Natural product-based Ebola virus entry inhibitors targeting the viral glycoprotein: A combined computational and experimental study.

Recurrent epidemics of hemorrhagic fever caused by Ebola virus frequently exceed 50% in fatalities making it one of the most dangerous human infections. The absence of effective anti-EBOV medications and their high transmissibility still make it an ongoing health concern worldwide. The Ebola glycoprotein (EBOV-GP) is a class I fusion protein that mediates viral attachment and membrane fusion. Thus, EBOV-GP is a prime target for treatment as it is directly involved in early infection. In this context, the aim of this study is to identify new effective natural-sourced inhibitors of EBOV-GP by utilizing a structure-based computational approach combined with experimental validation. Two large natural chemical libraries were prescreened to assure drug-likeness and safety. Then, compound selection was guided by a validated pharmacophore model and Molecular docking. Eleven hit compounds were first considered for the conserved binding pocket of EBOV-GP and were found to produce stable contacts. To further investigate these selected hits, we used in vitro inhibitory assays to assess their biological potency, as well as molecular dynamics (MD) simulations to evaluate their binding stability over time. Compound CNP0349608.0 showed the most potential activity, with IC50 values of 1.72 μM, selectivity index of 12.26, and specificity index of 11.65, respectively. The MD trajectory of compound CNP0349608.0 confirmed stable binding, preserved hydrogen bond networks, and minimal fluctuations within the EBOV-GP pocket supporting the compound's robust affinity. These results suggest that CNP0349608.0 has the potential to inhibit EBOV infection by GP offering new avenues for antiviral drug development against Ebola virus.