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Allosteric modulator

An allosteric modulator is a ligand that binds to a specific allosteric site on a target protein, such as a receptor, which is topographically distinct from the orthosteric (primary ligand-binding) site, thereby altering the protein's conformation to modulate the binding affinity, efficacy, or signaling properties of the orthosteric ligand without directly competing for the active site.^[1] These modulators typically exert their effects only in the presence of an endogenous agonist, providing a saturable ceiling to their action that preserves physiological signaling patterns and reduces the risk of receptor hyperactivation.^[1] In pharmacology, allosteric modulators represent an emerging paradigm in drug discovery, particularly for challenging targets like G protein-coupled receptors (GPCRs), where they enable subtype selectivity by binding to less conserved allosteric sites and allow for fine-tuned regulation akin to a "dimmer switch" rather than binary on/off control offered by traditional orthosteric ligands.^[2] They are classified primarily into positive allosteric modulators (PAMs), which enhance the orthosteric ligand's potency or efficacy; negative allosteric modulators (NAMs), which diminish it; and silent allosteric modulators (SAMs), which occupy the site without altering function, though additional subtypes like ago-PAMs (with intrinsic agonist activity) and neutral allosteric ligands also exist.^[1]^[3] The therapeutic potential of allosteric modulators spans diverse diseases, including central nervous system disorders (e.g., schizophrenia and Parkinson's via dopamine or mGluR targets), endocrine conditions (e.g., hyperparathyroidism), infectious diseases (e.g., HIV), and metabolic issues (e.g., diabetes), with advantages such as reduced side effects and the ability to probe-dependent biased signaling that targets specific pathways.^[2]^[3] Approved examples include cinacalcet, a PAM of the calcium-sensing receptor for treating secondary hyperparathyroidism, and maraviroc, a NAM of the CCR5 chemokine receptor for HIV entry inhibition, while numerous candidates like mGluR5 NAMs (e.g., dipraglurant) are in clinical development for conditions such as depression and neuropathic pain.^[1]^[3]

Fundamentals

Definition and Basic Principles

An allosteric modulator is a ligand that binds to a site on a receptor or enzyme distinct from the orthosteric site, thereby altering the receptor's response to its endogenous ligand or agonist without directly activating or inhibiting the receptor itself.^[4] This binding modulates the affinity or efficacy of the orthosteric ligand, influencing downstream signaling or enzymatic activity through indirect means.^[5] The orthosteric site refers to the primary binding location for the endogenous agonist, while the allosteric site is a secondary, topographically distinct region that enables this regulatory effect.^[6] The fundamental principle of allostery involves a conformational change in the protein structure upon modulator binding, which propagates through the molecule—often between distant sites—to affect the orthosteric site's properties.^[2] This phenomenon underpins cooperativity, where binding at one site enhances (positive cooperativity) or diminishes (negative cooperativity) the binding or activity at another site, allowing fine-tuned regulation of protein function.^[7] A seminal conceptualization of allostery came from the Monod-Wyman-Changeux (MWC) model proposed in 1965, which describes proteins as existing in equilibrium between tense (T) and relaxed (R) conformational states, with ligands shifting this equilibrium to promote cooperative interactions, as exemplified in hemoglobin's oxygen binding.^[8] A classic example of allosteric modulation is provided by benzodiazepines, which bind to an allosteric site on GABA_A receptors to enhance the receptor's response to the neurotransmitter GABA, increasing inhibitory signaling in the central nervous system without directly gating the ion channel.^[9] This illustrates how allosteric modulators can achieve subtype-specific effects while preserving the receptor's natural activation profile.^[10]

