Structural Determinants for High-Affinity Zolpidem Binding to GABA-A receptors

Sancar, Feyza; Ericksen, Spencer S.; Kucken, Amy M.; Teissére, Jeremy A.; Czajkowski, Cynthia

doi:10.1124/mol.106.029595

Cited by 53 publications

(45 citation statements)

References 38 publications

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“…The lack of correlation with residue volume suggests that the effect of this mutation may relate to conformational changes associated with receptor activation, rather than binding, which may not be reflected by our model. In a recent study, Sancar et al (2007) reported automated docking of FNZ and zolpidem, which resulted in a FNZ position that differs significantly from our results. In this model, the N1-methyl substituent is directed toward the membrane and is buried in the binding site, the carboxyl group is in close proximity to ␥ 2 Arg144 and ␣ 1 Thr206, and a fluorine atom is located next to ␣ 1 Tyr209, with ␥ 2 Thr193 and ␥ 2 Arg194 located close to C5-phenyl moiety.…”

Section: Discussioncontrasting

confidence: 57%

“…This may indicate the existence of an additional favorable orientation in which the BZ directly contacts this residue, as proposed by Sancar et al (2007); however, the introduction of nonaromatic ␥ 2 F77L, Fig. 9.…”

Section: Discussionmentioning

confidence: 98%

“…In this model, the N1-methyl substituent is directed toward the membrane and is buried in the binding site, the carboxyl group is in close proximity to ␥ 2 Arg144 and ␣ 1 Thr206, and a fluorine atom is located next to ␣ 1 Tyr209, with ␥ 2 Thr193 and ␥ 2 Arg194 located close to C5-phenyl moiety. Sancar et al (2007) reported that the ␥ 2 R194D mutation produced no change in [ 3 H]FNZ binding affinity, whereas Padgett and Lummis (2008) found that ␥ 2 R194N and ␥ 2 R194K mutations reduced maximum DZ potentiation of ␣ 1 ␤ 2 ␥ 2 receptors by 2.5-and 4-fold, respectively, whereas mutation of the neighboring residue ␥ 2 Ser195 to threonine reduced DZ potentiation by 5-fold. These results, which indicate that mutations of loop F influence BZD efficacy rather than potency, suggest that conformational changes within loop F are coupled to receptor activation.…”

Section: Discussionmentioning

confidence: 99%

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Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Berezhnoy

Gibbs²,

Farb³

2009

Mol Pharmacol

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Positive allosteric modulation of the GABA A receptor (GABA A R) via the benzodiazepine recognition site is the mechanism whereby diverse chemical classes of therapeutic agents act to reduce anxiety, induce and maintain sleep, reduce seizures, and induce conscious sedation. The binding of such therapeutic agents to this allosteric modulatory site increases the affinity of GABA for the agonist recognition site. A major unanswered question, however, relates to how positive allosteric modulators dock in the 1,4-benzodiazepine (BZD) recognition site. In the present study, the X-ray structure of an acetylcholine binding protein from the snail Lymnea stagnalis and the results from site-directed affinity-labeling studies were used as the basis for modeling of the BZD binding pocket at the ␣ 1 /␥ 2 subunit interface. A tethered BZD was introduced into the binding pocket, and molecular simulations were carried out to yield a set of candidate orientations of the BZD ligand in the binding pocket. Candidate orientations were refined based on known structureactivity and stereospecificity characteristics of BZDs and the impact of the ␣ 1 H101R mutation. Results favor a model in which the BZD molecule is oriented such that the C5-phenyl substituent extends approximately parallel to the plane of the membrane rather than parallel to the ion channel. Application of this computational modeling strategy, which integrates sitedirected affinity labeling with structure-activity knowledge to create a molecular model of the docking of active ligands in the binding pocket, may provide a basis for the design of more selective GABA A R modulators with enhanced therapeutic potential.

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Section: Discussioncontrasting

confidence: 57%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

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Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Berezhnoy

Gibbs²,

Farb³

2009

Mol Pharmacol

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“…Thus, these results strongly suggest that amino acid differences in the N terminus of mouse and human 5-HT 3A Rs exert their differential actions by affecting gating, not binding. These loops also have been shown to play a significant role in modulation of GABA-induced currents by BZDs and other drugs binding at the BZD binding site on the GABA A R (Sancar et al, 2007;Padgett and Lummis, 2008). The role of loops C and F in the GABA-BZD modulatory mechanism differs from the proposed role of these loops in colchicine modulation in that loops C and F probably induce conformational changes that affect gating of the 5-HT 3A R. In the GABA A Rs, these loops are thought to not only affect gating but also to play a direct role in stabilization of the BZD binding site.…”

Section: Discussionmentioning

confidence: 99%

Colchicine: A Novel Positive Allosteric Modulator of the Human 5-Hydroxytryptamine_3AReceptor

