Targeting 3Cpro of Enterovirus D68 with Medicinal Phytocompounds Using Structure-Based Molecular Screening and Molecular Simulation Approaches to Rescue the Host Immune Response

Abstract

Purpose: Enterovirus D68 (EV-D68) is a viral pathogen recognized for its role in inducing severe respiratory illnesses and its link to the development of acute flaccid myelitis (AFM) in children. The 3 C protease (3Cpro) of Enterovirus D68 disrupts TRIF, impairing NF-κB and IFN-β signaling, evading host immunity. EV-D68 also inhibits IRF7 and interferes with MDA5-MAVS interaction, hindering RLR pathway-mediated IFN signaling. Methods: Recognizing the key role of 3Cpro in modulating host immune responses, we employed structure-based drug design combined with molecular dynamics simulations to comprehensively screen phytochemical databases and pinpoint promising compounds with the potential to inhibit EV-D68 3Cpro, thereby supporting immune system restoration. Results: Our analysis identified lead compounds with high docking score such as EA-5317333 (-9.268 kcal/mol) and EA-76313109 (-8.618 kcal/mol) from East African Natural Products Database, NA-5320945 (-7.902 kcal/mol) and NA-101630512 (-7.570 kcal/mol) from North African Natural Products Database, SA-25245604 (-8.899 kcal/mol) and SA-9064 (-7.538 kcal/mol) from South African Natural Compounds Database, NE-5280343 (-7.845) and NE-162817590 (-7.264 kcal/mol) from North-East African Natural Products Database, TCM-71665623 (-8.324 kcal/mol) and TCM-163019889 (-8.414 kcal/mol) from Traditional Chinese Medicines Database as lead compounds. Furthermore, the stronger binding affinity of these lead compounds with the 3Cpro was validated by the results of molecular dynamics (MD) simulation, binding free energy calculation and dissociation constant analysis. The selected compounds exhibited favorable ADMET properties, including high solubility in water, strong gastrointestinal absorption, and no signs of liver toxicity, aligning well with Lipinski’s rule of five. Conclusion: Taken together, these findings provide compelling evidence to support the design of novel therapeutics directed at disrupting the immune evasion strategies employed by the EVD68 virus.