Haffez2017 - RAR interaction with synthetic analogues

  public model
Model Identifier
BIOMD0000000629
Short description
Haffez2017 - RAR interaction with synthetic analogues

This model is described in the article:

Hesham Haffez, David R. Chisholm, Roy Valentine, Ehmke Pohl, Christopher Redfern and Andrew Whiting
MedChemComm

Abstract:

All-trans-retinoic acid (ATRA) and its synthetic analogues EC23 and EC19 direct cellular differentiation by interacting as ligands for the retinoic acid receptor (RARα, β and γ) family of nuclear receptor proteins. To date, a number of crystal structures of natural and synthetic ligands complexed to their target proteins have been solved, providing molecular level snap-shots of ligand binding. However, a deeper understanding of receptor and ligand flexibility and conformational freedom is required to develop stable and effective ATRA analogues for clinical use. Therefore, we have used molecular modelling techniques to define RAR interactions with ATRA and two synthetic analogues, EC19 and EC23, and compared their predicted biochemical activities to experimental measurements of relative ligand affinity and recruitment of coactivator proteins. A comprehensive molecular docking approach that explored the conformational space of the ligands indicated that ATRA is able to bind the three RAR proteins in a number of conformations with one extended structure being favoured. In contrast the biologically-distinct isomer, 9-cis-retinoic acid (9CRA), showed significantly less conformational flexibility in the RAR binding pockets. These findings were used to inform docking studies of the synthetic retinoids EC23 and EC19, and their respective methyl esters. EC23 was found to be an excellent mimic for ATRA, and occupied similar binding modes to ATRA in all three target RAR proteins. In comparison, EC19 exhibited an alternative binding mode which reduces the strength of key polar interactions in RARα/γ but is well-suited to the larger RARβ binding pocket. In contrast, docking of the corresponding esters revealed the loss of key polar interactions which may explain the much reduced biological activity. Our computational results were complemented using an in vitro binding assay based on FRET measurements, which showed that EC23 was a strongly binding, pan-agonist of the RARs, while EC19 exhibited specificity for RARβ, as predicted by the docking studies. These findings can account for the distinct behaviour of EC23 and EC19 in cellular differentiation assays, and additionally, the methods described herein can be further applied to the understanding of the molecular basis for the selectivity of different retinoids to RARα, β and γ.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Format
SBML (L2V4)
Related Publication
  • The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors
  • Hesham Haffez, David R. Chisholm, Roy Valentine, Ehmke Pohl, Christopher Redfern and Andrew Whiting
  • MedChemComm , DOI: 10.1039/C6MD00680A
  • Department of Chemistry Durham University, Department of Biosciences & Biophysical Sciences,Durham University, Northern Institute for Cancer Research, Medical School, Newcastle University, Department of Biochemistry and Molecular Biology, Pharmacy College, Helwan University and High Force Research Ltd., Bowburn North Industrial Estate, Bowburn, Durham
  • All-trans-retinoic acid (ATRA) and its synthetic analogues EC23 and EC19 direct cellular differentiation by interacting as ligands for the retinoic acid receptor (RARα, β and γ) family of nuclear receptor proteins. To date, a number of crystal structures of natural and synthetic ligands complexed to their target proteins have been solved, providing molecular level snap-shots of ligand binding. However, a deeper understanding of receptor and ligand flexibility and conformational freedom is required to develop stable and effective ATRA analogues for clinical use. Therefore, we have used molecular modelling techniques to define RAR interactions with ATRA and two synthetic analogues, EC19 and EC23, and compared their predicted biochemical activities to experimental measurements of relative ligand affinity and recruitment of coactivator proteins. A comprehensive molecular docking approach that explored the conformational space of the ligands indicated that ATRA is able to bind the three RAR proteins in a number of conformations with one extended structure being favoured. In contrast the biologically-distinct isomer, 9-cis-retinoic acid (9CRA), showed significantly less conformational flexibility in the RAR binding pockets. These findings were used to inform docking studies of the synthetic retinoids EC23 and EC19, and their respective methyl esters. EC23 was found to be an excellent mimic for ATRA, and occupied similar binding modes to ATRA in all three target RAR proteins. In comparison, EC19 exhibited an alternative binding mode which reduces the strength of key polar interactions in RARα/γ but is well-suited to the larger RARβ binding pocket. In contrast, docking of the corresponding esters revealed the loss of key polar interactions which may explain the much reduced biological activity. Our computational results were complemented using an in vitro binding assay based on FRET measurements, which showed that EC23 was a strongly binding, pan-agonist of the RARs, while EC19 exhibited specificity for RARβ, as predicted by the docking studies. These findings can account for the distinct behaviour of EC23 and EC19 in cellular differentiation assays, and additionally, the methods described herein can be further applied to the understanding of the molecular basis for the selectivity of different retinoids to RARα, β and γ.
Contributors
Hesham Haffez, administrator