Comparison to Orthosteric Ligands

Orthosteric ligands bind directly to the primary active site of a receptor, also known as the orthosteric site, where they compete with endogenous agonists or antagonists for binding, thereby mimicking or blocking the natural ligand's interaction.^[11] In contrast, allosteric modulators bind to distinct secondary sites, known as allosteric sites, which are topographically separate from the orthosteric site, allowing non-competitive binding that does not directly displace the endogenous ligand.^[2] This fundamental difference in binding location enables allosteric modulators to influence receptor function without interfering with the orthosteric site's occupancy by the agonist.^[12] Regarding effect profiles, orthosteric agonists activate receptors by fully emulating the endogenous ligand's action, while orthosteric antagonists completely inhibit it, often leading to on/off binary responses.^[13] Allosteric modulators, however, lack intrinsic efficacy and instead fine-tune the receptor's response to the orthosteric ligand by altering its affinity or efficacy, resulting in graded modulation rather than direct activation or blockade.^[14] For instance, positive allosteric modulators enhance the orthosteric ligand's potency or maximal effect, whereas negative allosteric modulators reduce it, providing a more nuanced control over signaling.^[15] Pharmacologically, the allosteric approach offers advantages by avoiding direct competition at the orthosteric site, which can reduce off-target effects since allosteric sites are often more receptor-specific and less conserved across subtypes.^[16] A key implication is the "ceiling effect," where allosteric modulation reaches a maximum influence regardless of increasing modulator concentration, due to the saturable nature of allosteric binding, thereby limiting potential toxicity from overdose.^[3] This contrasts with orthosteric ligands, which can produce dose-proportional effects without such inherent safeguards.^[17] Structurally, orthosteric sites in G protein-coupled receptors (GPCRs) are typically located within the transmembrane helix bundle, forming a pocket that accommodates the endogenous ligand, while allosteric sites are often found in extracellular loops or intracellular domains, facilitating conformational changes without overlapping the primary binding region.^[18] These distinct locations contribute to the non-competitive nature of allosteric interactions, allowing simultaneous binding and cooperative effects on receptor dynamics.^[13]

Types

Positive Allosteric Modulators

Positive allosteric modulators (PAMs) are ligands that bind to sites distinct from the orthosteric agonist-binding site on a receptor, thereby enhancing the receptor's response to the endogenous agonist. Typical PAMs do not directly activate the receptor on their own, though subtypes such as ago-PAMs possess intrinsic agonist activity.^[19] These modulators can potentiate signaling by increasing the affinity of the agonist for the receptor, its efficacy in eliciting a response, or both, leading to amplified physiological effects at endogenous agonist concentrations.^[20] PAMs that primarily modulate affinity produce a leftward shift in the agonist dose-response curve, indicating that lower agonist concentrations are sufficient to achieve half-maximal response, while those modulating efficacy increase the maximal response amplitude without altering agonist potency, enabling fuller receptor activation even at saturating agonist levels.^[21]^[22] This allows for more physiological tuning of receptor activity compared to orthosteric agonists.^[4] Prominent examples of PAMs include compounds targeting metabotropic glutamate receptors (mGluRs), such as SAR218645, a selective mGluR2 PAM investigated for its potential in treating schizophrenia by enhancing glutamate signaling to alleviate cognitive and negative symptoms.^[23] Similarly, zolpidem serves as a subtype-selective PAM of GABA_A receptors, preferentially modulating α1-containing subtypes to promote sedation and treat sleep disorders like insomnia by augmenting GABA-mediated inhibition.^[24] Endogenous PAMs also play key physiological roles, exemplified by cholesterol, which acts as a positive allosteric effector on various ion channels, such as nicotinic acetylcholine receptors and GABA_A receptors, by stabilizing open-channel conformations and enhancing agonist-induced currents to fine-tune neuronal excitability.^[25]

Negative and Silent Allosteric Modulators

Negative allosteric modulators (NAMs) are ligands that bind to an allosteric site on a receptor, topographically distinct from the orthosteric agonist-binding site, and decrease the affinity, efficacy, or both of the orthosteric agonist for the receptor. This binding stabilizes inactive receptor conformations or increases the energy barrier for activation, resulting in reduced receptor signaling without intrinsic agonist activity of their own. In functional assays, NAMs typically produce a rightward shift in the agonist dose-response curve, reflecting decreased agonist affinity, and/or a reduction in the maximal response, indicating suppressed efficacy.^[1]^[26]^[27]^[28] A prominent example of NAMs is the class of calcilytics, which act as antagonists of the calcium-sensing receptor (CaSR), a G protein-coupled receptor (GPCR) that regulates parathyroid hormone (PTH) secretion and calcium homeostasis. By decreasing CaSR sensitivity to extracellular calcium, calcilytics transiently increase PTH levels, promoting bone formation and potentially treating osteoporosis without the sustained hypercalcemia risks associated with PTH analogs. Compounds like NPSP795 have demonstrated this effect in preclinical models by inducing rapid PTH release and enhancing bone mineral density.^[29]^[30] Silent allosteric modulators (SAMs), also known as neutral allosteric ligands, bind to the same allosteric site as other modulators but exert no detectable effect on orthosteric agonist affinity or efficacy in standard functional assays. Instead, SAMs competitively occupy the allosteric site to prevent binding or activity of positive or negative allosteric modulators, effectively blocking their influence on receptor signaling. However, SAMs may reveal modulatory effects under probe-dependent conditions, where their impact varies with the specific orthosteric agonist or signaling pathway probed, due to differences in receptor conformational states induced by various ligands.^[27]^[19]^[31] In chemokine receptors, such as CXCR1 and CXCR2, SAMs have been explored for their potential to inhibit pathological inflammation by blocking allosteric enhancement of chemokine signaling without disrupting baseline immune responses; for instance, certain non-peptide ligands exhibit silent properties in assays using full-length chemokines but may show modulation with chemokine fragments. This probe dependence underscores how SAMs can appear neutral in routine screens yet influence biased signaling or heterodimer interactions in disease contexts like cancer or autoimmune disorders.^[27]^[32] NAMs and SAMs differ fundamentally in their functional impact: NAMs actively suppress agonist-induced responses by altering receptor dynamics, whereas SAMs remain functionally inert toward orthosteric ligands under normal conditions but serve as gatekeepers against other allosteric influences, with their silence potentially unmasked by probe-specific or biased assay conditions. For contrast, while positive allosteric modulators enhance agonist potency or maximal effect, NAMs provide targeted inhibition useful in hyperactive receptor pathologies. An example of a NAM in a neurological context is cannabidiol, which acts as a negative allosteric modulator at the 5-HT2A receptor, reducing serotonin-induced signaling and showing promise in modulating psychosis-like behaviors without broad dopaminergic interference.^[33]

