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Sarma P, Banerjee R, Shukla AK. Structural snapshot of a β-arrestin-biased receptor. Trends Pharmacol Sci 2023; 44:1-3. [PMID: 36057461 PMCID: PMC7614537 DOI: 10.1016/j.tips.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 01/06/2023]
Abstract
Atypical chemokine receptor subtype 3 (ACKR3), a chemokine receptor, couples selectively to β-arrestins (βarrs) but not to G proteins despite having seven transmembrane (7TM) helix architecture. Yen et al. present cryogenic-electron microscopy (cryo-EM) structures of agonist-bound ACKR3, elucidating a distinct chemokine-binding mechanism, and offering a structural template to probe the transducer-coupling bias at this receptor.
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77
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Naressi RG, Schechtman D, Malnic B. Odorant receptors as potential drug targets. Trends Pharmacol Sci 2023; 44:11-14. [PMID: 35999088 DOI: 10.1016/j.tips.2022.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 12/27/2022]
Abstract
Odorant receptors (ORs) belong to a large family of G protein-coupled receptors (GPCRs) that are highly expressed by olfactory sensory neurons of the nose. Accumulating evidence indicates that they are also expressed in a variety of nonolfactory tissues, which makes them new potential drug targets. Here we discuss the challenges and strategies to target these receptors.
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78
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Kamadar JH, Kumari DR, Kapadiya KM. Recent Studies on Serotonin 5-HT 2A Receptor Antagonists in Medicinal Chemistry: A Last Decades Survey. Mini Rev Med Chem 2023; 23:1859-1870. [PMID: 37157202 DOI: 10.2174/1389557523666230508162439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/17/2022] [Accepted: 01/04/2023] [Indexed: 05/10/2023]
Abstract
In the last decades, much attention has been paid to the functioning of receptors to understand better how they work with various chemical motifs. Among different families, G-proteincoupled receptor (GPCR) families have drawn much attention in the twenty-first century. They are the most prominent signal transducer across the cell membrane, comprising thousand-odd proteins. One of the members of GPCRs is the serotonin 2A (5-HT2A) receptor, which has been associated with complex etiological mental illnesses. In this survey, we collected data on 5-HT2A, i.e., the role of 5- HT2A receptors in human and animal analogy, various binding site functionalities, advanced effects, and synthetic aspects.
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79
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Jakowiecki J, Orzeł U, Gliździnska A, Możajew M, Filipek S. Specificities of Protein Homology Modeling for Allosteric Drug Design. Methods Mol Biol 2023; 2627:339-348. [PMID: 36959457 DOI: 10.1007/978-1-0716-2974-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The allosteric binding sites are usually located in the flexible areas of proteins, which are hardly visible in the crystal structures. However, there are notable exceptions like allosteric sites in receptors in class B and C of GPCRs, which are located within a well-defined bundle of transmembrane helices. Class B and C evolved from class A and even after swapping of orthosteric and allosteric sites the central binding site persisted and it can be used for easy design of allosteric drugs. However, studying the ligand binding to the allosteric sites in the most populated class A of GPCRs is still a challenge, since they are located mostly in unresolved parts of the receptor's structure, and especially N-terminus. This chapter provides an example of cannabinoid CB1 receptor N-terminal homology modeling, ligand-guided modeling of the allosteric site in GABA receptor, as well as C-linker modeling in the potassium ion channels where the allosteric phospholipid ligand PIP2 is bound.
