A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening

Area of Science:

• Virology
• Structural Biology
• Drug Discovery

Background:

• Dengue virus poses a significant global health threat, necessitating the development of effective antiviral treatments.
• The dengue virus RNA-dependent RNA polymerase is a critical target for antiviral drug development.

Purpose of the Study:

• To identify novel small molecules that bind to the dengue virus serotype 3 RNA-dependent RNA polymerase.
• To characterize the binding site and its functional importance for enzyme activity.

Main Methods:

• Fragment-based screening using X-ray crystallography.
• Biophysical characterization using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC).
• Enzyme inhibition assays.

Main Results:

• A single fragment hit was identified from a screen of 1,400 compounds, binding to a novel pocket in the polymerase palm subdomain.
• This pocket is conserved across all four dengue virus serotypes.
• The fragment binds to the polymerase in solution, and related compounds show improved binding affinity, suggesting potential for rational design.
• Fragment binding correlated with inhibition of enzyme activity, indicating functional importance.

Conclusions:

• A novel, functionally important binding pocket on the dengue virus RNA-dependent RNA polymerase has been identified.
• The identified fragment serves as a promising starting point for structure-based drug design against dengue virus.
• Further optimization of related compounds could lead to potent antiviral agents.