Mechanisms of Action

Modulation of Ligand Binding and Unbinding

Allosteric modulators exert their effects on orthosteric ligand binding primarily by altering the kinetic parameters of association and dissociation. The association rate constant (k_on) reflects the speed at which the ligand binds to the receptor, while the dissociation rate constant (k_off) determines how quickly it unbinds, with the equilibrium dissociation constant (K_d) given by K_d = k_off / k_on. Positive allosteric modulators (PAMs) often decrease k_off for orthosteric agonists, thereby prolonging ligand residence time on the receptor and increasing apparent affinity without substantially affecting k_on.^[34] This stabilization of the bound state has been observed in metabotropic glutamate receptor 2 (mGlu2), where PAMs like LY487379 reduce the k_off of glutamate, correlating with enhanced functional potency.^[34] In contrast, negative allosteric modulators (NAMs) typically accelerate agonist unbinding by increasing k_off, which can diminish affinity and shorten residence time, as demonstrated in single-molecule fluorescence studies of G protein-coupled receptors (GPCRs) where NAMs expedited agonist dissociation rates by factors of 2- to 4-fold.^[35] The reciprocal nature of allosteric interactions is captured by the cooperativity factor α, which quantifies the extent to which binding of one ligand influences the affinity of the other:

\alpha = \frac{K_A \cdot K_B}{K_{AB} \cdot K_{BA}}

where K_A is the equilibrium dissociation constant of the orthosteric ligand alone, K_B is that of the allosteric modulator alone, K_{AB} is the dissociation constant of the orthosteric ligand in the presence of saturating allosteric modulator, and K_{BA} is the dissociation constant of the allosteric modulator in the presence of saturating orthosteric ligand.^[36] Values of α > 1 indicate positive cooperativity, resulting in decreased K_{AB} (higher orthosteric affinity) and decreased K_{BA} (higher allosteric affinity), whereas α < 1 signifies negative cooperativity with the opposite effects.^[36] This factor arises from coupled changes in binding free energies and can manifest asymmetrically in kinetics, where the modulator may slow orthosteric k_off while the orthosteric ligand reciprocally slows allosteric k_off, but effects on k_on are often oppositely directed due to entropic contributions in the transition state.^[37] In simplified models for binding assays, the apparent affinity of the orthosteric ligand can be modulated by the allosteric modulator through cooperativity, leading to leftward shifts in IC50 values for PAMs and rightward shifts for NAMs in radioligand competition assays.^[38] These models account for non-equilibrium conditions, emphasizing that allosteric effects on kinetics can produce probe-dependent outcomes, where the observed shift in IC50 reflects both equilibrium cooperativity and differential impacts on k_on and k_off.^[38] Experimental validation of these kinetic modulations frequently employs fluorescence-based assays to monitor real-time binding dynamics in GPCRs. For instance, fluorescence resonance energy transfer (FRET) and total internal reflection fluorescence (TIRF) microscopy have revealed that PAMs can slow orthosteric agonist dissociation in cells expressing muscarinic receptors.^[39] Similarly, studies on adenosine A1 receptors have shown NAMs increasing k_off of orthosteric ligands, confirming kinetic contributions to reduced binding affinity.^[40] These approaches highlight the practical utility of kinetic profiling in dissecting allosteric mechanisms beyond equilibrium measurements. These binding kinetic alterations often arise from subtle conformational adjustments in the receptor that propagate between sites.^[39]