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80
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Vitale RM, Iannotti FA, Florio T. Editorial: "Small molecules targeting transmembrane receptors and ion channels in drug discovery". Front Mol Biosci 2023; 10:1183713. [PMID: 37200869 PMCID: PMC10185887 DOI: 10.3389/fmolb.2023.1183713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023] Open
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81
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Ragini, Sakshi, Saini A, Mani I. Endocytosis and signaling of 5-HT1A receptor. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:113-123. [PMID: 36813354 DOI: 10.1016/bs.pmbts.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The neurotransmitter serotonin (also known as 5-hydroxytryptamine, 5-HT) regulates many important physiological as well as pathological functions in the body like psychoemotional, sensation, blood circulation, food intake, autonomic, memory, sleep, pain, etc. 5-HT binds to its receptor 5-HT1A to initiate GTP exchange at the Gi/o protein, which activates the receptor G protein complex. G protein subunits attach to different effectors and generate various responses, such as inhibition of adenyl cyclase enzyme and regulates the opening of Ca++ and K+ ion channels. Activated signalling cascades activate protein kinase C (PKC) (a second messenger), which further induces the detachment of Gβγ-dependent receptor signaling and leads to 5-HT1A internalization. After internalization, 5-HT1A receptor attaches to the Ras-ERK1/2 pathway. The receptor further trafficks to the lysosome for degradation. Receptor skips the trafficking to the lysosomal compartments and undergoes dephosphorylation. Dephosphorylated receptors now recycled back to the cell membrane. In this chapter, we have discussed the internalization, trafficking and signaling of the 5-HT1A receptor.
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82
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Liu C, He H, Tian J, Ma Y. Challenges and Solutions in the Recombinant Expression of Membrane Proteins. Protein Pept Lett 2023; 30:806-820. [PMID: 37861035 DOI: 10.2174/0109298665264728230920070145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 10/21/2023]
Abstract
Membrane proteins are important components of the proteome and play key roles in many biological processes, such as signal transduction, material transport, cell recognition, etc. Membrane proteins are involved in several fields, and more and more researchers want to understand them. However, the structural properties of membrane proteins make their recombinant expression yield low. This adversely affects the study of the structure and function of membrane proteins. Therefore, it is crucial to have a comprehensive and up-to-date understanding of membrane protein recombinant expression. Based on the current stage of research on membrane proteins, the article describes the current challenges faced by membrane protein recombinant expression and the solutions that can be applied to lay the foundation for a better study of membrane proteins in the future.
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83
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Bouma J, Soethoudt M, van Gils N, Xia L, van der Stelt M, Heitman LH. Cellular Assay to Study β-Arrestin Recruitment by the Cannabinoid Receptors 1 and 2. Methods Mol Biol 2023; 2576:189-199. [PMID: 36152187 DOI: 10.1007/978-1-0716-2728-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cannabinoid receptor 1 (CB1R) and cannabinoid receptor 2 (CB2R) are G protein-coupled receptors (GPCRs) that activate a variety of pathways upon activation by (partial) agonists including the G protein pathway and the recruitment of β-arrestins. Differences in the activation level of these pathways lead to biased signaling. Here, we describe a detailed protocol to characterize the potency and efficacy of ligands to induce or inhibit β-arrestin recruitment to the human CB1R and CB2R using the PathHunter® assay. This is a cellular assay that uses a β-galactosidase complementation system which has a chemiluminescent read-out and can be performed in 384-well plates. We have successfully used this assay to characterize a set of reference ligands (both agonists, antagonists, and an inverse agonist) on human CB1R and CB2R, of which some examples will be presented here.
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84
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Ben Abu N, Ben Shoshan-Galeczki Y, Malach E, Y Niv M. The T1R3 subunit of the sweet taste receptor is activated by D2O in transmembrane domain-dependent manner. Chem Senses 2023; 48:bjad032. [PMID: 37589415 DOI: 10.1093/chemse/bjad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Indexed: 08/18/2023] Open
Abstract
Deuterium oxide (D2O) is water in which the heavier and rare isotope deuterium replaces both hydrogens. We have previously shown that D2O has a distinctly sweet taste, mediated by the T1R2/T1R3 sweet taste receptor. Here, we explore the effect of heavy water on T1R2 and T1R3 subunits. We show that D2O activates T1R3-transfected HEK293T cells similarly to T1R2/T1R3-transfected cells. The response to glucose dissolved in D2O is higher than in water. Mutations of phenylalanine at position 7305.40 in the transmembrane domain of T1R3 to alanine, leucine, or tyrosine impair or diminish activation by D2O, suggesting a critical role for T1R3 TMD domain in relaying the heavy water signal.
