Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses

Abstract

AbstractMajor efforts have been underway to develop broad-spectrum high potency capsid binders that inhibit the life cycle of enteroviruses, a large group (family Picornaviridae) whose members include poliovirus, coxsackieviruses, echoviruses, numbered enteroviruses, and rhinoviruses. These diverse viruses cause a wide variety of illnesses, ranging from the mild common cold to hand-foot-and-mouth disease, myocarditis, pancreatitis, aseptic meningitis, and encephalitis. So-called classical capsid binders target a surface exposed hydrophobic pocket in one of the viral coat proteins (VP1) to prevent the genome uncoating process. However, efficacy, toxicity, emergence of drug-resistant viruses, and existence of certain enteroviral species that lack the VP1 pocket limit their clinical benefit. Recently, we identified a new druggable site at a conserved interface formed by multiple capsid proteins, the VP1-VP3 interprotomer pocket. To further study the properties that confer druggability at this site, we have determined high-resolution cryo-electron microscopy structures of two enteroviruses, coxsackieviruses B3 and B4, complexed with interprotomer-targeting compounds, CP17 and CP48 respectively. Until now, there has been no structure available for Coxsackievirus B4 despite the fact that the virus has long been implicated in the development of insulin-dependent diabetes mellitus. At better than 3 Å resolution, we could identify the detailed interactions that facilitate ligand binding. Both compounds target the same three conserved residues, each from a different polypeptide chain, to form a virion-stabilizing network inside the pocket. We measured the in silico binding energy for both inhibitors when anchored to the network and found a global stabilizing effect on the order of thousands of kcal/mol under saturating conditions (60 total sites per virion). Intriguingly, a recent X-ray structure has revealed that glutathione targets the same network within the interprotomer site of bovine enterovirus F3, where it is thought to facilitate virus assembly. In summary, our findings provide the structural basis for how a newly designed class of capsid binders target and stabilize enteroviruses. Future efforts to chemically optimize drugs for enhanced targeting to the interprotomer pocket is a promising endeavor in the fight against enteroviruses, especially given the possibility of synergistic effects when used in combination with classical VP1 binders like pleconaril.