Influence on Receptor Conformation and Signaling

Allosteric modulators exert their effects by binding to sites distinct from the orthosteric ligand-binding pocket, thereby inducing or stabilizing specific conformational states of the receptor that alter its functional properties. Positive allosteric modulators (PAMs) preferentially stabilize the active conformation (R*) of the receptor, enhancing the probability of orthosteric agonist-induced activation, while negative allosteric modulators (NAMs) favor the inactive conformation (R), reducing the receptor's responsiveness to agonists.^[41] This conformational selection is captured in the extended ternary complex model, which describes how allosteric modulators shift the equilibrium between inactive (R) and active (R*) receptor states in the presence of orthosteric ligands and G-proteins, thereby modulating the formation of the agonist-receptor-G-protein ternary complex.^[42] These conformational changes directly influence downstream signaling pathways by altering the receptor's interactions with intracellular effectors. For instance, PAMs can enhance G-protein coupling efficiency, increasing the activation of second messengers such as cyclic AMP in G_s-coupled receptors, or promote ion flux in ligand-gated ion channels.^[43] Conversely, NAMs suppress these interactions, reducing G-protein dissociation and subsequent signaling. In addition, allosteric binding can prevent receptor desensitization by inhibiting key regulatory mechanisms, such as phosphorylation by G-protein-coupled receptor kinases (GRKs) or β-arrestin recruitment, which would otherwise uncouple the receptor from G-proteins or promote internalization.^[44] For example, in AMPA receptors, positive allosteric modulators like cyclothiazide stabilize the open-channel state by disrupting the dimer interface rearrangements that underlie desensitization, thereby prolonging ion conductance without altering agonist binding kinetics.^[45] Allosteric modulators can also induce biased signaling, selectively favoring certain downstream pathways over others to produce pathway-specific effects. In G-protein-coupled receptors (GPCRs), this bias manifests as differential recruitment of G-proteins versus β-arrestins; for instance, certain PAMs may enhance G-protein-mediated signaling while suppressing β-arrestin-dependent pathways, leading to distinct cellular outcomes compared to orthosteric agonists.^[46] This allosteric control over signaling ensembles arises from the stabilization of intermediate conformational states that differentially engage effectors, providing a mechanism for fine-tuned regulation of receptor activity.^[43]

Binding Sites and Molecular Interactions

Identification and Characterization of Sites

The identification and characterization of allosteric binding sites on G protein-coupled receptors (GPCRs) and other targets relies on a combination of experimental and computational techniques to map potential pockets distinct from orthosteric sites. These methods enable the discovery of sites that can modulate receptor function without competing directly with endogenous ligands, offering opportunities for subtype-selective drug design. Key challenges include distinguishing allosteric sites from transient pockets and validating their functional relevance, which requires integrating structural, biochemical, and pharmacological data.^[47] Experimental techniques such as X-ray crystallography have been pivotal in visualizing allosteric binding sites at atomic resolution, often revealing cryptic pockets that open upon conformational changes. For instance, high-resolution structures of GPCRs co-crystallized with allosteric modulators have identified transmembrane and extracellular vestibule sites, providing templates for rational design. Cryo-electron microscopy (cryo-EM) complements crystallography by capturing dynamic states in near-native conditions, particularly for complexes with G proteins or arrestins, where allosteric sites at intracellular interfaces become apparent. Nuclear magnetic resonance (NMR) spectroscopy further aids in probing site flexibility and ligand-induced conformational shifts in solution, especially for smaller receptor domains or peptide modulators. To confirm the functional importance of identified residues, site-directed mutagenesis is routinely employed, introducing point mutations to disrupt binding and assess impacts on modulator potency via radioligand or functional assays.^[47]^[48]^[49]^[50] Computational approaches accelerate site prediction by simulating receptor dynamics and screening libraries for potential binders. Molecular docking tools, such as Glide within the Schrödinger suite, predict allosteric pocket occupancy by sampling ligand poses in receptor models derived from homology or experimental structures. Molecular dynamics (MD) simulations reveal transient pockets that stabilize upon ligand binding, often identifying lipid-facing or intracellular sites not evident in static structures. Fragment-based screening, combining virtual docking with biophysical validation like surface plasmon resonance or mass spectrometry, has successfully detected low-affinity fragments in allosteric sites, serving as starting points for optimization. A historical milestone was the 2014 determination of the first crystal structure of an allosteric site in a class C GPCR, the mGlu1 receptor transmembrane domain bound to a negative allosteric modulator, which illuminated a conserved pocket for modulator design across metabotropic glutamate receptors.^[51]^[52]^[53]^[54] Once potential sites are mapped, characterization involves functional assays to validate allosteric effects and probe dependence, where modulator activity varies with the orthosteric ligand used. High-throughput platforms like FLIPR calcium imaging measure real-time changes in intracellular calcium flux in cells expressing the receptor, allowing quantification of modulation on agonist-induced responses. These assays confirm site specificity by testing shifts in EC50 or maximal efficacy across different probes, ensuring the site supports non-competitive interactions. Integrating these data refines models of site-residue interactions, guiding iterative optimization of modulators.^[55]^[56]