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85
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Papageorgiou L, Christou E, Louka E, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. ADRA2B and HTR1A: An Updated Study of the Biogenic Amine Receptors Reveals Novel Conserved Motifs Which Play Key Role in Mental Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:79-99. [PMID: 37525034 DOI: 10.1007/978-3-031-31978-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Mental disorders are strongly connected with several psychiatric conditions including depression, bipolar disorder, schizophrenia, eating disorder, and suicides. There are many biological conditions and pathways that define these complicated illnesses. For example, eating disorders are complex mental health conditions that require the intervention of geneticists, psychiatrists, and medical experts in order to alleviate their symptoms. A patient with suicidal ideation should first be identified and consequently monitored by a similar team of specialists. Both genetics and epigenetics can shed light on eating disorders and suicides as they are found in the main core of such investigations. In the present study, an analysis has been performed on two specific members of the GPCR family toward drawing conclusions regarding their functionality and implementation in mental disorders. Specifically, evolutionary and structural studies on the adrenoceptor alpha 2b (ADRA2B) and the 5-hydroxytryptamine receptor 1A (HTR1A) have been carried out. Both receptors are classified in the biogenic amine receptors sub-cluster of the GPCRs and have been connected in many studies with mental diseases and malnutrition conditions. The major goal of this study is the investigation of conserved motifs among biogenic amine receptors that play an important role in this family signaling pathway, through an updated evolutionary analysis and the correlation of this information with the structural features of the HTR1A and ADRA2B. Furthermore, the structural comparison of ADRA2B, HTR1A, and other members of GPCRs related to mental disorders is performed.
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86
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Nag JK, Appasamy P, Sedley S, Malka H, Rudina T, Bar-Shavit R. RNF43 induces the turnover of protease-activated receptor 2 in colon cancer. FASEB J 2023; 37:e22675. [PMID: 36468684 DOI: 10.1096/fj.202200858rr] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/30/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022]
Abstract
Post-translational modification of G-protein coupled receptors (GPCRs) plays a central role in tissue hemostasis and cancer. The molecular mechanism of post-translational regulation of protease-activated receptors (PARs), a subgroup of GPCRs is yet understudied. Here we show that the cell-surface transmembrane E3 ubiquitin ligase ring finger 43 (RNF43) is a negative feedback regulator of PAR2 , impacting PAR2 -induced signaling and colon cancer growth. RNF43 co-associates with PAR2 , promoting its membrane elimination and degradation as shown by reduced cell surface biotinylated PAR2 levels and polyubiquitination. PAR2 degradation is rescued by R-spondin2 in the presence of leucine-rich repeat-containing G-protein-coupled receptor5 (LGR5). In fact, PAR2 acts jointly with LGR5, as recapitulated by increased β-catenin levels, transcriptional activity, phospho-LRP6, and anchorage-independent colony growth in agar. Animal models of the chemically induced AOM/DSS colon cancer of wt versus Par2/f2rl1 KO mice as also the 'spleen-liver' colon cancer metastasis, allocated a central role for PAR2 in colon cancer growth and development. RNF43 is abundantly expressed in the Par2/f2rl1 KO-treated AOM/DSS colon tissues while its level is very low to nearly null in colon cancer adenocarcinomas of the wt mice. The same result is obtained in the 'spleen-liver' model of spleen-inoculated cells, metastasized to the liver. High RNF43 expression is observed in the liver upon shRNA -Par2 silencing. "Limited-dilution-assay" performed in mice in-vivo, assigned PAR2 as a member of the cancer stem cell niche compartment. Collectively, we elucidate an original regulation of PAR2 oncogene, a member of cancer stem cells, by RNF43 ubiquitin ligase. It impacts β-catenin signaling and colon cancer growth.
