This chapter considers biased signaling as a natural function of GPCRs in the form of probe dependence. Thus, any ligand that changes the conformation of the receptor (agonist, antagonist, allosteric modulator) has the potential to change the natural signaling of the receptor through diverse conformational alterations in the receptor structure. Given this, selectivity is discussed in terms of varying intrinsic efficacy and selective stabilization of receptor states with methods to detect and measure these effects. Lastly, the translation of in vitro to complex in vivo systems will be considered.

This paper discusses how targeted pharmacologic experiments can elucidate the mechanism of allosteric receptor inhibitors (NAMs) to identify NAMs that may have exceptionally useful properties and target residence times in vivo. Specifically, experiments can be done to identify positive allosteric modulator (PAM) antagonists, NAMs that increase the affinity of the receptor for the agonist but decrease agonist efficacy. These molecules would be predicted to have long receptor offset times in vivo (in the presence of ambient concentrations of agonist) and favorable receptor residence times for therapy and also selectively target agonist prebound receptors. Flux analysis is used to demonstrate the salient properties of PAM antagonists and their favorable pharmacodynamic effects for blocking physiological signals.

The alarming rates of deaths due to opioid overdose present an urgent need for safer opioid analgesics. Positive allosteric modulators (PAMs) of opioid receptors (ORs) offer a promising approach to enhance opioid efficacy while reducing risks of overdose. In this study, we unveil the selective mechanism of PAM modulation of the OR family through structure elucidation of the δ-opioid receptor and μ-opioid receptor (μOR) bound to orthosteric agonists and PAMs BMS986187 (BMS187) and BMS986122 (BMS122). In addition, we uncovered an unexpected but conserved allosteric site across the transmembrane helices TM2 to TM4 of ORs, occupied by BMS187 but not BMS122. Leveraging these structural insights, we designed 9-(5-(4-chlorophenyl)furan-2-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione (MPAM-15), whose αβ cooperativity factor is 33-fold higher than BMS122 and threefold higher than BMS187, indicating markedly stronger positive allosterism. Animal studies demonstrate that MPAM-15 shows excellent brain penetration and enhances morphine-induced antinociception without exacerbating respiratory depression or constipation. Molecular dynamics simulations revealed that MPAM-15 promotes and stabilizes the conformational equilibrium of μOR toward the canonical active state, providing a mechanistic basis for its enhanced allosteric potency. These discoveries substantially advance our understanding of OR allosteric mechanism and pave the way for the structure-based development of allosteric opioid analgesics.

BACKGROUND AND PURPOSE:Binding kinetics are essentially based on rate constants. Yet, this view has been challenged by the idea that 'binding fluxes' are dynamic and therefore more relevant. Those fluxes refer to the rate at which a target/receptor changes from one state into another through ligand/drug binding or a conformational change. Besides acting as building blocks for many algebraic expressions, they also determine how the concentration of each individual target state evolves over time. Here we show that such fluxes offer additional opportunities for understanding and predicting ligand binding. EXPERIMENTAL APPROACH:Simulated binding data are obtained by solving the relevant set of flux-based differential equations for increasingly complex ligand binding models over very small time intervals by Euler's method. As input, they require only ligand concentration(s) and rate constants. KEY RESULTS:Compared to often-complex algebraic expressions, binding fluxes allow more intuitive/inductive insight into different aspects of ligand binding such as the occurrence of transient binding overshoots and the effect of a closing lid over the ligand's binding pocket on ligand dissociation. These examples disclose fundamental principles that govern ligand binding and, above all, they highlight the essential role of rate constants in all the examined binding models. CONCLUSIONS AND IMPLICATIONS:Binding fluxes and rate constants complement each other: They respectively indicate how and why binding processes evolve in a certain fashion. The presented flux-based approaches have the advantage to address pre-equilibrium as well as equilibrium conditions and can be applied to any ligand-binding model.

A mathematical model is described that enables calculation of drug concentration gradients within structured tissues for high affinity molecules that are taken up by cells. Access of drugs to the complete tissue mass may be prevented by high affinity binding, receptor re-binding, avid permeation into the cell and restricted diffusion (high tissue tortuosity). Varying parameters such as affinity and kinetic constants (association and dissociation rate constants) may be a strategy to manipulate affinity and penetration into structured tissues.

While potency of drugs has been considered the main criterion defining therapeutic utility in vivo, target residence time (RT, the time the ligand associates with the target in vivo) is also important, and studies have shown that in some cases, it is more important than potency. New data in this area have contributed toward the substantive detection and manipulation of RT for therapeutic increased value on the following two fronts: (1) new and better techniques to assess ligand-target kinetics and (2) new appreciation of ligand types (i.e. allosteric modulators) and mechanisms of ligand binding including the temporal implications of binding to cryptic pockets on GPCRs. These data will be discussed.

