5T9W

Discovery of a Potent Cyclophilin Inhibitor (Compound 5) based on Structural Simplification of Sanglifehrin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

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
  • Primary Citation of Related Structures:  
    5T9U, 5T9W, 5T9Z, 5TA2, 5TA4

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase AA164Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78E
Query on 78E

Download CCD File 
A
3-[(3-hydroxyphenyl)methyl]-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone
C30 H42 N4 O6
ZXIFDXMZMTULOX-WDJUPVIMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
78EKd:  2600   nM  Binding MOAD
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.864α = 90
b = 84.514β = 90
c = 68.533γ = 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