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87
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Di Pizio A, Bermudez M, De Graaf C, Jockers R. Editorial: Peptide-binding GPCRs coming of age. Front Endocrinol (Lausanne) 2023; 14:1189508. [PMID: 37152971 PMCID: PMC10161729 DOI: 10.3389/fendo.2023.1189508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
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88
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Li Y, Gao H, Zhang H, Yu R, Feng F, Tang J, Li B. Characterization and expression profiling of G protein-coupled receptors ( GPCRs) in Spodoptera litura (Lepidoptera: Noctuidae). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101018. [PMID: 35994891 DOI: 10.1016/j.cbd.2022.101018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 01/27/2023]
Abstract
Spodoptera litura is a highly destructive omnivorous pest, and they caused serious damage to various crops. G protein-coupled receptors (GPCRs) mediate dozens of physiological processes including reproduction, development, life span and behaviors, but the information of these receptors has been lacking in S. litura. Here, we methodically identified 122 GPCRs in S. litura and made an assay of their expression patterns in different tissues. Comparing the identified GPCRs with homologous genes of other insects, it is obvious that the subfamily A2 (biogenic amine receptors) and the subfamily A3 (neuropeptide and protein hormone receptors) of S. litura have expanded to a certain extent, which may be related to the omnivorous nature and drought environment resistance of S. litura. Besides, the large Methuselah (Mth)/Methuselah-like (Mthl) subfamily of S. litura may be involved in many physiological functions such as longevity and stress response. Apart from duplicate receptors, the loss of parathyroid hormone receptor (PTHR) and the bride of sevenless (Boss) receptor in the lepidopteran insects may imply a new pattern of wing formation and energy metabolism in lepidopteran insects. In addition, the high expression level of GPCRs in different tissues reflects the functional diversity of GPCRs regulating. Systemic identification and initial characterization of GPCRs in S. litura provide a basis for further studies to reveal the functions of these receptors in regulating physiology and behavior.
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89
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Forde B, Yao L, Shaha R, Murphy S, Lunjani N, O'Mahony L. Immunomodulation by foods and microbes: Unravelling the molecular tango. Allergy 2022; 77:3513-3526. [PMID: 35892227 PMCID: PMC10087875 DOI: 10.1111/all.15455] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 01/28/2023]
Abstract
Metabolic health and immune function are intimately connected via diet and the microbiota. Nearly 90% of all immune cells in the body are associated with the gastrointestinal tract and these immune cells are continuously exposed to a wide range of microbes and microbial-derived compounds, with important systemic ramifications. Microbial dysbiosis has consistently been observed in patients with atopic dermatitis, food allergy and asthma and the molecular mechanisms linking changes in microbial populations with disease risk and disease endotypes are being intensively investigated. The discovery of novel bacterial metabolites that impact immune function is at the forefront of host-microbe research. Co-evolution of microbial communities within their hosts has resulted in intertwined metabolic pathways that affect physiological and pathological processes. However, recent dietary and lifestyle changes are thought to negatively influence interactions between microbes and their host. This review provides an overview of some of the critical metabolite-receptor interactions that have been recently described, which may underpin the immunomodulatory effects of the microbiota, and are of relevance for allergy, asthma and infectious diseases.
