International Journal of Molecular Sciences

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Open AccessEditorial

Allosteric Modulators of G Protein-Coupled Receptors

by Alexander Shpakov

Int. J. Mol. Sci. 2022, 23(6), 2934; https://doi.org/10.3390/ijms23062934 - 8 Mar 2022

Cited by 2 | Viewed by 1743

Abstract

The G protein-coupled receptors (GPCRs) are the largest group of membrane receptor proteins that are targeted by more than 30% of drugs [...] Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

Research

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18 pages, 4082 KiB

Open AccessArticle

The Molecular Mechanism of Positive Allosteric Modulation at the Dopamine D1 Receptor

by Alexander Goldberg, Bing Xie and Lei Shi

Int. J. Mol. Sci. 2023, 24(16), 12848; https://doi.org/10.3390/ijms241612848 - 16 Aug 2023

Cited by 1 | Viewed by 960

Abstract

The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds [...] Read more.

The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na⁺-binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207’s allosteric action at the D1R paves the way for the rational design of more potent and effective allosteric modulators. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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16 pages, 5244 KiB

Open AccessArticle

Search for Structural Basis of Interactions of Biogenic Amines with Human TAAR1 and TAAR6 Receptors

by Anna V. Glyakina, Constantine D. Pavlov, Julia V. Sopova, Raul R. Gainetdinov, Elena I. Leonova and Oxana V. Galzitskaya

Int. J. Mol. Sci. 2022, 23(1), 209; https://doi.org/10.3390/ijms23010209 - 25 Dec 2021

Cited by 7 | Viewed by 2878

Abstract

The identification and characterization of ligand-receptor binding sites are important for drug development. Trace amine-associated receptors (TAARs, members of the class A GPCR family) can interact with different biogenic amines and their metabolites, but the structural basis for their recognition by the TAARs [...] Read more.

The identification and characterization of ligand-receptor binding sites are important for drug development. Trace amine-associated receptors (TAARs, members of the class A GPCR family) can interact with different biogenic amines and their metabolites, but the structural basis for their recognition by the TAARs is not well understood. In this work, we have revealed for the first time a group of conserved motifs (fingerprints) characterizing TAARs and studied the docking of aromatic (β-phenylethylamine, tyramine) and aliphatic (putrescine and cadaverine) ligands, including gamma-aminobutyric acid, with human TAAR1 and TAAR6 receptors. We have identified orthosteric binding sites for TAAR1 (Asp68, Asp102, Asp284) and TAAR6 (Asp78, Asp112, Asp202). By analyzing the binding results of 7500 structures, we determined that putrescine and cadaverine bind to TAAR1 at one site, Asp68 + Asp102, and to TAAR6 at two sites, Asp78 + Asp112 and Asp112 + Asp202. Tyramine binds to TAAR6 at the same two sites as putrescine and cadaverine and does not bind to TAAR1 at the selected Asp residues. β-Phenylethylamine and gamma-aminobutyric acid do not bind to the TAAR1 and TAAR6 receptors at the selected Asp residues. The search for ligands targeting allosteric and orthosteric sites of TAARs has excellent pharmaceutical potential. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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11 pages, 2421 KiB

Open AccessArticle

Living-Cell Diffracted X-ray Tracking Analysis Confirmed Internal Salt Bridge Is Critical for Ligand-Induced Twisting Motion of Serotonin Receptors

by Kazuhiro Mio, Shoko Fujimura, Masaki Ishihara, Masahiro Kuramochi, Hiroshi Sekiguchi, Tai Kubo and Yuji C. Sasaki

Int. J. Mol. Sci. 2021, 22(10), 5285; https://doi.org/10.3390/ijms22105285 - 17 May 2021

Cited by 10 | Viewed by 2043

Abstract

Serotonin receptors play important roles in neuronal excitation, emotion, platelet aggregation, and vasoconstriction. The serotonin receptor subtype 2A (5-HT_2AR) is a Gq-coupled GPCR, which activate phospholipase C. Although the structures and functions of 5-HT_2ARs have been well studied, little [...] Read more.