This chapter considers biased signaling as a natural function of G protein-coupled receptors (GPCRs) in the form of probe dependence. Thus, any ligand that changes the conformation of the receptor (agonist, antagonist, or allosteric modulator) has the potential to change the natural signaling of the receptor through unequal conformational alterations in the receptor structure. This gives an added dimension to agonist selectivity beyond extracellular recognition, namely the ability of agonists to emphasize certain signaling pathways in the cell at the expense of others. Given this, selectivity is discussed in terms of varying intrinsic efficacy and selective stabilization of receptor states with methods to detect and measure these effects. Last, the translation of in vitro to complex in vivo systems will be considered.

The therapeutic effects of allosteric modulators on neurotransmission are described. The two unique features of allosteric modulators are: (1) separate binding sites on proteins, and (2) the production of altered receptor conformation upon binding. The effects of positive allosteric modulators (PAMs), negative allosteric modulators (NAMs) and PAM-Antagonists are described in relation to effects on neural pathways. The quantification of allosteric effects and ascription of parameters to allosteric modulators through comparison to the functional allosteric model also is described.

Opioid receptors, a subfamily of G protein-coupled receptors (GPCRs), are key therapeutic targets. In the canonical GPCR activation model, agonist binding is required for receptor–G protein complex formation, while antagonists prevent G protein coupling. However, many GPCRs exhibit basal activity, allowing G protein association without an agonist. The pharmacological impact of agonist-free receptor–G protein complexes is poorly understood. Here we present biochemical evidence that certain κ-opioid receptor (KOR) inverse agonists can act via KOR–Gi protein complexes. To investigate this phenomenon, we determined cryo-EM structures of KOR–Gi protein complexes with three inverse agonists: JDTic, norBNI and GB18, corresponding to structures of inverse agonist-bound GPCR–G protein complexes. Remarkably, the orthosteric binding pocket resembles the G protein-free ‘inactive’ receptor conformation, while the receptor remains coupled to the G protein. In summary, our work challenges the canonical model of receptor antagonism and offers crucial insights into GPCR pharmacology. This study uncovers that certain κ-opioid receptor inverse agonists form receptor–G protein complexes, even in inactive states, challenging the classic GPCR activation model.

Sodium ions are classically conceptualized as negative allosteric modulators for G protein-coupled receptors, although there have been reports of either positive allosteric modulation or no effect of sodium on GPCR function. Here, we identified opposing actions of sodium on μ and κ opioid receptors. We utilized a variety of methods including radioligand binding, real-time conformational monitoring of transitions using bioluminescence resonance energy transfer, and signaling assays using the TRUPATH resource. At the μ receptors, sodium behaved as a negative allosteric modulator of binding, conformational transitions, and signaling. Intriguingly, bitopic μ agonists displayed transducer-specific effects on conformational transitions and signaling sodium concentrations. By contrast, at the κ opioid receptor, sodium negatively modulated agonist binding and positively modulated conformational transitions and signaling. Taken together, these findings support the notion that the differential sensitivities to sodium concentrations will result in opposing effects on the cell surface and intracellular signaling.

Olfactory receptors are members of class A (rhodopsin-like) family of G protein-coupled receptors (GPCRs). Their expression and function have been increasingly studied in nonolfactory tissues, and many have been identified as potential therapeutic targets. In this manuscript, we focus on the discovery of novel ligands for the olfactory receptor family 51 subfamily E2 (OR51E2). We performed an artificial intelligence-based virtual drug screen of a ∼2.2 million small molecule library. Cell-based functional assay identified compound 80 (C80) as an antagonist and inverse agonist, and detailed pharmacological analysis revealed C80 acts as a negative allosteric modulator by significantly decreasing the agonist efficacy, while having a minimal effect on receptor affinity for agonist. C80 binds to an allosteric binding site formed by a network of nine residues localized in the intracellular parts of transmembrane domains 3, 5, 6, 7, and H8, which also partially overlaps with a G protein binding site. Mutational experiments of residues involved in C80 binding uncovered the significance of the C2406.37 position in blocking the activation-related conformational change and keeping the receptor in the inactive form. Our study provides a mechanistic understanding of the negative allosteric action of C80 on agonist-ctivated OR51E2. We believe the identification of the antagonist of OR51E2 will enable a multitude of studies aiming to determine the functional role of this receptor in specific biologic processes. SIGNIFICANCE STATEMENT OR51E2 has been implicated in various biological processes, and its antagonists that can effectively modulate its activity have therapeutic potential. Here we report the discovery of a negative allosteric modulator of OR51E2 and provide a mechanistic understanding of its action. We demonstrate that this modulator has an inhibitory effect on the efficacy of the agonist for the receptor and reveal a network of nine residues that constitute its binding pocket, which also partially overlaps with the G protein binding site.