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90
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Farmer JP, Mistry SN, Laughton CA, Holliday ND. Development of fluorescent peptide G protein-coupled receptor activation biosensors for NanoBRET characterization of intracellular allosteric modulators. FASEB J 2022; 36:e22576. [PMID: 36183332 DOI: 10.1096/fj.202201024r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are widely therapeutically targeted, and recent advances in allosteric modulator development at these receptors offer further potential for exploitation. Intracellular allosteric modulators (IAM) represent a class of ligands that bind to the receptor-effector interface (e.g., G protein) and inhibit agonist responses noncompetitively. This potentially offers greater selectivity between receptor subtypes compared to classical orthosteric ligands. However, while examples of IAM ligands are well described, a more general methodology for assessing compound interactions at the IAM site is lacking. Here, fluorescent labeled peptides based on the Gα peptide C terminus are developed as novel binding and activation biosensors for the GPCR-IAM site. In TR-FRET binding studies, unlabeled peptides derived from the Gαs subunit were first characterized for their ability to positively modulate agonist affinity at the β2 -adrenoceptor. On this basis, a tetramethylrhodamine (TMR) labeled tracer was synthesized based on the 19 amino acid Gαs peptide (TMR-Gαs19cha18, where cha = cyclohexylalanine). Using NanoBRET technology to detect binding, TMR-Gαs19cha18 was recruited to Gs coupled β2 -adrenoceptor and EP2 receptors in an agonist-dependent manner, but not the Gi-coupled CXCR2 receptor. Moreover, NanoBRET competition binding assays using TMR-Gαs19cha18 enabled direct assessment of the affinity of unlabeled ligands for β2 -adrenoceptor IAM site. Thus, the NanoBRET platform using fluorescent-labeled G protein peptide mimetics offers novel potential for medium-throughput screens to identify IAMs, applicable across GPCRs coupled to a G protein class. Using the same platform, Gs peptide biosensors also represent useful tools to probe orthosteric agonist efficacy and the dynamics of receptor activation.
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91
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Jakubík J, Randáková A. Insights into the operational model of agonism of receptor dimers. Expert Opin Drug Discov 2022; 17:1181-1191. [PMID: 36369915 DOI: 10.1080/17460441.2023.2147502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Accurate ranking of efficacies and potencies of agonists is essential in the discovery of new selective agonists. For the purpose of system-independent ranking of agonists, the operational model of agonism (OMA) has become a standard. Many receptors function as oligomers which makes functional responses more complex, requiring an extension of the original OMA. AREAS COVERED Explicit equations of the operational model of agonism of receptor dimers (OMARD) were derived. The OMARD can be applied to any receptor possessing two orthosteric sites. The behavior of OMARD was analyzed to demonstrate its complexity and relation to experimental data. Properties of OMARD and OMA equations were compared to demonstrate their pros and cons. EXPERT OPINION Extension of OMA by slope factors gives simple equations of functional response that are easy to fit experimental data but results may be inaccurate because of exponentiation of operational efficacy. Also, such equations cannot accommodate bell-shaped curves. Explicit equations of OMARD give accurate results but are complex and tedious to fit experimental data. All operational models use inter-dependent parameters that are a hurdle in the fitting. A good understanding of OMARD behavior helps to overcome such obstacles.
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92
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Chiesa L, Kellenberger E. One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data. J Cheminform 2022; 14:74. [PMID: 36309734 PMCID: PMC9617447 DOI: 10.1186/s13321-022-00654-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
G protein-coupled receptors are involved in many biological processes, relaying the extracellular signal inside the cell. Signaling is regulated by the interactions between receptors and their ligands, it can be stimulated by agonists, or inhibited by antagonists or inverse agonists. The development of a new drug targeting a member of this family requires to take into account the pharmacological profile of the designed ligands in order to elicit the desired response. The structure-based virtual screening of chemical libraries may prioritize a specific class of ligands by combining docking results and ligand binding information provided by crystallographic structures. The performance of the method depends on the relevance of the structural data, in particular the conformation of the targeted site, the binding mode of the reference ligand, and the approach used to compare the interactions formed by the docked ligand with those formed by the reference ligand in the crystallographic structure. Here, we propose a new method based on the conformational dynamics of a single protein–ligand reference complex to improve the biased selection of ligands with specific pharmacological properties in a structure-based virtual screening exercise. Interactions patterns between a reference agonist and the receptor, here exemplified on the β2 adrenergic receptor, were extracted from molecular dynamics simulations of the agonist/receptor complex and encoded in graphs used to train a one-class machine learning classifier. Different conditions were tested: low to high affinity agonists, varying simulation duration, considering or ignoring hydrophobic contacts, and tuning of the classifier parametrization. The best models applied to post-process raw data from retrospective virtual screening obtained by docking of test libraries effectively filtered out irrelevant poses, discarding inactive and non-agonist ligands while identifying agonists. Taken together, our results suggest that consistency of the binding mode during the simulation is a key to the success of the method.
