5f3t

Publication Abstract from PubMed

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 8 identified a single hit that bound in a novel pocket in the protein. This pocket is located in the polymerase palm sub-domain 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.

A Conserved Pocket in the Dengue Virus Polymerase Identified Through Fragment-Based Screening.,Noble CG, Lim SP, Arora R, Yokokawa F, Nilar S, Seh CC, Wright SK, Benson TE, Smith PW, Shi PY J Biol Chem. 2016 Feb 12. pii: jbc.M115.710731. PMID:26872970^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.