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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024; 23:626-644. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
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.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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2
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Pradhan B, Pavan M, Fisher CL, Salmaso V, Wan TC, Keyes RF, Rollison N, Suresh RR, Kumar TS, Gao ZG, Smith BC, Auchampach JA, Jacobson KA. Lipid Trolling to Optimize A 3 Adenosine Receptor-Positive Allosteric Modulators (PAMs). J Med Chem 2024; 67:12221-12247. [PMID: 38959401 DOI: 10.1021/acs.jmedchem.4c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
A3 adenosine receptor (A3AR) positive allosteric modulators (PAMs) (2,4-disubstituted-1H-imidazo[4,5-c]quinolin-4-amines) allosterically increase the Emax of A3AR agonists, but not potency, due to concurrent orthosteric antagonism. Following mutagenesis/homology modeling of the proposed lipid-exposed allosteric binding site on the cytosolic side, we functionalized the scaffold, including heteroatom substitutions and exocyclic phenylamine extensions, to increase allosteric binding. Strategically appended linear alkyl-alkynyl chains with terminal amino/guanidino groups improved allosteric effects at both human and mouse A3ARs. The chain length, functionality, and attachment position were varied to modulate A3AR PAM activity. For example, 26 (MRS8247, p-alkyne-linked 8 methylenes) and homologues increased agonist Cl-IB-MECA's Emax and potency ([35S]GTPγS binding). The putative mechanism involves a flexible, terminally cationic chain penetrating the lipid environment for stable electrostatic anchoring to cytosolic phospholipid head groups, suggesting "lipid trolling", supported by molecular dynamic simulation of the active-state model. Thus, we have improved A3AR PAM activity through rational design based on an extrahelical, lipidic binding site.
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Affiliation(s)
- Balaram Pradhan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Matteo Pavan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Courtney L Fisher
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy
| | - Tina C Wan
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Robert F Keyes
- Department of Biochemistry and the Program in Chemical Biology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Noah Rollison
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - T Santhosh Kumar
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Brian C Smith
- Department of Biochemistry and the Program in Chemical Biology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - John A Auchampach
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
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3
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Zhang M, Chen T, Lu X, Lan X, Chen Z, Lu S. G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery. Signal Transduct Target Ther 2024; 9:88. [PMID: 38594257 PMCID: PMC11004190 DOI: 10.1038/s41392-024-01803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.
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Affiliation(s)
- Mingyang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China
| | - Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Fisher CL, Pavan M, Salmaso V, Keyes RF, Wan TC, Pradhan B, Gao ZG, Smith BC, Jacobson KA, Auchampach JA. Extrahelical Binding Site for a 1 H-Imidazo[4,5-c]quinolin-4-amine A 3 Adenosine Receptor Positive Allosteric Modulator on Helix 8 and Distal Portions of Transmembrane Domains 1 and 7. Mol Pharmacol 2024; 105:213-223. [PMID: 38182432 PMCID: PMC10877738 DOI: 10.1124/molpharm.123.000784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
This study describes the localization and computational prediction of a binding site for the A3 adenosine receptor (A3AR) positive allosteric modulator 2-cyclohexyl-1H-imidazo[4,5-c]quinolin-4-(3,4-dichlorophenyl)amine (LUF6000). The work reveals an extrahelical lipid-facing binding pocket disparate from the orthosteric binding site that encompasses transmembrane domain (TMD) 1, TMD7, and Helix (H) 8, which was predicted by molecular modeling and validated by mutagenesis. According to the model, the nearly planar 1H-imidazo[4,5-c]quinolinamine ring system lies parallel to the transmembrane segments, inserted into an aromatic cage formed by π-π stacking interactions with the side chains of Y2847.55 in TMD7 and Y2938.54 in H8 and by π-NH bonding between Y2847.55 and the exocyclic amine. The 2-cyclohexyl group is positioned "upward" within a small hydrophobic subpocket created by residues in TMDs 1 and 7, while the 3,4-dichlorophenyl group extends toward the lipid interface. An H-bond between the N-1 amine of the heterocycle and the carbonyl of G291.49 further stabilizes the interaction. Molecular dynamics simulations predicted two metastable intermediates, one resembling a pose determined by molecular docking and a second involving transient interactions with Y2938.54; in simulations, each of these intermediates converges into the final bound state. Structure-activity-relationships for replacement of either of the identified exocyclic or endocyclic amines with heteroatoms lacking H-bond donating ability were consistent with the hypothetical pose. Thus, we characterized an allosteric pocket for 1H-imidazo[4,5-c]quinolin-4-amines that is consistent with data generated by orthogonal methods, which will aid in the rational design of improved A3AR positive allosteric modulators. SIGNIFICANCE STATEMENT: Orthosteric A3AR agonists have advanced in clinical trials for inflammatory conditions, liver diseases, and cancer. Thus, the clinical appeal of selective receptor activation could extend to allosteric enhancers, which would induce site- and time-specific activation in the affected tissue. By identifying the allosteric site for known positive allosteric modulators, structure-based drug discovery modalities can be enabled to enhance the pharmacological properties of the 1H-imidazo[4,5-c]quinolin-4-amine class of A3AR positive allosteric modulators.