Probe Dependence and Specificity

Probe dependence refers to the phenomenon where the effect of an allosteric modulator on receptor function varies depending on the orthosteric ligand (probe) used to assess activity. This occurs because allosteric modulators can differentially influence the binding affinity or efficacy of distinct orthosteric ligands, even at the same receptor. For instance, a modulator might enhance the affinity of one agonist while having no effect or even reducing the affinity of another, leading to context-specific outcomes in functional assays.^[57] The underlying mechanisms for probe dependence include the existence of multiple allosteric sites on the receptor or the dynamic nature of receptor conformational ensembles, where the modulator stabilizes different states that interact variably with orthosteric probes. In G protein-coupled receptors (GPCRs), such as the μ-opioid receptor, structural studies have revealed that probe-dependent effects arise from how allosteric ligands alter the receptor's energy landscape, favoring conformations that either cooperate or compete with specific orthosteric ligands. This variability complicates the classification of modulators as positive (PAMs) or negative (NAMs), as their behavior is probe-specific rather than intrinsic.^[58]^[59] Quantitative assessment of probe dependence often employs cooperativity indices, such as the binding cooperativity factor α, where log(α) values quantify the magnitude and direction of modulation for a given orthosteric probe. Positive log(α) (>0) indicates affinity enhancement (PAM-like), while negative values (<0) denote reduction (NAM-like), and these can differ significantly across probes; for example, in muscarinic receptors, log(α) shifts from positive to neutral depending on the agonist used. Efficacy modulation is similarly captured by β factors in extended operational models, highlighting how probe choice affects both binding and signaling outcomes.^[38]^[60] In the context of negative allosteric modulators (NAMs) at opioid receptors, probe dependence manifests in differential impacts on therapeutic versus adverse effects, such as enhanced analgesia with one agonist probe while mitigating respiratory depression with another due to biased conformational stabilization. For example, certain NAMs at the μ-opioid receptor exhibit probe-dependent antagonism, reducing respiratory depression induced by high-efficacy agonists like fentanyl without fully blocking analgesia from endogenous opioids. This selectivity arises from the modulator's influence on distinct signaling pathways activated by different probes.^[58]^[61] Achieving specificity remains a key challenge for allosteric modulators, as they often exhibit cross-reactivity across closely related receptor subtypes, such as between GABA_A and glycine receptors, which share allosteric sites sensitive to modulators like volatile anesthetics. This off-target binding can lead to unintended effects, complicating therapeutic development. Strategies to enhance specificity include the design of bitopic ligands, which combine orthosteric and allosteric pharmacophores in a single molecule to achieve higher subtype selectivity by exploiting unique site geometries across receptors. For instance, bitopic ligands at muscarinic receptors demonstrate improved discrimination between M1 and M2 subtypes compared to pure allosteric agents.^[62]^[63]^[64]

Interactions with Orthosteric Ligands

Effects on Agonist Affinity

Allosteric modulators exert their effects on agonist affinity through non-competitive interactions that alter the binding equilibrium of orthosteric ligands via allosteric coupling between distinct sites on the receptor. This coupling induces conformational changes that either stabilize or destabilize the agonist-bound state, leading to shifts in the apparent dissociation constant (K_D) or half-maximal effective concentration (EC_{50}) without directly competing for the orthosteric site. Positive allosteric modulators (PAMs) enhance agonist affinity, typically manifesting as a leftward shift in concentration-response curves (decreased EC_{50}), while negative allosteric modulators (NAMs) reduce affinity, producing rightward shifts (increased EC_{50}). These shifts are concentration-dependent and reflect the degree of cooperativity between the modulator and agonist binding events.^[65] Quantitative assessment of affinity modulation employs models such as the allosteric ternary complex model, which describes the observed agonist affinity in the presence of a modulator. The apparent dissociation constant for the agonist (A) is given by:

