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

We performed a fragment screen on the dengue virus serotype 3 RNA-dependent RNA polymerase using x-ray crystallography. A screen of 1,400 fragments in pools of eight identified a single hit that bound in a novel pocket in the protein. This pocket is located in the polymerase palm subdomain and conse...

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Bibliographic Details
Published in:The Journal of biological chemistry 2016-04, Vol.291 (16), p.8541-8548
Main Authors: Noble, Christian G., Lim, Siew Pheng, Arora, Rishi, Yokokawa, Fumiaki, Nilar, Shahul, Seh, Cheah Chen, Wright, S.Kirk, Benson, Timothy E., Smith, Paul W., Shi, Pei-Yong
Format: Article
Language:English
Subjects:
Catalytic Domain
crystallography
Crystallography, X-Ray
dengue virus (DENV)
Dengue Virus - enzymology
DNA-Directed RNA Polymerases - chemistry
enzyme inhibitor
flavivirus
inhibitor
Molecular Biophysics
Protein Structure, Tertiary
RNA polymerase
viral polymerase
Viral Proteins - chemistry
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Summary:We performed a fragment screen on the dengue virus serotype 3 RNA-dependent RNA polymerase using x-ray crystallography. A screen of 1,400 fragments in pools of eight identified a single hit that bound in a novel pocket in the protein. This pocket is located in the polymerase palm subdomain and conserved across the four serotypes of dengue virus. The compound binds to the polymerase in solution as evidenced by surface plasmon resonance and isothermal titration calorimetry analyses. Related compounds where a phenyl is replaced by a thiophene show higher affinity binding, indicating the potential for rational design. Importantly, inhibition of enzyme activity correlated with the binding affinity, showing that the pocket is functionally important for polymerase activity. This fragment is an excellent starting point for optimization through rational structure-based design.
ISSN:0021-9258
1083-351X
DOI:10.1074/jbc.M115.710731