Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library

Abstract

Potent Ebolavirus (EBOV) inhibitors will help to curtail outbreaks such as that which occurred in 2014–16 in West Africa. EBOV has on its surface a single glycoprotein (GP) critical for viral entry and membrane fusion. Recent high-resolution complexes of EBOV GP with a variety of approved drugs revealed that binding to a common cavity prevented fusion of the virus and endosomal membranes, inhibiting virus infection. We performed docking experiments, screening a database of natural compounds to identify those likely to bind at this site. Using both inhibition assays of HIV-1-derived pseudovirus cell entry and structural analyses of the complexes of the compounds with GP, we show here that two of these compounds attach in the common binding cavity, out of eight tested. In both cases, two molecules bind in the cavity. The two compounds are chemically similar, but the tighter binder has an additional chlorine atom that forms good halogen bonds to the protein and achieves an IC 50 of 50 nM, making it the most potent GP-binding EBOV inhibitor yet identified, validating our screening approach for the discovery of novel antiviral compounds.

Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines

“…1A, right). Even in the high-resolution GP∆muc structures (66,72,73), the HR2 stalk still contains less helical content than most coiled-coils in the Protein Data Bank (PDB), ~15 aa vs ~30 aa, and becomes less regular and unwound towards the C terminus, suggesting an inherent instability in HR2 (Fig. 1D, left).…”

“…Corning). Based on recent studies on EBOV infectivity in various cell lines(72, 105), HEK293T cells or TZM-bl cells were used for ebolavirus-pp neutralization assays. Briefly, HEK293T cells or TZM-bl cells at 1×104 were added to each well and the plate was incubated at 37°C for 48 h.After incubation, overlying media was removed, and cells were lysed.…”

A virion-based assay for glycoprotein thermostability reveals key determinants of filovirus entry and its inhibition

“…Among the SERMs known to inhibit EBOV entry, only toremifene has been tested for its effect on GP stability (32)(33)(34)57). Here, we tested two additional SERMs and structural analogs of toremifene-clomifene and ospemifene.…”

Two Achilles' Heels of the Ebolavirus Glycoprotein?

“…Experimental studies around the Ebolavirus disease, both fundamental and clinical, have been reported extensively in recent years . For instance, a set of Ebolavirus GP experimental structures were reported [14][15][16][115][116][117], including both apo (unliganded) structure of Ebolavirus GP, and also high-resolution complex structures of GP with a series of directly interacting compounds (including a variety of approved drugs) and also its neutralizing antibodies (Tables 1 and 2).…”