K_A^{app} = K_A \frac{1 + \frac{[B]}{K_B}}{1 + \alpha \frac{[B]}{K_B}}

where K_A and K_B are the equilibrium dissociation constants of the agonist and modulator (B), respectively, and \alpha is the allosteric cooperativity factor (\alpha > 1 for PAMs, increasing affinity; \alpha < 1 for NAMs, decreasing affinity; \alpha = 1 for neutral effects). Dose-ratio analyses, adapted from classical Schild plots for allosteric contexts, quantify these interactions by plotting \log(\text{dose ratio} - 1) against \log[\text{modulator}], where slopes deviating from unity indicate non-competitive allosteric behavior rather than orthosteric antagonism.^[65]^[66] In experimental assays, such as radioligand competition binding studies, allosteric modulators demonstrate their affinity effects through parallel shifts in agonist saturation curves. For instance, PAMs cause leftward shifts in the binding isotherm of a labeled agonist (e.g., the PAM JNJ-46281222 increases glutamate affinity ~5-fold at mGlu2 by reducing the dissociation rate constant), while maintaining the maximum number of binding sites (B_{\max}), confirming selective modulation of binding strength without altering receptor density. NAMs produce analogous rightward shifts, often with similar parallelism in binding assays.^[67]^[55] A representative receptor-specific example involves PAMs of the metabotropic glutamate receptor subtype 2 (mGluR2), which enhance glutamate affinity (e.g., via \alpha values >1 in ternary complex analyses), thereby potentiating synaptic glutamate signaling and eliciting anxiolytic-like effects in rodent models of anxiety without the sedation associated with orthosteric agonists.^[68]

Effects on Agonist Efficacy

Allosteric modulators influence agonist efficacy by altering the maximal functional response (E_max) elicited by orthosteric agonists at their receptors, without necessarily affecting binding affinity. Positive allosteric modulators (PAMs) enhance agonist efficacy by stabilizing the active receptor conformation, thereby increasing the proportion of receptors that can transduce a signal upon agonist binding, which raises the observed E_max in dose-response curves.^[21] This effect arises from the modulator's ability to increase the residence time of the receptor in the active state, promoting more efficient coupling to downstream effectors such as G proteins or ion channels.^[69] In contrast, negative allosteric modulators (NAMs) reduce agonist efficacy by favoring inactive or less responsive receptor states, lowering E_max and potentially converting full agonists into partial ones, even at saturating agonist concentrations.^[11] A subset of PAMs, known as ago-PAMs, exhibit partial intrinsic agonist activity in the absence of orthosteric ligand, directly eliciting a submaximal response while also potentiating agonist efficacy when co-applied.^[70] This dual action allows ago-PAMs to activate receptors independently but with lower efficiency than orthosteric agonists, while enhancing the E_max of co-administered agonists through allosteric stabilization of active conformations.^[71] The extended operational model of allosterically modulated agonism (OMAM) quantifies this allosteric modulation of efficacy via a cooperativity factor β representing the modulator's effect on operational efficacy, distinct from affinity modulation by α. In this framework, the apparent maximal response in the presence of the modulator is given by:

E_{\max}^{\prime} = \frac{\beta \tau_A E_{\max}}{\beta \tau_A + 1}

where τ_A is the operational efficacy of the agonist A, E_{\max} is the system maximum, and β scales efficacy (β > 1 for PAMs enhancing efficacy; β < 1 for NAMs reducing it).^[38] This model distinguishes efficacy effects from affinity changes, as shifts in E_max occur independently of alterations in the agonist's EC_50. Functional assays commonly demonstrate these efficacy modulations through changes in peak response amplitude without parallel shifts in agonist potency. For instance, in cAMP accumulation assays for G protein-coupled receptors, PAMs increase the maximal cAMP production induced by agonists like glutamate at mGluR5, reflecting enhanced G protein coupling efficiency.^[72] Similarly, electrophysiological recordings in ligand-gated ion channels reveal amplified current amplitudes; benzodiazepines, as PAMs at GABA_A receptors, boost the maximal chloride conductance evoked by GABA, enhancing inhibitory neurotransmission without altering GABA's EC_50, which underlies their sedative effects.^[73] These assays highlight how efficacy modulation fine-tunes receptor signaling ceilings, offering a mechanistic basis for therapeutic selectivity.^[74]

