Profiling of flaviviral NS2B-NS3 protease specificity provides a structural basis for the development of selective chemical tools that differentiate Dengue from Zika and West Nile viruses

Antiviral Res. 2020 Mar;175:104731. doi: 10.1016/j.antiviral.2020.104731. Epub 2020 Jan 31.


West Nile virus (WNV) and Dengue virus (DENV) are mosquito-borne pathogenic flaviviruses. The NS2B-NS3 proteases found in these viruses are responsible for polyprotein processing and are therefore considered promising medical targets. Another ortholog of these proteases is found in Zika virus (ZIKV). In this work, we applied a combinatorial chemistry approach - Hybrid Combinatorial Substrate Library (HyCoSuL), to compare the substrate specificity profile at the P4-P1 positions of the NS2B-NS3 proteases found in all three viruses. The obtained data demonstrate that Zika and West Nile virus NS2B-NS3 proteases display highly overlapping substrate specificity in all binding pockets, while the Dengue ortholog has slightly different preferences toward natural and unnatural amino acids at the P2 and P4 positions. We used this information to extract specific peptide sequences recognized by the Dengue NS2B-NS3 protease. Next, we applied this knowledge to design a selective substrate and activity-based probe for the Dengue NS2B-NS3 protease. Our work provides a structural framework for the design of inhibitors, which could be used as a lead structure for drug development efforts.

Keywords: Dengue; Proteolytic enzyme; Serine hydrolase; Substrate specificity; West Nile; Zika.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Combinatorial Chemistry Techniques
  • Dengue Virus / chemistry
  • Dengue Virus / enzymology*
  • Drug Development
  • Kinetics
  • Models, Molecular*
  • RNA Helicases / chemistry
  • RNA Helicases / metabolism
  • Serine Endopeptidases / chemistry
  • Serine Endopeptidases / metabolism
  • Structure-Activity Relationship
  • Substrate Specificity
  • Viral Nonstructural Proteins / chemistry
  • Viral Nonstructural Proteins / metabolism*
  • West Nile virus / chemistry
  • West Nile virus / enzymology*
  • Zika Virus / chemistry
  • Zika Virus / enzymology*


  • NS2B protein, flavivirus
  • NS3 protein, flavivirus
  • Viral Nonstructural Proteins
  • Serine Endopeptidases
  • RNA Helicases