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93
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Orecchioni M, Matsunami H, Ley K. Olfactory receptors in macrophages and inflammation. Front Immunol 2022; 13:1029244. [PMID: 36311776 PMCID: PMC9606742 DOI: 10.3389/fimmu.2022.1029244] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/23/2022] [Indexed: 12/30/2022] Open
Abstract
Olfactory receptors (ORs) that bind odorous ligands are the largest family of G-protein-coupled receptors. In the olfactory epithelium, approximately 400 and 1,100 members are expressed in humans and mice, respectively. Growing evidence suggests the extranasal functions of ORs. Here, we review OR expression and function in macrophages, specialized innate immune cells involved in the detection, phagocytosis, and destruction of cellular debris and pathogens as well as the initiation of inflammatory responses. RNA sequencing data in mice suggest that up to 580 ORs may be expressed in macrophages. Macrophage OR expression is increased after treatment with the Toll-like receptor 4 ligand lipopolysaccharide, which also induces the transcription of inflammasome components. Triggering human OR6A2 or its mouse orthologue Olfr2 with their cognate ligand octanal induces inflammasome assembly and the secretion of IL-1β, which exacerbates atherosclerosis. Octanal is positively correlated with blood lipids like low-density lipoprotein -cholesterol in humans. Another OR, Olfr78, is activated by lactate, which promotes the generation of tumor-associated macrophages that dampen the immune response and promote tumor progression. Olfactory receptors in macrophages are a rich source of untapped opportunity for modulating inflammation. It is not known which of the many ORs expressed in macrophages promote or modulate inflammation. Progress in this area also requires deorphanizing more ORs and determining the sources of their ligands.
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Jiménez-Rosés M, Morgan BA, Jimenez Sigstad M, Tran TDZ, Srivastava R, Bunsuz A, Borrega-Román L, Hompluem P, Cullum SA, Harwood CR, Koers EJ, Sykes DA, Styles IB, Veprintsev DB. Combined docking and machine learning identify key molecular determinants of ligand pharmacological activity on β2 adrenoceptor. Pharmacol Res Perspect 2022; 10:e00994. [PMID: 36029004 PMCID: PMC9418666 DOI: 10.1002/prp2.994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/21/2022] [Indexed: 11/06/2022] Open
Abstract
G protein‐coupled receptors (GPCRs) are valuable therapeutic targets for many diseases. A central question of GPCR drug discovery is to understand what determines the agonism or antagonism of ligands that bind them. Ligands exert their action via the interactions in the ligand binding pocket. We hypothesized that there is a common set of receptor interactions made by ligands of diverse structures that mediate their action and that among a large dataset of different ligands, the functionally important interactions will be over‐represented. We computationally docked ~2700 known β2AR ligands to multiple β2AR structures, generating ca 75 000 docking poses and predicted all atomic interactions between the receptor and the ligand. We used machine learning (ML) techniques to identify specific interactions that correlate with the agonist or antagonist activity of these ligands. We demonstrate with the application of ML methods that it is possible to identify the key interactions associated with agonism or antagonism of ligands. The most representative interactions for agonist ligands involve K972.68×67, F194ECL2, S2035.42×43, S2045.43×44, S2075.46×641, H2966.58×58, and K3057.32×31. Meanwhile, the antagonist ligands made interactions with W2866.48×48 and Y3167.43×42, both residues considered to be important in GPCR activation. The interpretation of ML analysis in human understandable form allowed us to construct an exquisitely detailed structure‐activity relationship that identifies small changes to the ligands that invert their pharmacological activity and thus helps to guide the drug discovery process. This approach can be readily applied to any drug target.