Serotonin receptors play important roles in neuronal excitation, emotion, platelet aggregation, and vasoconstriction. The serotonin receptor subtype 2A (5-HT_2AR) is a Gq-coupled GPCR, which activate phospholipase C. Although the structures and functions of 5-HT_2ARs have been well studied, little has been known about their real-time dynamics. In this study, we analyzed the intramolecular motion of the 5-HT_2AR in living cells using the diffracted X-ray tracking (DXT) technique. The DXT is a very precise single-molecular analytical technique, which tracks diffraction spots from the gold nanocrystals labeled on the protein surface. Trajectory analysis provides insight into protein dynamics. The 5-HT_2ARs were transiently expressed in HEK 293 cells, and the gold nanocrystals were attached to the N-terminal introduced FLAG-tag via anti-FLAG antibodies. The motions were recorded with a frame rate of 100 μs per frame. A lifetime filtering technique demonstrated that the unliganded receptors contain high mobility population with clockwise twisting. This rotation was, however, abolished by either a full agonist α-methylserotonin or an inverse agonist ketanserin. Mutation analysis revealed that the “ionic lock” between the DRY motif in the third transmembrane segment and a negatively charged residue of the sixth transmembrane segment is essential for the torsional motion at the N-terminus of the receptor. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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21 pages, 2935 KiB

Open AccessArticle

Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors

by Pedro Renault and Jesús Giraldo

Int. J. Mol. Sci. 2021, 22(1), 187; https://doi.org/10.3390/ijms22010187 - 27 Dec 2020

Cited by 6 | Viewed by 3313

Abstract

G protein-coupled Receptors (GPCRs) play a central role in many physiological processes and, consequently, constitute important drug targets. In particular, the search for allosteric drugs has recently drawn attention, since they could be more selective and lead to fewer side effects. Accordingly, computational [...] Read more.

G protein-coupled Receptors (GPCRs) play a central role in many physiological processes and, consequently, constitute important drug targets. In particular, the search for allosteric drugs has recently drawn attention, since they could be more selective and lead to fewer side effects. Accordingly, computational tools have been used to estimate the druggability of allosteric sites in these receptors. In spite of many successful results, the problem is still challenging, particularly the prediction of hydrophobic sites in the interface between the protein and the membrane. In this work, we propose a complementary approach, based on dynamical correlations. Our basic hypothesis was that allosteric sites are strongly coupled to regions of the receptor that undergo important conformational changes upon activation. Therefore, using ensembles of experimental structures, normal mode analysis and molecular dynamics simulations we calculated correlations between internal fluctuations of different sites and a collective variable describing the activation state of the receptor. Then, we ranked the sites based on the strength of their coupling to the collective dynamics. In the β2 adrenergic (β2AR), glucagon (GCGR) and M2 muscarinic receptors, this procedure allowed us to correctly identify known allosteric sites, suggesting it has predictive value. Our results indicate that this dynamics-based approach can be a complementary tool to the existing toolbox to characterize allosteric sites in GPCRs. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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28 pages, 5444 KiB

Open AccessArticle

Comparative Study of the Steroidogenic Effects of Human Chorionic Gonadotropin and Thieno[2,3-D]pyrimidine-Based Allosteric Agonist of Luteinizing Hormone Receptor in Young Adult, Aging and Diabetic Male Rats

by Andrey A. Bakhtyukov, Kira V. Derkach, Maxim A. Gureev, Dmitry V. Dar’in, Viktor N. Sorokoumov, Irina V. Romanova, Irina Yu. Morina, Anna M. Stepochkina and Alexander O. Shpakov

Int. J. Mol. Sci. 2020, 21(20), 7493; https://doi.org/10.3390/ijms21207493 - 11 Oct 2020

Cited by 21 | Viewed by 3014

Abstract

Low-molecular-weight agonists of luteinizing hormone (LH)/human chorionic gonadotropin (hCG) receptor (LHCGR), which interact with LHCGR transmembrane allosteric site and, in comparison with gonadotropins, more selectively activate intracellular effectors, are currently being developed. Meanwhile, their effects on testicular steroidogenesis have not been studied. The [...] Read more.

