5TA2

Discovery of a Potent Cyclophilin Inhibitor (Compound 7) based on Structural Simplification of Sanglifehrin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of Potent Cyclophilin Inhibitors Based on the Structural Simplification of Sanglifehrin A.

Steadman, V.A.Pettit, S.B.Poullennec, K.G.Lazarides, L.Keats, A.J.Dean, D.K.Stanway, S.J.Austin, C.A.Sanvoisin, J.A.Watt, G.M.Fliri, H.G.Liclican, A.C.Jin, D.Wong, M.H.Leavitt, S.A.Lee, Y.J.Tian, Y.Frey, C.R.Appleby, T.C.Schmitz, U.Jansa, P.Mackman, R.L.Schultz, B.E.

(2017) J Med Chem 60: 1000-1017

  • DOI: 10.1021/acs.jmedchem.6b01329
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cyclophilin inhibition has been a target for the treatment of hepatitis C and other diseases, but the generation of potent, drug-like molecules through chemical synthesis has been challenging. In this study, a set of macrocyclic cyclophilin inhibitor ...

    Cyclophilin inhibition has been a target for the treatment of hepatitis C and other diseases, but the generation of potent, drug-like molecules through chemical synthesis has been challenging. In this study, a set of macrocyclic cyclophilin inhibitors was synthesized based on the core structure of the natural product sanglifehrin A. Initial compound optimization identified the valine-m-tyrosine-piperazic acid tripeptide (Val-m-Tyr-Pip) in the sanglifehrin core, stereocenters at C14 and C15, and the hydroxyl group of the m-tyrosine (m-Tyr) residue as key contributors to compound potency. Replacing the C18-C21 diene unit of sanglifehrin with a styryl group led to potent compounds that displayed a novel binding mode in which the styrene moiety engaged in a π-stacking interaction with Arg55 of cyclophilin A (Cyp A), and the m-Tyr residue was displaced into solvent. This observation allowed further simplifications of the scaffold to generate new lead compounds in the search for orally bioavailable cyclophilin inhibitors.


    Organizational Affiliation

    Gilead Sciences , 333 Lakeside Drive, Foster City, California 94404, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase A
A
163Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78X
Query on 78X

Download CCD File 
A
11-[(3-hydroxyphenyl)methyl]-18-methoxy-2,17-dimethyl-14-(propan-2-yl)-3-oxa-9,12,15,28-tetraazatricyclo[21.3.1.1~5,9~]octacosa-1(27),21,23,25-tetraene-4,10,13,16-tetrone
C36 H48 N4 O7
SDVRVWXKFPHKSR-IBVKFTFISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
78XKd:  11   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.249α = 90
b = 52.356β = 90
c = 81.774γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-02-15
    Changes: Database references
  • Version 1.3: 2017-03-29
    Changes: Structure summary