Oliveira-Pierce

Zhang

Machu

2009

J Pharmacol Exp Ther

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The actions of colchicine were examined with the two-electrode voltage-clamp technique and radioligand binding assays in mouse and human 5-hydroxytryptamine 3A receptors (5-HT 3A Rs) expressed in Xenopus laevis oocytes. Colchicine inhibited 5-hydroxytryptamine (5-HT)-evoked currents in oocytes expressing mouse 5-HT 3A Rs, with an IC 50 of 59.5 Ϯ 3 M. In contrast to the mouse receptor, coapplication of colchicine with 5-HT (Ͻ1 M) strongly enhanced 5-HT-evoked currents in oocytes expressing human 5-HT 3A Rs. Colchicine applied alone did not induce a detectable current. In the presence of 0.5 M 5-HT, the potentiation was concentration-dependent and reached the maximum (ϳ100%) when 750 M colchicine was applied. However, colchicine-dependent inhibition can be observed at 5-HT concentrations Ͼ 1 M. In oocyte membranes expressing mouse or human receptors, binding studies with colchicine, suggesting that actions of colchicine do not occur at the ligand binding domain. Functional effects of colchicine on both receptors occurred in the absence of preincubation and after cold temperature incubation, suggesting that the microtubule-depolymerizing effects of colchicine play no role in modulation of receptor function. Studies with interspecies chimeric receptors demonstrated that the distal one third of the N terminus is responsible for the bidirectional modulation by colchicine. Collectively, these results suggest that colchicine modulates receptor function through loops C and/or F through a gating mechanism.The 5-hydroxytryptamine 3 receptor (5-HT 3 R) belongs to the superfamily of ligand-gated ion channels (LGICs) (Maricq et al., 1991) and shares a number of structural and functional homologies with other members, such as the nicotinic acetylcholine receptor (nAChR), GABA receptor (GABA A R), and glycine receptor (GlyR) (Grenningloh et al., 1987;. To date, five 5-HT 3 receptor subunits have been cloned (A-E) (Maricq et al., 1991;Belelli et al., 1995;Niesler et al., 2007). Receptors composed of A-homomers and A/B-heteromers have been shown to have functional significance in the central and peripheral nervous systems (for review, see Thompson and Lummis, 2006), and a recent study reported expression of functional A/C-, A/D-, and A/E-heteromers (Niesler et al., 2007). The ligand binding domain (LBD) is located in the N terminus at the interface between subunits and consists of six loops, A to F. Loops A to C form the principal component of the LBD, and loops D to F form the complementary component of the LBD (for review, see Thompson and Lummis, 2006). Homology models using the acetylcholine-binding protein and biochemical studies have identified important residues for ligand binding on both the primary (loops A-C) and the complementary (loops D-F) interfaces of the binding site (Schreiter et al., 2003;Thompson et al., 2005).The homomeric 5-HT 3A R is a good model system for exploring the ligand recognition sites of LGICs. Significant homology exists between the 5-HT 3A Rs among the six cloned species (80 -95%). It is...

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“…see Ref. 6), the molecular mechanism by which benzodiazepines mediate their effects is not yet clear.…”

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confidence: 99%

The F-loop of the GABAA Receptor γ2 Subunit Contributes to Benzodiazepine Modulation

Padgett¹,

Lummis

2008

Journal of Biological Chemistry

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H]flumazenil binding affinity, suggesting they do not affect GABA or benzodiazepine binding characteristics; we therefore propose that they are involved in the diazepam-mediated conformational change that results in an increased response to GABA. Homology models of the receptor binding pocket in agonist-bound and unbound states suggest that the F-loop is flexible and has different orientations in the two states. Considering our data in relation to these models, we find that the F-loop residues could contribute to hydrogen bond networks and hydrophobic interactions with neighboring residues that change during receptor activation.

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Structural Determinants for High-Affinity Zolpidem Binding to GABA-A receptors

Abstract: The imidazopyridine zolpidem (Ambien)

Cited by 53 publications

References 38 publications

Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Colchicine: A Novel Positive Allosteric Modulator of the Human 5-Hydroxytryptamine_3AReceptor

The F-loop of the GABAA Receptor γ2 Subunit Contributes to Benzodiazepine Modulation

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Structural Determinants for High-Affinity Zolpidem Binding to GABA-A receptors

Abstract: The imidazopyridine zolpidem (Ambien)

Cited by 53 publications

References 38 publications

Docking of 1,4-Benzodiazepines in the α1/γ2GABAAReceptor Modulator Site

Docking of 1,4-Benzodiazepines in the α1/γ2GABAAReceptor Modulator Site

Colchicine: A Novel Positive Allosteric Modulator of the Human 5-Hydroxytryptamine3AReceptor

The F-loop of the GABAA Receptor γ2 Subunit Contributes to Benzodiazepine Modulation

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Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Colchicine: A Novel Positive Allosteric Modulator of the Human 5-Hydroxytryptamine_3AReceptor