In silico and in vitro screening of newly designed compounds against coxsackivirus A16 and enterovirus A71

Abstract

Outbreaks of hand, foot, and mouth disease (HFMD) occur around the world. It is caused by the Coxsackievirus-A16 (CV-A16) and Enterovirus-A71 (EV-A71) that belong to the Enterovirus genus. Unfortunately, neither an anti-HFMD drug nor a vaccine is currently available. Rupintrivir, one of the drug candidates for HFMD treatment, has been attractive for the development of its analogs with broad biological activities. This drug is an inhibitor for 3C protease of CV-A16 and EV-A71, an enzyme that plays a crucial role in the viral replication process. ). In the present study, we focused on designing 50 novel rupintrivir analogs against CV-A16 and EV-A71 3Cpro using computational tools. From their predicted binding affinities, the five com-pounds with functional group modifications at P1′, P2, P3, and P4 sites, namely P1′-1, P2-m3, P3-4, P4-5, and P4-19, could bind with both CV-A16 and EV-A71 3Cpro better than rupintrivir. Subsequently, these five analogs were studied by 500 ns molecular dynamics simulations. Among them, P2-m3, the derivative with meta-aminomethyl-benzyl group at the P2 site, showed the greatest potential to interact with the 3Cpro target by delivering the highest number of inter-molecular hydrogen bonds and contact atoms. It formed the hydrogen bonds with L127 and K130 residues at the P2 site stronger than rupintrivir, supported by significantly lower MM/PB(GB)SA binding free energies. The P2-m3 was suggested to be synthesized and tested the biological activity. Moreover, we found new potential compounds against 3C protease of EV-A71 and CV-A16 from flavonoids by using pharmacophore-based virtual screening. Among 39 flavonoids, diosmin, epigallocatechin gallate, EGCG, and RTH-011 showed high binding affinity against EV-A71 and CV-A16. In addition, we found that EGCG showed the highest potent efficacy (EC50) at the values of 12.86 ± 1.30 µM and 15.54 ± 1.50 µM for EV-A71 and CV-A16, respectively, while diosmin showed EC50 at the values of 21.01±1.57 µM and 30.68 ± 3.25 µM for EV-A71 and CV-A16, respectively. Both compounds no toxic (CC50 > 250 µM and > 500 µM for EGCG and diosmin, respectively) against RD cells were obtained. Moreover, the MD simulation analysis revealed that EGCG had higher the binding affinity than diosmin supported by significantly lower SIE binding free energies, higher number contact atom and higher number of key biding residue which similar to rupintrivir. We suggested that the EGCG compounds are effective in inhibiting EV-A71 and CV-A16 3C protease.