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95
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Sinha S, Tam B, Wang SM. Applications of Molecular Dynamics Simulation in Protein Study. MEMBRANES 2022; 12:membranes12090844. [PMID: 36135863 PMCID: PMC9505860 DOI: 10.3390/membranes12090844] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 05/29/2023]
Abstract
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction, enzymatic reactions and drug-protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.
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Agonist concentration-dependent changes in FPR1 conformation lead to biased signaling for selective activation of phagocyte functions. Proc Natl Acad Sci U S A 2022; 119:e2201249119. [PMID: 35878025 PMCID: PMC9351494 DOI: 10.1073/pnas.2201249119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The bacteria-derived formyl peptide fMet-Leu-Phe (fMLF) is a potent chemoattractant of phagocytes that induces chemotaxis at subnanomolar concentrations. At higher concentrations, fMLF inhibits chemotaxis while stimulating degranulation and superoxide production, allowing phagocytes to kill invading bacteria. How an agonist activates distinct cellular functions at different concentrations remains unclear. Using a bioluminescence resonance energy transfer-based FPR1 biosensor, we found that fMLF at subnanomolar and micromolar concentrations induced distinct conformational changes in FPR1, a Gi-coupled chemoattractant receptor that activates various phagocyte functions. Neutrophil-like HL-60 cells exposed to subnanomolar concentrations of fMLF polarized rapidly and migrated along a chemoattractant concentration gradient. These cells also developed an intracellular Ca2+ concentration gradient. In comparison, high nanomolar and micromolar concentrations of fMLF triggered the PLC-β/diacyl glycerol/inositol trisphosphate pathway downstream of the heterotrimeric Gi proteins, leading to Ca2+ mobilization from intracellular stores and Ca2+ influx from extracellular milieu. A robust and uniform rise in cytoplasmic Ca2+ level was required for degranulation and superoxide production but disrupted cytoplasmic Ca2+ concentration gradient and inhibited chemotaxis. In addition, elevated ERK1/2 phosphorylation and β-arrestin2 membrane translocation were associated with diminished chemotaxis in the presence of fMLF above 1 nM. These findings suggest a mechanism for FPR1 agonist concentration-dependent signaling that leads to a switch from migration to bactericidal activities in phagocytes.
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Pandey P, Kaur G, Babu K. Crosstalk between neurons and glia through G-protein coupled receptors: Insights from Caenorhabditis elegans. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:119-144. [PMID: 36357074 DOI: 10.1016/bs.pmbts.2022.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The past decades have witnessed a dogmatic shift from glia as supporting cells in the nervous system to their active roles in neurocentric functions. Neurons and glia communicate and show bidirectional responses through tripartite synapses. Studies across species indicate that neurotransmitters released by neurons are perceived by glial receptors, which allow for gliotransmitter release. These gliotransmitters can result in activation of neurons via neuronal GPCR receptors. However, studies of these molecular interactions are in their infancy. Caenorhabditis elegans has a conserved neuron-glia architectural repertoire with molecular and functional resemblance to mammals. Further, glia in C. elegans can be manipulated through ablation and mutations allowing for deciphering of glial dependent processes in vivo at single glial resolutions. Here, we will review recent findings from vertebrate and invertebrate organisms with a focus on how C. elegans can be used to advance our understanding of neuron-glia interactions through GPCRs.
