title: A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening.
abstract: 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.
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670, christian.noble@novartis.com.
authors.forename: Christian G
authors.initials: CG
authors.lastname: Noble
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.
authors.forename: Siew Pheng
authors.initials: SP
authors.lastname: Lim
authors.affiliation: the Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, and.
authors.forename: Rishi
authors.initials: R
authors.lastname: Arora
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Yokokawa
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.
authors.forename: Shahul
authors.initials: S
authors.lastname: Nilar
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.
authors.forename: Cheah Chen
authors.initials: CC
authors.lastname: Seh
authors.affiliation: the Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, and.
authors.forename: S Kirk
authors.initials: SK
authors.lastname: Wright
authors.affiliation: the Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, and.
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Benson
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.
authors.forename: Paul W
authors.initials: PW
authors.lastname: Smith
authors.affiliation: From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670, the Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555 peshi@utmb.edu.
authors.forename: Pei-Yong
authors.initials: PY
authors.lastname: Shi
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D003716:Dengue Virus / Q000201:enzymology*; D017434:Protein Structure, Tertiary; D014764:Viral Proteins / Q000737:chemistry*
chemical_list: D014764:Viral Proteins; D012321:DNA-Directed RNA Polymerases
keywords: RNA polymerase; crystallography; dengue virus (DENV); enzyme inhibitor; flavivirus; inhibitor; viral polymerase