Identification and In Silico Binding Study of a Highly Potent DENV NS2B-NS3 Covalent Inhibitor

Dengue virus (DENV), an arthropod-borne flavivirus, has developed rapidly in the past few decades and becoming the most widespread arbovirus in the world. The vital role of NS2B-NS3 in virus replication and maturation of viral proteins makes it the most promising target for anti-DENV drug discovery. In the current work, a potent NS2B-NS3 covalent inhibitor 23 (IC 50 = 6.0 nM, k inac / K i = 1581 M –1 s –1 ) was discovered through the chemical modification of a published covalent inhibitor 1 (IC 50 = 500 nM, k inac / K i = 156.1 M –1 s –1 ), followed by in vitro assay. Further comprehensive structure–activity relationship analysis through covalent docking and molecular dynamics simulation provides informative understanding of the binding modes of covalent inhibitors targeting NS2B-NS3.