives, suggesting a favorable pharmacokinetic profile. Toxicity studies indicated that the majority of compounds belong to toxicity class 5 with high LD₅₀ values (5000 mg/kg), reflecting low acute toxicity. Results: Molecular docking analysis showed that most derivatives exhibited stronger binding affinity than the standard drug (-8.7 kcal/mol), with MB-2 (-9.8 kcal/mol), MB-5 (-9.7 kcal/mol), and MB-7 (-9.6 kcal/mol) demonstrating the highest affinity. Interaction analysis revealed that hydrogen bonding, π-π stacking, hydrophobic interactions, and π-sulfur interactions play key roles in stabilizing ligand-protein complexes, particularly involving residues such as PHE399, MET395, LEU400, and THR1711. Conclusion: Overall, the study identifies MB-2, MB-5, and MB-7 as promising candidates with enhanced binding affinity, favorable pharmacokinetic properties, and acceptable safety profiles. These findings provide valuable insights for the rational design of novel antiarrhythmic agents and warrant further validation through molecular dynamics simulations and experimental studies.