A conserved pocket in the dengue virus polymerase identified through fragment-based screening

Christian G. Noble, Siew Pheng Lim, Rishi Arora, Fumiaki Yokokawa, Shahul Nilar, Cheah Chen Seh, S. Kirk Wright, Timothy E. Benson, Paul W. Smith, Pei-Yong Shi

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)8541-8548
Number of pages8
JournalJournal of Biological Chemistry
Volume291
Issue number16
DOIs
StatePublished - Apr 15 2016

Fingerprint

Dengue Virus
Viruses
Screening
Enzyme inhibition
RNA Replicase
Thiophenes
Calorimetry
Crystallography
Surface Plasmon Resonance
Enzyme activity
Surface plasmon resonance
Titration
X-Rays
X rays
Enzymes
Proteins
Serogroup

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

A conserved pocket in the dengue virus polymerase identified through fragment-based screening. / 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.

In: Journal of Biological Chemistry, Vol. 291, No. 16, 15.04.2016, p. 8541-8548.

Research output: Contribution to journalArticle

Noble, CG, Lim, SP, Arora, R, Yokokawa, F, Nilar, S, Seh, CC, Wright, SK, Benson, TE, Smith, PW & Shi, P-Y 2016, 'A conserved pocket in the dengue virus polymerase identified through fragment-based screening', Journal of Biological Chemistry, vol. 291, no. 16, pp. 8541-8548. https://doi.org/10.1074/jbc.M115.710731
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. / A conserved pocket in the dengue virus polymerase identified through fragment-based screening. In: Journal of Biological Chemistry. 2016 ; Vol. 291, No. 16. pp. 8541-8548.
@article{e0c63c6753064f148641bc42b802f167,
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.",
author = "Noble, {Christian G.} and Lim, {Siew Pheng} and Rishi Arora and Fumiaki Yokokawa and Shahul Nilar and Seh, {Cheah Chen} and Wright, {S. Kirk} and Benson, {Timothy E.} and Smith, {Paul W.} and Pei-Yong Shi",
year = "2016",
month = "4",
day = "15",
doi = "10.1074/jbc.M115.710731",
language = "English (US)",
volume = "291",
pages = "8541--8548",
journal = "Journal of Biological Chemistry",
issn = "0021-9258",
publisher = "American Society for Biochemistry and Molecular Biology Inc.",
number = "16",

}

TY - JOUR

T1 - A conserved pocket in the dengue virus polymerase identified through fragment-based screening

AU - Noble, Christian G.

AU - Lim, Siew Pheng

AU - Arora, Rishi

AU - Yokokawa, Fumiaki

AU - Nilar, Shahul

AU - Seh, Cheah Chen

AU - Wright, S. Kirk

AU - Benson, Timothy E.

AU - Smith, Paul W.

AU - Shi, Pei-Yong

PY - 2016/4/15

Y1 - 2016/4/15

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84963995644&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84963995644&partnerID=8YFLogxK

U2 - 10.1074/jbc.M115.710731

DO - 10.1074/jbc.M115.710731

M3 - Article

VL - 291

SP - 8541

EP - 8548

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 16

ER -