A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses

Abstract

Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are “capsid binders” that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhibitors and by means of cryo–electron microscopy (EM), followed by resistance selection and reverse genetics, we discovered a hitherto unknown druggable pocket that is formed by viral proteins VP1 and VP3 and that is conserved across entero-/rhinovirus species. We propose that these inhibitors stabilize a key region of the virion, thereby preventing the conformational expansion needed for viral RNA release. A medicinal chemistry effort resulted in the identification of analogues targeting this pocket with broad-spectrum activity against Coxsackieviruses B (CVBs) and compounds with activity against enteroviruses (EV) of groups C and D, and even rhinoviruses (RV). Our findings provide novel insights in the biology of the entry of entero-/rhinoviruses and open new avenues for the design of broad-spectrum antivirals against these pathogens.

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

“…CP17 is a benzenesulfanomide derivative that potently inhibits the CVB3 Nancy strain in cells (EC50 0.7 ± 0.1 µM) via a direct interaction with the capsid that increases virion thermostability by 1.5 and 2.1 log10 TCID50/mL at 46°C and 49°C, respectively (Abdelnabi et al, 2019). A 4.0 Å cryo-EM structure of CP17 in complex with CVB3 Nancy (EMD-0103) revealed that the site of binding is located at a conserved VP1-VP3 interprotomer interface, but the low resolution of the map prevented identification of the detailed interactions within the pocket.…”

“…To further investigate and confirm the activity and structural basis for how inhibitors bind at the interprotomer pocket, we determined a structure of CVB4 in the presence of a commercially available analog, which we refer to as CP48. This particular inhibitor was found to be active against all six serotypes of CVBs, and completely inhibited poliovirus type 1 replication at a concentration of 144 μM (Abdelnabi et al, 2019). We chose to work with CVB4 because no structure exists for this important human pathogen.…”

“…However, clinical development has been thwarted because of issues related to efficacy and toxicity, as well as emergence of drug-resistant viruses (Thibaut et al, 2012). Recently, we discovered a second druggable pocket at a conserved VP1-VP3 interprotomer interface in the viral capsid (Abdelnabi et al, 2019). This interface is in a region of the capsid that undergoes quaternary conformational changes to promote disassembly and release of the virion's genome into the host cell.…”

2019 meeting of the global virus network

“…As for entero/rhinoviruses, besides the target for capsid binders like pocapavir (Thibout et al, 2012), the researchers at the Rega Institute have found a novel druggable pocket formed by the viral proteins VP1 and VP2 in the virus capsid and have now identified analogs targeting this pocket with broad spectrum activity (Abdelnabi et al, 2019). Also described was a novel class of tryptophan dendrimers targeting the capsid five-fold vertex were found to inhibit EV-A71 replication at low nanomolar to high picomolar concentrations in vitro (Sun et al, 2019).…”

A benzene-mapping approach for uncovering cryptic pockets in membrane-bound proteins

“…Nevertheless, the applicability of the method and the proposed parameters to a benzene molecule remains to be addressed, particularly with regards to aggregation, depth of entry into the membrane, and the stringency of the repulsion distance parameter. 6 Using pocket mapping for viral proteins is an attractive area of study with the potential to utilize transient pocket discovery for targeted antiviral drug design and for identifying conserved but hidden antibody-binding epitopes [28][29][30] . Flaviviruses are a family of enveloped, single-stranded RNA viruses that include a range of vector-borne human pathogens such as DENV, Zika virus, yellow fever virus, or Japanese and tick-borne encephalitis virus 31 .…”