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Affiliation(s)
- Courtney L Fisher
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Matteo Pavan
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Veronica Salmaso
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Robert F Keyes
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Tina C Wan
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Balaram Pradhan
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Zhan-Guo Gao
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Brian C Smith
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - Kenneth A Jacobson
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
| | - John A Auchampach
- Departments of Pharmacology & Toxicology and the Cardiovascular Center (C.L.F., T.C.W., J.A.A.) and Biochemistry and the Program in Chemical Biology (R.F.K., B.C.S.), Medical College of Wisconsin, Milwaukee, Wisconsin; Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (M.P., V.S., B.P., Z.-G.G., K.A.J.); and Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy (V.S.)
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5
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Kenakin T. Allostery: The Good, the Bad, and the Ugly. J Pharmacol Exp Ther 2024; 388:110-120. [PMID: 37918859 DOI: 10.1124/jpet.123.001838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
With the advent of functional screening, more allosteric molecules are being discovered and developed as possible therapeutic entities. Allosteric proteins are unique because of two specific properties: 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 systems 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 scientific procedures to characterize these are unique and require 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 techniques required to optimize the discovery process for allosteric molecules.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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Zha J, He J, Wu C, Zhang M, Liu X, Zhang J. Designing drugs and chemical probes with the dualsteric approach. Chem Soc Rev 2023; 52:8651-8677. [PMID: 37990599 DOI: 10.1039/d3cs00650f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.
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Affiliation(s)
- Jinyin Zha
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jixiao He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengwei Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyang Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Liu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang M, Lan X, Li X, Lu S. Pharmacologically targeting intracellular allosteric sites of GPCRs for drug discovery. Drug Discov Today 2023; 28:103803. [PMID: 37852356 DOI: 10.1016/j.drudis.2023.103803] [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: 09/12/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
G-protein-coupled receptors (GPCRs) are a family of cell surface proteins that can sense a variety of extracellular stimuli and mediate multiple signaling transduction pathways involved in human physiology. Recent advances in GPCR structural biology have revealed a relatively conserved intracellular allosteric site in multiple GPCRs, which can be utilized to modulate receptors from the inside. This novel intracellular site partially overlaps with the G-protein and β-arrestin coupling sites, providing a novel avenue for biological intervention. Here, we review evidence available for GPCR structures complexed with intracellular small-molecule allosteric modulators, elucidating drug-target interactions and allosteric mechanisms. Moreover, we highlight the potential of intracellular allosteric modulators in achieving biased signaling, which provides insights into biased allosteric mechanisms.
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Affiliation(s)
- Mingyang Zhang
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaobing Lan
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China.
| | - Shaoyong Lu
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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8
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Girych M, Kulig W, Enkavi G, Vattulainen I. How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harb Perspect Biol 2023; 15:a041419. [PMID: 37487628 PMCID: PMC10547395 DOI: 10.1101/cshperspect.a041419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized by the fact that in many neuropathological diseases there are significant deviations in the lipid composition of nerve membranes compared to healthy individuals. The lipid composition of neuromembranes can significantly affect the function of receptors by regulating the physical properties of the membrane or by affecting specific interactions between receptors and lipids. In addition, it is worth noting that the ligand-binding pocket of many receptors is located inside the cell membrane, due to which lipids can even modulate the binding of ligands to their receptors. These mechanisms highlight the importance of lipids in the regulation of membrane receptor activation and function. In this article, we focus on two major protein families: G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) and discuss how lipids affect their function in neuronal membranes, elucidating the basic mechanisms underlying neuronal function and dysfunction.