Low-molecular-weight agonists of luteinizing hormone (LH)/human chorionic gonadotropin (hCG) receptor (LHCGR), which interact with LHCGR transmembrane allosteric site and, in comparison with gonadotropins, more selectively activate intracellular effectors, are currently being developed. Meanwhile, their effects on testicular steroidogenesis have not been studied. The purpose of this work is to perform a comparative study of the effects of 5-amino-N-tert-butyl-4-(3-(1-methylpyrazole-4-carboxamido)phenyl)-2-(methylthio)thieno[2,3-d] pyrimidine-6-carboxamide (TP4/2), a LHCGR allosteric agonist developed by us, and hCG on adenylyl cyclase activity in rat testicular membranes, testosterone levels, testicular steroidogenesis and spermatogenesis in young (four-month-old), aging (18-month-old) and diabetic male Wistar rats. Type 1 diabetes was caused by a single streptozotocin (50 mg/kg) injection. TP4/2 (20 mg/kg/day) and hCG (20 IU/rat/day) were administered for 5 days. TP4/2 was less effective in adenylyl cyclase stimulation and ability to activate steroidogenesis when administered once into rats. On the 3rd–5th day, TP4/2 and hCG steroidogenic effects in young adult, aging and diabetic rats were comparable. Unlike hCG, TP4/2 did not inhibit LHCGR gene expression and did not hyperstimulate the testicular steroidogenesis system, moderately increasing steroidogenic proteins gene expression and testosterone production. In aging and diabetic testes, TP4/2 improved spermatogenesis. Thus, during five-day administration, TP4/2 steadily stimulates testicular steroidogenesis, and can be used to prevent androgen deficiency in aging and diabetes. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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Review

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18 pages, 2865 KiB

Open AccessReview

Allosteric Modulation of GPCRs of Class A by Cholesterol

by Jan Jakubík and Esam E. El-Fakahany

Int. J. Mol. Sci. 2021, 22(4), 1953; https://doi.org/10.3390/ijms22041953 - 16 Feb 2021

Cited by 35 | Viewed by 5265

Abstract

G-protein coupled receptors (GPCRs) are membrane proteins that convey extracellular signals to the cellular milieu. They represent a target for more than 30% of currently marketed drugs. Here we review the effects of membrane cholesterol on the function of GPCRs of Class A. [...] Read more.

G-protein coupled receptors (GPCRs) are membrane proteins that convey extracellular signals to the cellular milieu. They represent a target for more than 30% of currently marketed drugs. Here we review the effects of membrane cholesterol on the function of GPCRs of Class A. We review both the specific effects of cholesterol mediated via its direct high-affinity binding to the receptor and non-specific effects mediated by cholesterol-induced changes in the properties of the membrane. Cholesterol binds to many GPCRs at both canonical and non-canonical binding sites. It allosterically affects ligand binding to and activation of GPCRs. Additionally, it changes the oligomerization state of GPCRs. In this review, we consider a perspective of the potential for the development of new therapies that are targeted at manipulating the level of membrane cholesterol or modulating cholesterol binding sites on to GPCRs. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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38 pages, 4880 KiB

Open AccessReview

Pharmacology of Free Fatty Acid Receptors and Their Allosteric Modulators

by Manuel Grundmann, Eckhard Bender, Jens Schamberger and Frank Eitner

Int. J. Mol. Sci. 2021, 22(4), 1763; https://doi.org/10.3390/ijms22041763 - 10 Feb 2021

Cited by 53 | Viewed by 6626

Abstract

The physiological function of free fatty acids (FFAs) has long been regarded as indirect in terms of their activities as educts and products in metabolic pathways. The observation that FFAs can also act as signaling molecules at FFA receptors (FFARs), a family of [...] Read more.

The physiological function of free fatty acids (FFAs) has long been regarded as indirect in terms of their activities as educts and products in metabolic pathways. The observation that FFAs can also act as signaling molecules at FFA receptors (FFARs), a family of G protein-coupled receptors (GPCRs), has changed the understanding of the interplay of metabolites and host responses. Free fatty acids of different chain lengths and saturation statuses activate FFARs as endogenous agonists via binding at the orthosteric receptor site. After FFAR deorphanization, researchers from the pharmaceutical industry as well as academia have identified several ligands targeting allosteric sites of FFARs with the aim of developing drugs to treat various diseases such as metabolic, (auto)inflammatory, infectious, endocrinological, cardiovascular, and renal disorders. GPCRs are the largest group of transmembrane proteins and constitute the most successful drug targets in medical history. To leverage the rich biology of this target class, the drug industry seeks alternative approaches to address GPCR signaling. Allosteric GPCR ligands are recognized as attractive modalities because of their auspicious pharmacological profiles compared to orthosteric ligands. While the majority of marketed GPCR drugs interact exclusively with the orthosteric binding site, allosteric mechanisms in GPCR biology stay medically underexploited, with only several allosteric ligands currently approved. This review summarizes the current knowledge on the biology of FFAR1 (GPR40), FFAR2 (GPR43), FFAR3 (GPR41), FFAR4 (GPR120), and GPR84, including structural aspects of FFAR1, and discusses the molecular pharmacology of FFAR allosteric ligands as well as the opportunities and challenges in research from the perspective of drug discovery. Full article

(This article belongs to the Special Issue Allosteric Modulators of GPCRs)

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