Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in “Super-Open” Conformation

Abstract

The Zika virus (ZIKV), a member of the Flaviviridae family, is considered a major health threat causing multiple cases of microcephaly in newborns and Guillain-Barré syndrome in adults. In this study, we targeted a transient, deep, and hydrophobic pocket of the “super-open” conformation of ZIKV NS2B-NS3 protease to overcome the limitations of the active site pocket. After virtual docking screening of approximately seven million compounds against the novel allosteric site, we selected the top six candidates and assessed them in enzymatic assays. Six candidates inhibited ZIKV NS2B-NS3 protease proteolytic activity at low micromolar concentrations. These six compounds, targeting the selected protease pocket conserved in ZIKV, serve as unique drug candidates and open new opportunities for possible treatment against several flavivirus infections.

Crystallographic fragment screening delivers diverse chemical scaffolds for Zika virus NS2B-NS3 protease inhibitor development

“…Our fragment screening data presented herein, helps to reduce this knowledge gap and map the allosteric site with structural details. Although the allosteric binding pocket we described is present in a closed conformation, it is in agreement with a proposed allosteric site reported previously 12, 18 , supporting the ligandability of the interface of C-terminal β-hairpin of NS2B and NS3. However, the diverse fragment scaffolds and distinct binding poses and interactions make it necessary that we acknowledge the challenges, as well as opportunities, for non-competitive inhibitor development.…”

“…The identification of several fragment hits in a potential allosteric binding site not only provides novel chemical matter for the development of potential allosteric inhibitors, but also helps to structurally characterise this putative allosteric site. Multiple allosteric sites of Flaviviral NS2B-NS3 protease have been proposed but without structural description 12, 18, 20 . Our fragment screening data presented herein, helps to reduce this knowledge gap and map the allosteric site with structural details.…”

“…These residues wrap around NS3 with the C-terminal residues forming a β-hairpin structurally contributing to the protease active site as well as participating in substrate recognition 8 . Structural studies have revealed several conformations of this unique two-component NS2B-NS3 protease, specifically a closed conformation 9 , an open conformation 10, 11 , and a super-open conformation 12 , depending on the dynamic interactions between NS2B and NS3. In the open conformation and super-open conformation, the C-terminal portion of NS2B is disordered and locates distant from the NS3 catalytic site, resulting in an unstructured substrate binding site.…”

Antiviral Activity of Flavonoids from Bauhinia holophylla Leaves against Zika virus

“…However, there are still no specific, safe, and effective drugs or vaccines to protect against ZIKV infection. There are only palliative treatments and symptom management [4,10,11]. NS2B-NS3 protease is essential for ZIKV replication, designating it as a potential target for treatment [10].…”

“…There are only palliative treatments and symptom management [4,10,11]. NS2B-NS3 protease is essential for ZIKV replication, designating it as a potential target for treatment [10].…”