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Affiliation(s)
- Mykhailo Girych
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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Zhang D, Liu Y, Zaidi SA, Xu L, Zhan Y, Chen A, Guo J, Huang X, Roth BL, Katritch V, Cherezov V, Zhang H. Structural insights into angiotensin receptor signaling modulation by balanced and biased agonists. EMBO J 2023; 42:e112940. [PMID: 37038975 PMCID: PMC10233375 DOI: 10.15252/embj.2022112940] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/22/2023] [Accepted: 03/21/2023] [Indexed: 04/12/2023] Open
Abstract
The peptide hormone angiotensin II regulates blood pressure mainly through the type 1 angiotensin II receptor AT1 R and its downstream signaling proteins Gq and β-arrestin. AT1 R blockers, clinically used as antihypertensive drugs, inhibit both signaling pathways, whereas AT1 R β-arrestin-biased agonists have shown great potential for the treatment of acute heart failure. Here, we present a cryo-electron microscopy (cryo-EM) structure of the human AT1 R in complex with a balanced agonist, Sar1 -AngII, and Gq protein at 2.9 Å resolution. This structure, together with extensive functional assays and computational modeling, reveals the molecular mechanisms for AT1 R signaling modulation and suggests that a major hydrogen bond network (MHN) inside the receptor serves as a key regulator of AT1 R signal transduction from the ligand-binding pocket to both Gq and β-arrestin pathways. Specifically, we found that the MHN mutations N1113.35 A and N2947.45 A induce biased signaling to Gq and β-arrestin, respectively. These insights should facilitate AT1 R structure-based drug discovery for the treatment of cardiovascular diseases.
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Affiliation(s)
- Dongqi Zhang
- Hangzhou Institute of Innovative Medicine, Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti‐Cancer Drug Research, College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
| | - Yongfeng Liu
- Department of PharmacologyUniversity of North Carolina School of MedicineChapel HillNCUSA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP)University of North Carolina School of MedicineChapel HillNCUSA
| | - Saheem A Zaidi
- Department of Quantitative and Computational BiologyUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Lingyi Xu
- Department of BiophysicsZhejiang University School of MedicineHangzhouChina
- Department of Neurology of the Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Yuting Zhan
- Hangzhou Institute of Innovative Medicine, Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti‐Cancer Drug Research, College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
| | - Anqi Chen
- Hangzhou Institute of Innovative Medicine, Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti‐Cancer Drug Research, College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
| | - Jiangtao Guo
- Department of BiophysicsZhejiang University School of MedicineHangzhouChina
- Department of Neurology of the Fourth Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Xi‐Ping Huang
- Department of PharmacologyUniversity of North Carolina School of MedicineChapel HillNCUSA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP)University of North Carolina School of MedicineChapel HillNCUSA
| | - Bryan L Roth
- Department of PharmacologyUniversity of North Carolina School of MedicineChapel HillNCUSA
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP)University of North Carolina School of MedicineChapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Vsevolod Katritch
- Department of Quantitative and Computational BiologyUniversity of Southern CaliforniaLos AngelesCAUSA
- Department of Chemistry, Bridge InstituteUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Vadim Cherezov
- Department of Chemistry, Bridge InstituteUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Haitao Zhang
- Hangzhou Institute of Innovative Medicine, Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti‐Cancer Drug Research, College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
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10
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Wang X, Hembre EJ, Goldsmith PJ, Beck JP, Svensson KA, Willard FS, Bruns RF. Mutual Cooperativity of Three Allosteric Sites on the Dopamine D1 Receptor. Mol Pharmacol 2023; 103:176-187. [PMID: 36804203 DOI: 10.1124/molpharm.122.000605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