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98
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Margulis E, Slavutsky Y, Lang T, Behrens M, Benjamini Y, Niv MY. BitterMatch: recommendation systems for matching molecules with bitter taste receptors. J Cheminform 2022; 14:45. [PMID: 35799226 PMCID: PMC9261901 DOI: 10.1186/s13321-022-00612-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/14/2022] [Indexed: 11/10/2022] Open
Abstract
Bitterness is an aversive cue elicited by thousands of chemically diverse compounds. Bitter taste may prevent consumption of foods and jeopardize drug compliance. The G protein-coupled receptors for bitter taste, TAS2Rs, have species-dependent number of subtypes and varying expression levels in extraoral tissues. Molecular recognition by TAS2R subtypes is physiologically important, and presents a challenging case study for ligand-receptor matchmaking. Inspired by hybrid recommendation systems, we developed a new set of similarity features, and created the BitterMatch algorithm that predicts associations of ligands to receptors with ~ 80% precision at ~ 50% recall. Associations for several compounds were tested in-vitro, resulting in 80% precision and 42% recall. The encouraging performance was achieved by including receptor properties and integrating experimentally determined ligand-receptor associations with chemical ligand-to-ligand similarities. BitterMatch can predict off-targets for bitter drugs, identify novel ligands and guide flavor design. The novel features capture information regarding the molecules and their receptors, which could inform various chemoinformatic tasks. Inclusion of neighbor-informed similarities improves as experimental data mounts, and provides a generalizable framework for molecule-biotarget matching.
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Wang H, Hetzer F, Huang W, Qu Q, Meyerowitz J, Kaindl J, Hübner H, Skiniotis G, Kobilka BK, Gmeiner P. Structure-Based Evolution of G Protein-Biased μ-Opioid Receptor Agonists. Angew Chem Int Ed Engl 2022; 61:e202200269. [PMID: 35385593 PMCID: PMC9322534 DOI: 10.1002/anie.202200269] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Indexed: 01/14/2023]
Abstract
The μ-opioid receptor (μOR) is the major target for opioid analgesics. Activation of μOR initiates signaling through G protein pathways as well as through β-arrestin recruitment. μOR agonists that are biased towards G protein signaling pathways demonstrate diminished side effects. PZM21, discovered by computational docking, is a G protein biased μOR agonist. Here we report the cryoEM structure of PZM21 bound μOR in complex with Gi protein. Structure-based evolution led to multiple PZM21 analogs with more pronounced Gi protein bias and increased lipophilicity to improve CNS penetration. Among them, FH210 shows extremely low potency and efficacy for arrestin recruitment. We further determined the cryoEM structure of FH210 bound to μOR in complex with Gi protein and confirmed its expected binding pose. The structural and pharmacological studies reveal a potential mechanism to reduce β-arrestin recruitment by the μOR, and hold promise for developing next-generation analgesics with fewer adverse effects.
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Sonawani A, Kharche S, Dasgupta D, Sengupta D. Insights into the dynamic interactions at chemokine-receptor interfaces and mechanistic models of chemokine binding. J Struct Biol 2022; 214:107877. [PMID: 35750237 DOI: 10.1016/j.jsb.2022.107877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Chemokine receptors are the central signaling hubs of several processes such as cell migration, chemotaxis and cell positioning. In this graphical review, we provide an overview of the structural and mechanistic principles governing chemokine recognition that are currently emerging. Structural models of chemokine-receptor co-complexes with endogenous chemokines, viral chemokines and therapeutics have been resolved that highlight multiple interaction sites, termed as CRS1, CRS1.5 etc. The first site of interaction has been shown to be the N-terminal domain of the receptors (CRS1 site). A large structural flexibility of the N-terminal domain has been reported that was supported by both experimental and simulation studies. Upon chemokine binding, the N-terminal domain appears to show constricted dynamics and opens up to interact with the chemokine via a large interface. The subsequent sites such as CRS1.5 and CRS2 sites have been structurally well resolved although differences arise such as the localization of the N-terminus of the ligand to a major or minor pocket of the orthosteric binding site. Several computational studies have highlighted the dynamic protein-protein interface at the CRS1 site that seemingly appears to resolve the differences in NMR and mutagenesis studies. Interestingly, the differential dynamics at the CRS1 site suggests a mixed model of binding with complex signatures of both conformational selection and induced fit models. Integrative experimental and computational approaches could help unravel the structural basis of promiscuity and specificity in chemokine-receptor binding and open up new avenues of therapeutic design.
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