Article Figures & Data
Figures
- Fig. 1.
Simple schematic illustrating the potential for different ligands to display either competitive or allosteric interactions depending on their binding sites relative to one another.
- Fig. 2.
Diagrammatic representation of different classes of allosteric sites and exemplar ligands of LGICs. ECD, extracellular domain; TMD, transmembrane domain; CD, cytoplasmic domain.
- Fig. 3.
Crystal structures of ligand-gated ion channels, showing the range of allosteric (or coagonist) binding sites. (A) Ethanol binding sites on the ethanol-sensitive mutant GLIC pentameric ligand gated ion channel (PDB ID 4HFE). (B) Ketamine bound to the GLIC pentameric ligand gated ion channel (PDB ID 4F8H). (C) GluN1/GluN2A ligand-binding domain in complex with GluN receptor coagonists glycine and glutamate (PDB ID 4NF8). (D) Crystal structure of amino terminal domains of the GluN receptor subunit GluN1 and GluN2B in complex with ifenprodil (PDB ID 3QEL). Crystal structure of a pentameric ligand gated ion channel Erminia ligand-gated ion channel in complex with GABA and flurazepam (E; PDB ID 2YOE) or zopiclone (F; PDB ID 4A97).
- Fig. 4.
(A) Side view of the crystal structure of the bacterial NaVAb VGIC (Payandeh et al., 2011). (Left) NaVAb crystal structure illustrating the voltage-sensing module (green), pore module (blue), and connecting S4–S5 linker (red) in the preopen state. (Right) The NavAb pore module in the preopen state, indicating amino acids implicated in the binding of channel pore blockers. The tight closure in the intracellular regions provides a structural explanation for use-dependent blockade by large or hydrophilic drugs, because they would bind more rapidly upon channel opening. The amino acid Phe203 plays a key role in governing drug access to this site. The other highlighted residues, Thr206 (blue), Met209 (green), and Val213 (orange) have been implicated as key contributors to the drug-binding pocket in mammalian NaV channels. (B) Diagrammatic representation of multiple distinct allosteric sites for neurotoxins and local anesthetics at voltage-gated sodium channels, with exemplar molecules listed. The channels comprise four homologous voltage-sensing domains (I–IV), each composed of six (S1–S6) segments, which surround a central pore. The locations of the different allosteric sites (Site 1–6 and the local anesthetic site) are indicated both with regards to their domain location (left) and their localization within a given intradomain module (right). TTX, tetrodotoxin; STX, saxitoxin.
- Fig. 5.
Topographically distinct but conformationally linked domains within GPCRs. (A) Structures of the chemokine CCR5 receptor bound to maraviroc (PDB ID 4MBS) and the corticotrophin releasing factor receptor (CRF1) bound to CP-376395 (PDB ID 4K5Y). (B) Structure of the M2 mAChR (PDB ID 4MQT) in complex with a positive allosteric modulator (LY02119620, purple), an agonist (iperoxo, yellow), and a nanobody (Nb9-8, green) that stabilizes an active state of the receptor.
- Fig. 6.
(A) Modular domain structure of NHRs. (B) Crystal structure of the PPARγ/RXR heterodimeric NHR (PDB ID 3DZY) bound to the orthosteric ligands retinoic acid and rosiglitazone, highlighting potential sites for allosteric modulation. AF, activation function.
- Fig. 7.
(A) Schematic representation of the allosteric transition mechanism proposed for intact epidermal growth factor receptor activation based on long timescale molecular dynamics simulations. EC, extracellular; JM, juxtramembrane. Transition from inactive to active states involves ligand-dependent reorientation of the C- versus N-terminal ends of the TM region. (B) Three-dimensional representation of the 4.2-Å crystal structure of the FGF receptor 2 (FGFR2) extracellular D2–D3 region in complex with FGF1 in the absence (left) or presence (right) of the allosteric modulator SSR1281129E (SSR). Although the molecule could not be resolved at this resolution, the change in B factors (which quantify changes in the vibrational motions of different parts of a structure) suggests an increase in the flexibility of the D3 region. The inset shows a predicted binding mode for the modulator in the D3 region based on free energy calculations and in silico docking. Reproduced, with permission, from Herbert et al. (2013).
- Fig. 8.
Work-flow charts to investigate a possible allosteric mechanism of action for a new chemical entity (N.C.E.) using binding (A) or functional (B) assays. Note, the reference probe ligand would typically be an orthosteric ligand (e.g., endogenous agonist) but can also be a well characterized allosteric ligand.