Metadata information

is
BioModels Database MODEL1702240000
BioModels Database BIOMD0000000629
hasTaxon
isDescribedBy

Curation status
Curated

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Model files

BIOMD0000000629_url.xml SBML L2V4 representation of Haffez2017 - RAR interaction with synthetic analogues 31.51 KB Preview | Download

Additional files

BIOMD0000000629.svg Auto-generated Reaction graph (SVG) 5.83 KB Preview | Download
BIOMD0000000629.m Auto-generated Octave file 3.58 KB Preview | Download
BIOMD0000000629.sci Auto-generated Scilab file 1.89 KB Preview | Download
SigmaplotFiles.zip These Files can be used with sigmaplot to reproduce the figures in the paper 84.90 KB Preview | Download
BIOMD0000000629.pdf Auto-generated PDF file 156.18 KB Preview | Download
BIOMD0000000629.xpp Auto-generated XPP file 1.72 KB Preview | Download
BIOMD0000000629-biopax2.owl Auto-generated BioPAX (Level 2) 8.51 KB Preview | Download
BIOMD0000000629.vcml Auto-generated VCML file 58.72 KB Preview | Download
BIOMD0000000629.png Auto-generated Reaction graph (PNG) 16.28 KB Preview | Download
BIOMD0000000629-biopax3.owl Auto-generated BioPAX (Level 3) 11.46 KB Preview | Download
BIOMD0000000629_urn.xml Auto-generated SBML file with URNs 31.33 KB Preview | Download

  • Model originally submitted by : Hesham Haffez
  • Submitted: Feb 24, 2017 8:26:15 PM
  • Last Modified: Dec 21, 2018 6:20:32 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Dec 21, 2018 6:20:32 PM
    • Submitted by: administrator
    • With comment: Include the additional files provided by the submitter in the original submission: SigmaplotFiles.zip
  • Version: 2 public model Download this version
    • Submitted on: Apr 20, 2017 3:49:49 PM
    • Submitted by: Hesham Haffez
    • With comment: Current version of Haffez2017 - RAR interaction with synthetic analogues
  • Version: 1 public model Download this version
    • Submitted on: Feb 24, 2017 8:26:15 PM
    • Submitted by: Hesham Haffez
    • With comment: Original import of RAR-retinoids biomodel

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
L

all-trans-retinoic acid
5.0E-4 ��mol
LR

all-trans-retinoic acid ; Retinoic acid receptor alpha
0.0 ��mol
R

Retinoic acid receptor alpha
0.0035 ��mol
CA

fluorescin ; peptide
30.0 ��mol
LRCA

all-trans-retinoic acid ; Retinoic acid receptor alpha
0.0 ��mol
Reactions
Reactions Rate Parameters
RAR_retinoids*(k1*L*R-k2*LR)

RAR_retinoids*(k1*L*R-k2*LR)
k1=0.6; k2=0.1
RAR_retinoids*(k1*LR*CA-k2*LRCA)

RAR_retinoids*(k1*LR*CA-k2*LRCA)
k2=0.2; k1=0.014
Curator's comment:
(added: 17 Mar 2017, 14:13:15, updated: 17 Mar 2017, 14:13:15)
We used COPASI 4.19 (Build 140) to reproduce figure 14 d from the paper. The simulation was run on COPASI and the plot was generated using R. The authors in the original paper have used COPASI to calculate the steady state values. These values were then used on SigmaPlot and a 3-parameter sigmoidal curve f = min + (max-min)/(1+10^(logEC50-x)) was used in generating this figure.