3TYV

SAR development and discovery of potent indole-based inhibitors of the hepatitis C virus NS5B polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Activity Relationship (SAR) Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus (HCV) NS5B Polymerase.

Chen, K.X.Vibulbhan, B.Yang, W.Sannigrahi, M.Velazquez, F.Chan, T.Y.Venkatraman, S.Anilkumar, G.N.Zeng, Q.Bennet, F.Jiang, Y.Lesburg, C.A.Duca, J.Pinto, P.Gavalas, S.Huang, Y.Wu, W.Selyutin, O.Agrawal, S.Feld, B.Huang, H.C.Li, C.Cheng, K.C.Shih, N.Y.Kozlowski, J.A.Rosenblum, S.B.Njoroge, F.G.

(2012) J Med Chem 55: 754-765

  • DOI: 10.1021/jm201258k
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Starting with the indole-based C-3 pyridone lead HCV polymerase inhibitor 2, extensive SAR studies were performed at different positions of the indole core. The best C-5 groups were found to be compact and nonpolar moieties and that the C-6 attachmen ...

    Starting with the indole-based C-3 pyridone lead HCV polymerase inhibitor 2, extensive SAR studies were performed at different positions of the indole core. The best C-5 groups were found to be compact and nonpolar moieties and that the C-6 attachments were not affecting potency. Limited N-1 benzyl-type substituent studies indicated that the best substitutions were fluoro or methyl groups at 2' or 5' positions of the benzyl group. To improve pharmacokinetic (PK) properties, acylsulfonamides were incorporated as acid isosteres at the C-2 position. Further optimization of the combination at N-1, C-2, C-5, and C-6 resulted in the identification of compound 56, which had an excellent potency in both NS5B enzyme (IC(50) = 0.008 μM) and cell-based replicon (EC(50) = 0.02 μM) assays and a good oral PK profile with area-under-the curve (AUC) of 14 and 8 μM·h in rats and dogs, respectively. X-ray structure of inhibitor 56 bound to the enzyme was also reported.


    Organizational Affiliation

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States. kxcn@yahoo.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
576Hepatitis C virus isolate HC-J4Mutation(s): 0 
Gene Names: NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HI3
Query on HI3

Download CCD File 
A, B
N-(cyclopropylsulfonyl)-1-(2,5-difluorobenzyl)-6-fluoro-5-methyl-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxamide
C25 H20 F3 N3 O4 S
GXKRHWPFLHJAKI-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HI3IC50:  8   nM  PDBBind
HI3IC50:  8   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.65α = 90
b = 106.72β = 90
c = 133.94γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
BUSTERrefinement
AutoPROCdata scaling
XDSdata reduction
SCALAdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description