Tables
- TABLE 1
Terms used to describe receptor allosterism and allosteric ligand actions (see also Note 1)
Term Suggested Use Orthosteric site The binding site/s on a receptor macromolecule that is/are recognized by the endogenous agonist/s for that receptor. Allosteric site A binding site on a receptor macromolecule that is nonoverlapping and spatially distinct from, but conformationally linked to, the orthosteric binding site. Orthosteric agonist A ligand that binds to the orthosteric site of a receptor and alters the receptor state, resulting in a biologic response. Conventional orthosteric agonists increase receptor activity, whereas orthosteric inverse agonists reduce it (see also Notes 2 and 3). Allosteric agonist A ligand that binds to an allosteric site on a receptor macromolecule and alters the receptor state, resulting in a biologic response. Conventional allosteric agonists increase receptor activity, whereas allosteric inverse agonists reduce it (see also Notes 4 and 5). Allosteric modulator A ligand that modifies the action of an orthosteric agonist, endogenous activator, or antagonist by combining with an allosteric site on the receptor macromolecule. A positive allosteric modulator (PAM) increases the action (affinity and/or efficacy) of an orthosteric agonist, activator, or antagonist, whereas a negative allosteric modulator (NAM) decreases the action (affinity and/or efficacy) of an orthosteric agonist, activator, or antagonist. Note that the term “modulator” is preferred to the terms “effector” or “regulator.” Neutral allosteric ligand A ligand that combines with an allosteric site on a receptor macromolecule but does not alter the action of a (given) orthosteric agonist, activator, or antagonist. The neutral allosteric ligand (NAL) can, however, prevent the binding of other allosteric ligands to the same allosteric site via a steric interaction and may be a positive or negative allosteric modulator of other orthosteric ligands, activators, or antagonists or allosteric ligands that bind to a different (second) allosteric site on the receptor macromolecule (see also Note 6). Neutral allosteric ligands have also been referred to as “silent allosteric modulators” (SAMs). Note, however, that the terms “neutral” and “ligand” are preferred to the terms “silent” and “modulator” for ligands with neutral cooperativity. This ensures conformity with prior terms, such as “neutral antagonist” and also reflects the fact that if a ligand is neutral, it is not "modulating." Bitopic ligand A hybrid molecule that concomitantly engages an orthosteric and an allosteric site on a receptor macromolecule via two pharmacologically active pharmacophores (one constituting an orthosteric ligand and the other an allosteric ligand; see also Note 7). Allosteric interaction An indirect interaction between ligands that bind to spatially distinct, nonoverlapping recognition sites on the receptor macromolecule mediated by a conformational change. Allosteric transition The isomerization of a receptor macromolecule between different conformational states. Competitive interaction An interaction between ligands that bind to the same recognition site or to recognition sites that overlap on the receptor macromolecule. A competitive interaction can occur between different orthosteric ligands or between different allosteric ligands provided that each class shares a similar recognition domain on the receptor macromolecule (see also Note 3). Homotropic interaction An allosteric interaction between structurally identical ligands. Heterotropic interaction An allosteric interaction between structurally different ligands. Target Class Target Ligand Proposed Ligand Descriptors GPCR Cannabinoid CB1 receptor Org27569 Org27569 is a PAM of CP55940 affinity but a NAM of CP55940 efficacy for mediating inhibition of cAMP accumulation. GPCR mGlu1 receptor CPCCOEt CPCCOEt is a NAL with respect to glutamate affinity but a NAM of glutamate efficacy in mediating intracellular calcium mobilization GPCR mGlu5 receptor M-5MPEP M-5MPEP is a NAL with respect to glutamate affinity and NAM of glutamate efficacy for stimulation of intracellular calcium mobilization and inositol phosphate accumulation GPCR CCR5 Aplaviroc Aplaviroc is a NAM of CCL3 affinity and a NAL with respect to CCL5 affinity; it is also a NAM of CCL3 and CCL5 efficacy to stimulate intracellular calcium mobilization. LGIC Benzodiazepine-sensitive GABAA receptors Diazepam Diazepam is a PAM of GABA affinity and chloride flux at benzodiazepine-sensitive GABAA receptors. LGIC GABAA receptor Flumazenil Flumazenil is a NAL with respect to GABA affinity and chloride flux at (most) GABAA receptor subtypes. LGIC GABAA receptor Pentobarbital Pentobarbital is a PAM of GABA affinity and chloride flux and an allosteric agonist with respect to GABAA receptor gating. LGIC nAChR Lidocaine Lidocaine is a PAM of acetylcholine affinity but a NAM of acetylcholine-mediated cation flux at the nAChR. LGIC NMDA (GluN1/GluN2A) TCN-201 TCN-201 is a NAM of glycine affinity and efficacy but a NAL of glutamate activity at the NMDA receptor. VGIC CaV1 BayK8644 BayK8644 is an allosteric agonist at CaV1 channels, a competitive antagonist of other dihydropyridines, a PAM with respect to diltiazem, and a NAM with respect to verapamil. RTK FGFR1 SSR128129E SSR128129E is NAL with respect to FGF2 affinity but a NAM of FGF2 efficacy to mediate phosphorylation of FRS2 and ERK1/2. It is a Type 3 tyrosine kinase inhibitor with respect to the ATP binding site. BayK8644, methyl 2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate; ERK1/2, extracellular signal-regulated kinase 1/2; FGFR1, FGF receptor 1; FRS2, fibroblast growth factor receptor substrate 2; M-5MPEP, 2-[(3-methoxyphenyl)ethynyl]-5-methylpyridine; NAL, neutral allosteric ligand (see also Note 10).
In this issue
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- Article
- Abstract
- I. Introduction
- II. A Brief Overview of Receptor Allosterism
- III. Definitions
- IV. Some Representative Examples of Allosteric Receptor Modulation
- V. Recommendations for Allosteric Ligand Classification
- VI. Classification of Endogenous Allosteric Ligands
- VII. Experimental Approaches for Validating an Allosteric Interaction
- Authorship Contributions
- Footnotes
- Abbreviations
- References
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