title: Analysis of Differential Efficacy and Affinity of GABAA(α1/α2) Selective Modulators.
abstract: Selective modulators of the γ-amino butyric acid (GABAA) family of receptors have the potential to treat a range of disease states related to cognition, pain, and anxiety. While the development of various α subunit-selective modulators is currently underway for the treatment of anxiety disorders, a mechanistic understanding of the correlation between their bioactivity and efficacy, based on ligand-target interactions, is currently still lacking. In order to alleviate this situation, in the current study we have analyzed, using ligand- and structure-based methods, a data set of 5440 GABAAmodulators. The Spearman correlation (ρ) between binding activity and efficacy of compounds was calculated to be 0.008 and 0.31 against the α1 and α2 subunits of GABA receptor, respectively; in other words, the compounds had little diversity in structure and bioactivity, but they differed significantly in efficacy. Two compounds were selected as a case study for detailed interaction analysis due to the small difference in their structures and affinities (ΔpKi(comp1_α1 - comp2_α1)= 0.45 log units, ΔpKi(comp1_α2 - comp2_α2)= 0 log units) as compared to larger relative efficacies (ΔRE(comp1_α1 - comp2_α1)= 1.03, ΔRE(comp1_α2 - comp2_α2)= 0.21). Docking analysis suggested that His-101 is involved in a characteristic interaction of the α1 receptor with both compounds 1 and 2. Residues such as Phe-77, Thr-142, Asn-60, and Arg-144 of the γ chain of the α1γ2 complex also showed interactions with heterocyclic rings of both compounds 1 and 2, but these interactions were disturbed in the case of α2γ2 complex docking results. Binding pocket stability analysis based on molecular dynamics identified three substitutions in the loop C region of the α2 subunit, namely, G200E, I201T, and V202I, causing a reduction in the flexibility of α2 compared to α1. These amino acids in α2, as compared to α1, were also observed to decrease the vibrational and dihedral entropy and to increase the hydrogen bond content in α2 in the apo state. However, freezing of both α1 and α2 was observed in the ligand-bound state, with an increased number of internal hydrogen bonds and increased entropy. Therefore, we hypothesize that the amino acid differences in the loop C region of α2 are responsible for conformational changes in the protein structure compared to α1, as well as for the binding modes of compounds and hence their functional signaling.
authors.affiliation: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, United Kingdom.
authors.forename: Qurrat U
authors.initials: QU
authors.lastname: Ain
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer NPRU , The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, United Kingdom.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Owen
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer NPRU , The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, United Kingdom.
authors.forename: Kiyoyuki
authors.initials: K
authors.lastname: Omoto
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer NPRU , The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, United Kingdom.
authors.forename: Rubben
authors.initials: R
authors.lastname: Torella
authors.affiliation: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, United Kingdom.
authors.forename: Krishna C
authors.initials: KC
authors.lastname: Bulusu
authors.affiliation: Worldwide Medicinal Chemistry, Pfizer NPRU , The Portway Building, Granta Park, Great Abington, Cambridge, CB21 6GS, United Kingdom.
authors.forename: David C
authors.initials: DC
authors.lastname: Pryde
authors.affiliation: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, United Kingdom.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Glen
authors.affiliation: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, United Kingdom.|Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.
authors.forename: Julian E
authors.initials: JE
authors.lastname: Fuchs
authors.affiliation: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, United Kingdom.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bender
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001569:Benzodiazepines / Q000494:pharmacology; D020148:Butyric Acid / Q000494:pharmacology; D058785:GABA-A Receptor Agonists / Q000494:pharmacology; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D018079:Receptors, GABA / Q000737:chemistry / Q000378:metabolism*
chemical_list: D058785:GABA-A Receptor Agonists; D018079:Receptors, GABA; D020148:Butyric Acid; D001569:Benzodiazepines
keywords: GABAA α1; GABAA α2; affinity modeling; benzodiazepines; proteochemometric modeling; relative efficacy; selective modulators