Comparison of templates for homology model of ρ1 GABA C  receptors: More insights to the orthosteric binding site’s structure and functionality

Naffaa, Moawiah M.; Chebib, Mary; Hibbs, David E.; Hanrahan, Jane R.

doi:10.1016/j.jmgm.2015.09.002

Cited by 10 publications

(26 citation statements)

References 66 publications

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“…The sequence identity between the GluCl template and the ρ1 and ρ2 receptors is 37% and 36.6%, and it is even higher when only the pore‐lining helices are considered (54.2% and 58.3%, respectively). Indeed, GluCl has been proposed to be the best template to model the structure of GABA A ρ receptors (Naffaa, Chebib, Hibbs, & Hanrahan, ). For the S2′G ρ1 and P2′S ρ2 mutant receptors, the mutation was introduced in silico using the Molefacture tool (version 1.3) in VMD (version 1.9.2; Humphrey, Dalke, & Schulten, ).…”

Section: Methodsmentioning

confidence: 99%

A photoswitchable GABA receptor channel blocker

Maleeva

Wutz

Rustler

et al. 2019

British J Pharmacology

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Background and Purpose Anion‐selective Cys‐loop receptors (GABA and glycine receptors) provide the main inhibitory drive in the CNS. Both types of receptor operate via chloride‐selective ion channels, though with different kinetics, pharmacological profiles, and localization. Disequilibrium in their function leads to a variety of disorders, which are often treated with allosteric modulators. The few available GABA and glycine receptor channel blockers effectively suppress inhibitory currents in neurons, but their systemic administration is highly toxic. With the aim of developing an efficient light‐controllable modulator of GABA receptors, we constructed azobenzene‐nitrazepam (Azo‐NZ1), which is composed of a nitrazepam moiety merged to an azobenzene photoisomerizable group. Experimental Approach The experiments were carried out on cultured cells expressing Cys‐loop receptors of known subunit composition and in brain slices using patch‐clamp. Site‐directed mutagenesis and molecular modelling approaches were applied to evaluate the mechanism of action of Azo‐NZ1. Key Results At visible light, being in trans‐configuration, Azo‐NZ1 blocked heteromeric α1/β2/γ2 GABAA receptors, ρ2 GABAA (GABAC), and α2 glycine receptors, whereas switching the compound into cis‐state by UV illumination restored the activity. Azo‐NZ1 successfully photomodulated GABAergic currents recorded from dentate gyrus neurons. We demonstrated that in trans‐configuration, Azo‐NZ1 blocks the Cl‐selective ion pore of GABA receptors interacting mainly with the 2′ level of the TM2 region. Conclusions and Implications Azo‐NZ1 is a soluble light‐driven Cl‐channel blocker, which allows photo‐modulation of the activity induced by anion‐selective Cys‐loop receptors. Azo‐NZ1 is able to control GABAergic postsynaptic currents and provides new opportunities to study inhibitory neurotransmission using patterned illumination.

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Section: Methodsmentioning

confidence: 99%

A photoswitchable GABA receptor channel blocker

Maleeva

Wutz

Rustler

et al. 2019

British J Pharmacology

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“…We then combined a mutation that eliminates ethanol inhibition (T6’Y) with a previously described mutation that may provide a potentiating binding site for alcohols (I15’S), and studied the effects of alcohols of different chain length on these mutants. We also built homology models of wild-type and mutated ρ1 receptors, based on the the wild-type GluCl, which has been identified as the best template to model the ρ1 receptor out of five different X-ray crystal structures 25 .…”

Section: Introductionmentioning

confidence: 99%

Identification of an Inhibitory Alcohol Binding Site in GABA_A ρ1 Receptors

Borghese

Ruiz

Lee

et al. 2015

ACS Chem. Neurosci.

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Alcohols inhibit γ-aminobutyric acid type A ρ1 receptor function. After introducing mutations in several positions of the second transmembrane helix in ρ1, we studied the effects of ethanol and hexanol on GABA responses using two-electrode voltage clamp electrophysiology in Xenopus laevis oocytes. The 6′ mutations produced the following effects on ethanol and hexanol responses: small increase or no change (T6′M), increased inhibition (T6′V) and small potentiation (T6′Y and T6′F). The 5′ mutations produced mainly increases in hexanol inhibition. Other mutations produced small (3′ and 9′) or no changes (2′ and L277 in the first transmembrane domain) in alcohol effects. These results suggest an inhibitory alcohol binding site near the 6′ position. Homology models of ρ1 receptors based on the X-ray structure of GluCl showed that the 2′, 5′, 6’ and 9′ residues were easily accessible from the ion pore, with 5′ and 6′ residues from neighboring subunits facing each other; L3′ and L277 also faced the neighboring subunit. We tested ethanol through octanol on single and double mutated ρ1 receptors [ρ1(I15′S), ρ1(T6′Y) and ρ1(T6′Y,I15′S)] to further characterize the inhibitory alcohol pocket in the wild-type ρ1 receptor. The pocket can only bind relatively short-chain alcohols and is eliminated by introducing Y in the 6’ position. Replacing the bulky 15′ residue with a smaller side chain introduced a potentiating binding site, more sensitive to long-chain than to short-chain alcohols. In conclusion, the net alcohol effect on the ρ1 receptor is determined by the sum of its actions on inhibitory and potentiating sites.

