New aryl hydrocarbon receptor homology model targeted to improve docking reliability

Ilaria Motto, Annalisa Bordogna, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-ARNT-Sim (PAS) containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). As no experimentally determined structures of the AhR ligand binding domain (LBD) are available and previous homology models were only derived from apo template structures, we developed a new model based on holo X-ray structures of the hypoxia-inducible factor 2α (HIF-2α) PAS B domain, targeted to improve the accuracy of the binding site for molecular docking applications. We experimentally confirmed the ability of two HIF-2α crystallographic ligands to bind to the mAhR with relatively high affinity and demonstrated that they are AhR agonists, thus justifying the use of the holo HIF-2α structures as templates. A specific modeling/docking approach was proposed to predict the binding modes of AhR ligands in the modeled LBD. It was validated by comparison of the calculated and the experimental binding affinities of active THS ligands and TCDD for the mAhR and by functional activity analysis using several mAhR mutants generated on the basis of the modeling results. Finally the ability of the proposed approach to reproduce the different affinities of TCDD for AhRs of different species was confirmed, and a first test of its reliability in virtual screening is carried out by analyzing the correlation between the calculated and experimental binding affinities of a set of 14 PCDDs.

Original languageEnglish (US)
Pages (from-to)2868-2881
Number of pages14
JournalJournal of Chemical Information and Modeling
Volume51
Issue number11
DOIs
StatePublished - Nov 28 2011

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Aryl Hydrocarbon Receptors
Hydrocarbons
Ligands
ability
Transcription factors
Poisons
Binding sites
Screening
Transcription Factors
Binding Sites
Impurities
X rays
1,4-dioxin
endothelial PAS domain-containing protein 1

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

Cite this

New aryl hydrocarbon receptor homology model targeted to improve docking reliability. / Motto, Ilaria; Bordogna, Annalisa; Soshilov, Anatoly A.; Denison, Michael S.; Bonati, Laura.

In: Journal of Chemical Information and Modeling, Vol. 51, No. 11, 28.11.2011, p. 2868-2881.

Research output: Contribution to journalArticle

Motto, Ilaria ; Bordogna, Annalisa ; Soshilov, Anatoly A. ; Denison, Michael S. ; Bonati, Laura. / New aryl hydrocarbon receptor homology model targeted to improve docking reliability. In: Journal of Chemical Information and Modeling. 2011 ; Vol. 51, No. 11. pp. 2868-2881.
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