With the advent of functional screening, more allosteric molecules are being discovered and developed as possible therapeutic enti-ties. Allosteric proteins are unique because of two specific proper-ties: 1) separate binding sites for allosteric modulators and guests and 2) mandatory alteration of receptor conformation upon binding of allosteric modulators. For G protein-coupled receptors, these properties produce many beneficial effects on pharmacologic sys-tems that are described here. Allosteric discovery campaigns also bring with them added considerations that must be addressed for the endeavor to be successful, and these are described herein as well. SIGNIFICANCE STATEMENT Recent years have seen the increasing presence of allosteric molecules as possible therapeutic drug candidates. The sci-entific procedures to characterize these are unique and re-quire special techniques, so it is imperative that scientists understand the new concepts involved in allosteric function. This review examines the reasons why allosteric molecules should be considered as new drug entities and the techni-ques required to optimize the discovery process for allosteric molecules.

Biased signalling is a natural result of GPCR allosteric function and should be expected from any and all synthetic and natural agonists. Therefore, it may be encountered in all agonist discovery projects and must be considered as a beneficial (or possible detrimental) feature of new candidate molecules. While bias is detected easily, the synoptic nature of GPCR signalling makes translation of simple in vitro bias to complex in vivo systems problematic. The practical outcome of this is a difficulty in predicting the therapeutic value of biased signalling due to the failure of translation of identified biased signalling to in vivo agonism. This is discussed in this review as well as some new ways forward to improve this translation process and better exploit this powerful pharmacologic mechanism.

Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the ‘quality’ of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more ‘efficacies’ of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development. Deeper pharmacological characterization of hit and lead compounds is being enabled by novel assays to characterize target behaviour as well as by advances in structural biology. This article discusses key factors in pharmacological characterization in the context of G protein-coupled receptors as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to increase the probability of them succeeding in clinical trials.

This chapter deals with the quantification of the effects of antagonists to yield empirical measures of antagonist potency. Beginning with the premise that there are two possible modes of action of antagonism; orthosteric blockade (occlusion of the agonist binding site) and allosteric modulation, this chapter focuses on orthosteric antagonism. Estimates of antagonist potency can be obtained for all modes of antagonism through a pA2 value and/or a pIC50 of antagonism of a fixed agonist effect. Patterns of antagonism are then discussed from the standpoint of using these to identify the mechanism of antagonist action (e.g., orthosteric antagonists producing steric hindrance of agonists). The chapter then discusses how these mechanisms can be used to identify the appropriate mathematical analysis to yield estimates of true system-independent antagonist potency that transcend cell type and measuring system.

Several non-caloric sweeteners exhibit a delay in sweetness onset and a sweetness linger after sampling. These temporal properties are thought to be the result of non-specific interactions with cell membranes and proteins in the oral cavity. Data and analysis presented in this report also support the potential involvement of receptor affinity and binding kinetics to this phenomenon. In general, affected sweeteners exhibit distinctly higher binding affinity compared to carbohydrate sweeteners, which do not have temporal issues. In addition, binding kinetic simulations illustrate much slower receptor binding association and dissociation kinetics for a set of non-caloric sweeteners presenting temporal issues, in comparison to carbohydrate sweeteners. So, the higher affinity of some non-caloric sweeteners, dictating lower use levels, and affecting binding kinetics, could contribute to their delay and linger in sweetness perception. Simple pharmacology principles could explain, at least in part, some of the temporal issues of sweeteners.

The NTSR1 neurotensin receptor (NTSR1) is a G protein-coupled receptor (GPCR) found in the brain and peripheral tissues with neurotensin (NTS) being its endogenous peptide ligand. In the brain, NTS modulates dopamine neuronal activity, induces opioid-independent analgesia, and regulates food intake. Recent studies indicate that biasing NTSR1 toward β-arrestin signaling can attenuate the actions of psychostimulants and other drugs of abuse. Here, we provide the cryoEM structures of NTSR1 ternary complexes with heterotrimeric Gq and GoA with and without the brain-penetrant small-molecule SBI-553. In functional studies, we discovered that SBI-553 displays complex allosteric actions exemplified by negative allosteric modulation for G proteins that are Gα subunit selective and positive allosteric modulation and agonism for β-arrestin translocation at NTSR1. Detailed structural analysis of the allosteric binding site illuminated the structural determinants for biased allosteric modulation of SBI-553 on NTSR1.