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“…Pentameric ligand‐gated ion channel receptor of GABA‐ρ homology model based on GluCl structure prepared has been previously described (Naffaa et al, ). A single ion channel showing the main domains with five identical subunits, coloured differently to show the intersubunit interfaces located between the principal (+) and complementary (−) sides.…”

Section: Cys‐loop Pentameric Ligand‐gated Ion Channelsmentioning

confidence: 99%

“…The amino acid sequence alignment of GABA‐ρ1, GABA‐ρ2 and GABA‐ρ3 subunits. Alignments were prepared as previously described (Naffaa et al, ). The amino acid sequence of various human GABA‐ρ receptors was obtained from the Universal Protein Resources ( http://www.uniprot.org/) (UniProt Consortium, 2013).…”

Section: Gaba‐ρ Receptorsmentioning

confidence: 99%

“…Homology models of GABA‐ρ receptors (Harrison and Lummis, ; Abdel‐Halim et al, ; Osolodkin et al, ; Tai et al, ; Naffaa et al, ) have been based on the five different LGIC crystal structures, AChBP, ELIC, GLIC, GABA A β 3 and GluCl (Brejc et al, ; Hilf and Dutzler, ; Chen et al, ; Hibbs and Gouaux, ; Miller and Aricescu, ). With the exception of AChBP, these crystal structures are of full ion channels, with varying percentages of residues conserved with GABA‐ρ.…”

Section: Structure and Function Of Gaba‐ρ1 Receptorsmentioning

confidence: 99%

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GABA‐ρ receptors: distinctive functions and molecular pharmacology

Naffaa

Hung

Chebib

et al. 2017

British J Pharmacology

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The homomeric GABA-ρ ligand-gated ion channels (also known as GABA or GABA -ρ receptors) are similar to heteromeric GABA receptors in structure, function and mechanism of action. However, their distinctive pharmacological properties and distribution make them of special interest. This review focuses on GABA-ρ ion channel structure, ligand selectivity toward ρ receptors over heteromeric GABA receptor sub-types and selectivity between different homomeric ρ sub-type receptors. Several GABA analogues show selectivity at homomeric GABA-ρ receptors over heteromeric GABA receptors. More recently, some synthetic ligands have been found to show selectivity at receptors formed from one ρ subtype over others. The unique pharmacological profiles of these agents are discussed in this review. The classical binding site of GABA within the orthosteric site of GABA-ρ homomeric receptors is discussed in detail regarding the loops and residues that constitute the binding site. The ligand-residue interactions in this classical binding and those of mutant receptors are discussed. The structure and conformations of GABA are discussed in regard to its flexibility and molecular properties. Although the binding mode of GABA is difficult to predict, several interactions between GABA and the receptor assist in predicting its potential conformation and mode of action. The structure-activity relationships of GABA and structurally key ligands at ρ receptors are described and discussed.

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Comparison of templates for homology model of ρ1 GABA C receptors: More insights to the orthosteric binding site’s structure and functionality

Cited by 10 publications

References 66 publications

A photoswitchable GABA receptor channel blocker

A photoswitchable GABA receptor channel blocker

Identification of an Inhibitory Alcohol Binding Site in GABA_A ρ1 Receptors

GABA‐ρ receptors: distinctive functions and molecular pharmacology

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Comparison of templates for homology model of ρ1 GABA C receptors: More insights to the orthosteric binding site’s structure and functionality

Cited by 10 publications

References 66 publications

A photoswitchable GABA receptor channel blocker

A photoswitchable GABA receptor channel blocker

Identification of an Inhibitory Alcohol Binding Site in GABAA ρ1 Receptors

GABA‐ρ receptors: distinctive functions and molecular pharmacology

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Product

Resources

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Identification of an Inhibitory Alcohol Binding Site in GABA_A ρ1 Receptors