Therapeutic Relevance

Advantages in Drug Design

Allosteric modulators offer enhanced subtype selectivity in drug design compared to orthosteric ligands, as allosteric binding sites are often less conserved across receptor subtypes, allowing for more precise targeting. For instance, positive allosteric modulators (PAMs) of the M4 muscarinic acetylcholine receptor (mAChR) demonstrate high selectivity over M1 and M3 subtypes, enabling potential treatment of schizophrenia without activating peripheral muscarinic receptors that contribute to side effects like salivation or bradycardia.^[75] This selectivity arises from structural differences in allosteric pockets, which vary more significantly between subtypes than the highly conserved orthosteric sites.^[76] A key advantage is the reduced risk of side effects due to the inherent "ceiling effect" of allosteric modulation, where the response saturates at physiological levels of the endogenous ligand, preventing excessive activation and overdose toxicity. Unlike orthosteric agonists, which can drive signaling beyond natural tones and lead to desensitization or toxicity, allosteric modulators preserve the spatiotemporal patterns of endogenous signaling, maintaining physiological control.^[3] This property is particularly beneficial for G protein-coupled receptors (GPCRs) in the central nervous system, where overactivation can cause adverse effects.^[21] Allosteric modulators can overcome resistance to orthosteric drugs caused by mutations at the active site, as they bind to distinct sites unaffected by such alterations, restoring or enhancing therapeutic efficacy. In cancer, for example, allosteric inhibitors of kinases like BCR-ABL1 have been combined with orthosteric inhibitors to resensitize resistant cells by modulating allosteric pathways that compensate for mutations.^[77] This approach is also relevant for viral receptors, where mutations confer drug resistance without impacting allosteric sites.^[78] Recent advances in the 2020s have improved the drug-like properties of allosteric ligands, particularly their pharmacokinetics, enabling better central nervous system (CNS) penetration for neurological indications. For example, the M1 mAChR PAM VU0467319 exhibits enhanced brain exposure and favorable oral bioavailability compared to earlier analogs, advancing it into clinical trials for Alzheimer's disease and schizophrenia while minimizing cholinergic adverse events.^[79] These optimizations, including reduced molecular weight and improved lipophilicity, facilitate the development of CNS-penetrant PAMs with superior therapeutic windows.^[80]

Clinical Applications and Examples

Allosteric modulators have found significant clinical utility in central nervous system (CNS) disorders, particularly through positive allosteric modulation (PAM) of ionotropic receptors. Benzodiazepines, such as diazepam and lorazepam, act as PAMs at the benzodiazepine site on GABA_A receptors, enhancing GABA-mediated inhibitory neurotransmission to alleviate symptoms of anxiety disorders.^[81] These agents have been a cornerstone of anxiolytic therapy since the 1960s, with their efficacy stemming from increased chloride influx and neuronal hyperpolarization without directly activating the receptor.^[10] Beyond CNS applications, allosteric modulators target endocrine pathways for metabolic disorders. Cinacalcet, a PAM of the calcium-sensing receptor (CaSR), was approved by the FDA in 2004 for treating secondary hyperparathyroidism in patients with chronic kidney disease on dialysis, where it sensitizes the receptor to extracellular calcium, thereby reducing parathyroid hormone secretion and serum calcium levels.^[82] Investigational negative allosteric modulators (NAMs) have been explored for neurodegenerative conditions. Basimglurant (RO4917523), a selective mGluR5 NAM, advanced to Phase II trials in the 2010s for fragile X syndrome and depression, showing limited efficacy that led to discontinuation of the program; it has also been investigated in preclinical models for Alzheimer's disease targeting amyloid-beta pathology. As of 2025, it is in Phase II/III trials for trigeminal neuralgia.^[83]^[84] Emerging applications span pain management and oncology. For chronic pain, allosteric modulators of acid-sensing ion channels (ASICs), such as heteroarylguanidines targeting ASIC1a and ASIC3, demonstrate analgesic potential by inhibiting proton-gated sodium influx in preclinical models of inflammatory and neuropathic pain.^[85] In oncology, allosteric NAMs for mutant epidermal growth factor receptor (EGFR), like EAI045 and JBJ-09-063, address resistance in non-small cell lung cancer by stabilizing inactive conformations of T790M and C797S mutants, showing efficacy in combination with orthosteric inhibitors in preclinical and early clinical studies.^[86]^[87] Recent advancements include neurosteroid-based PAMs for mood disorders. Zuranolone (SAGE-217), a GABAA receptor PAM, was approved by the FDA in 2023 and the EMA in 2025 for postpartum depression and completed Phase III trials for major depressive disorder, with approval pending as of November 2025, offering rapid antidepressant effects through enhanced inhibitory signaling comparable to intravenous brexanolone.^[88]^[89]^[90]^[91]

Challenges in Development

Selectivity and Safety Concerns

One major challenge in developing allosteric modulators is selectivity, arising from the conservation of allosteric binding sites across related protein families, which can promote polypharmacology and off-target effects. For instance, allosteric sites in G protein-coupled receptors (GPCRs), a common target for such modulators, exhibit structural similarities that allow ligands to bind multiple receptor subtypes or even unrelated proteins, potentially leading to unintended pharmacological actions. In the case of positive allosteric modulators (PAMs) of GABA_A receptors, such as benzodiazepines, off-target binding to non-α1 subtypes or other ion channels can exacerbate sedation beyond therapeutic levels, contributing to adverse events like excessive drowsiness or cognitive impairment.^[92]^[73] Safety concerns with negative allosteric modulators (NAMs) include the risk of inverse agonism, where these compounds not only block agonist activity but also suppress constitutive receptor signaling, potentially altering receptor expression levels over time. Although inverse agonism typically leads to compensatory upregulation in constitutively active systems,^[93]^[55] Additionally, probe dependence—the phenomenon where an allosteric modulator's effect varies depending on the orthosteric agonist used—can result in unpredictable in vivo outcomes, as the modulator may enhance or inhibit signaling differently across endogenous ligands or physiological conditions, complicating translation from in vitro assays to clinical efficacy and safety.^[93]^[55] Toxicological profiles of early allosteric modulators highlight specific risks, such as hepatotoxicity observed with certain mGluR5 NAMs developed in the 2010s. For example, acetylene-based compounds like raseglurant (RO4917523) were withdrawn from clinical development due to elevated liver enzyme levels and hepatic injury in patients during long-term use.^[94]^[95] To mitigate cardiac risks, hERG channel assays are routinely employed in preclinical screening of allosteric modulators, as inhibition of this potassium channel can prolong the QT interval and increase arrhythmia susceptibility, a concern for many small-molecule modulators regardless of mechanism.^[94]^[95] Regulatory oversight emphasizes evaluating abuse potential for allosteric modulators targeting opioid receptors, given their capacity to enhance or alter endogenous ligand effects. The FDA's 2017 guidance on assessing abuse potential requires comprehensive preclinical and clinical studies for such compounds, including those acting allosterically, to identify risks of dependence or misuse similar to orthosteric opioids; updated emphases in subsequent reviews underscore monitoring for biased signaling that might retain rewarding properties.^[96]^[97]

Strategies for Discovery and Optimization

The discovery of allosteric modulators relies on advanced screening methods that enable the identification of compounds interacting with non-orthosteric sites. High-throughput assays utilizing bioluminescent resonance energy transfer (BRET) have emerged as a powerful tool for detecting allosteric effects in real-time, particularly for G protein-coupled receptors (GPCRs) and ion channels, by monitoring conformational changes or protein-protein interactions without the interference of orthosteric ligands.^[98] For instance, NanoBRET platforms facilitate the screening of modulators that disrupt or enhance interactions like those between KRAS and downstream effectors, allowing for the prioritization of selective hits in cellular contexts.^[99] Complementing these experimental approaches, AI-driven virtual screening has accelerated site prediction since 2021, leveraging models like AlphaFold to predict allosteric pockets in proteins lacking experimental structures, thereby guiding docking simulations for novel modulators.^[100] This integration has proven effective in identifying potential allosteric sites on GPCRs, where AI-generated models rival cryo-EM data in hit discovery campaigns.^[101] Optimization of lead allosteric modulators emphasizes structure-based design, incorporating high-resolution cryo-EM structures to refine binding poses and enhance potency. Iterative docking and molecular dynamics simulations against cryo-EM-derived allosteric pockets, such as those in the adenosine A1 receptor, have yielded positive allosteric modulators with improved selectivity by targeting extrahelical sites.^[102] Similarly, cryo-EM has illuminated modulator-bound conformations in Class A, B, and C GPCRs, enabling the design of compounds that stabilize specific states while minimizing off-target effects.^[103] To further boost specificity, the development of bitopic ligands—molecules that simultaneously engage orthosteric and allosteric sites—has gained traction, as these dual-acting agents amplify affinity and subtype selectivity in targets like GPCRs.^[104] For example, bitopic modulators of the cannabinoid CB2 receptor demonstrate enhanced functional bias, reducing unwanted signaling pathways compared to single-site ligands.^[105] Looking ahead, strategies increasingly target allosteric modulation in historically undruggable proteins, exemplified by the 2021 FDA approval of sotorasib, a negative allosteric modulator (NAM) that covalently binds the switch-II pocket of KRAS G12C to lock it in an inactive GDP-bound state, offering a paradigm for oncology applications.^[106] Pharmacogenomics further supports personalized approaches by identifying genetic variants in GPCR allosteric sites that influence modulator efficacy, allowing tailored dosing to optimize therapeutic responses and mitigate adverse effects.^[107] As of 2025, emerging trends focus on biased allosteric modulators that selectively activate pathway-specific signaling, particularly in immunotherapy, where PAR2 NAMs promote anti-tumor immune responses by repressing immunosuppressive pathways without broad receptor antagonism.^[108]

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