An amine-containing molecule called Compound A has been reported by a group from Bristol-Myers Squibb to act as a positive allosteric modulator (PAM) at the dopamine D1 receptor. We synthesized the more active enantiomer of Compound A (BMS-A1) and compared it with the D1 PAMs DETQ and MLS6585, which are known to bind to intracellular loop 2 and the extracellular portion of transmembrane helix 7, respectively. Results from D1/D5 chimeras indicated that PAM activity of BMS-A1 tracked with the presence of D1 sequence in the N-terminal/extracellular region of the D1 receptor, a unique location compared with either of the other PAMs. In pairwise combinations, BMS-A1 potentiated the small allo-agonist activity of each of the other PAMs, while the triple PAM combination (in the absence of dopamine) produced a cAMP response about 64% of the maximum produced by dopamine. Each of the pairwise PAM combinations produced a much larger leftward shift of the dopamine EC50 than either single PAM alone. All three PAMs in combination produced a 1000-fold leftward shift of the dopamine curve. These results demonstrate the presence of three non-overlapping allosteric sites that cooperatively stabilize the same activated state of the human D1 receptor. SIGNIFICANCE STATEMENT: Deficiencies in dopamine D1 receptor activation are seen in Parkinson disease and other neuropsychiatric disorders. In this study, three positive allosteric modulators of the dopamine D1 receptor were found to bind to distinct and separate sites, interacting synergistically with each other and dopamine, with the triple combination causing a 1000-fold leftward shift of the response to dopamine. These results showcase multiple opportunities to modulate D1 tone and highlight new pharmacological approaches for allosteric modulation of G-protein-coupled receptors.
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Affiliation(s)
- Xushan Wang
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Erik J Hembre
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Paul J Goldsmith
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - James P Beck
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Kjell A Svensson
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Francis S Willard
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
| | - Robert F Bruns
- Lilly Research Laboratories, Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana
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11
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Harrington AW, Liu C, Phillips N, Nepomuceno D, Kuei C, Chang J, Chen W, Sutton SW, O'Malley D, Pham L, Yao X, Sun S, Bonaventure P. Identification and characterization of select oxysterols as ligands for GPR17. Br J Pharmacol 2023; 180:401-421. [PMID: 36214386 DOI: 10.1111/bph.15969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND AND PURPOSE G-protein coupled receptor 17 (GPR17) is an orphan receptor involved in the process of myelination, due to its ability to inhibit the maturation of oligodendrocyte progenitor cells (OPCs) into myelinating oligodendrocytes. Despite multiple claims that the biological ligand has been identified, it remains an orphan receptor. EXPERIMENTAL APPROACH Seventy-seven oxysterols were screened in a cell-free [35 S]GTPγS binding assay using membranes from cells expressing GPR17. The positive hits were characterized using adenosine 3',5' cyclic monophosphate (cAMP), inositol monophosphate (IP1) and calcium mobilization assays, with results confirmed in rat primary oligodendrocytes. Rat and pig brain extracts were separated by high-performance liquid chromatography (HPLC) and endogenous activator(s) were identified in receptor activation assays. Gene expression studies of GPR17, and CYP46A1 (cytochrome P450 family 46 subfamily A member 1) enzymes responsible for the conversion of cholesterol into specific oxysterols, were performed using quantitative real-time PCR. KEY RESULTS Five oxysterols were able to stimulate GPR17 activity, including the brain cholesterol, 24(S)-hydroxycholesterol (24S-HC). A specific brain fraction from rat and pig extracts containing 24S-HC activates GPR17 in vitro. Expression of Gpr17 during mouse brain development correlates with the expression of Cyp46a1 and the levels of 24S-HC itself. Other active oxysterols have low brain concentrations below effective ranges. CONCLUSIONS AND IMPLICATIONS Oxysterols, including but not limited to 24S-HC, could be physiological activators for GPR17 and thus potentially regulate OPC differentiation and myelination through activation of the receptor.
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Affiliation(s)
| | - Changlu Liu
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Naomi Phillips
- Janssen Research & Development, LLC, San Diego, California, USA
| | | | - Chester Kuei
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Joseph Chang
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Weixuan Chen
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Steven W Sutton
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Daniel O'Malley
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Ly Pham
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Xiang Yao
- Janssen Research & Development, LLC, San Diego, California, USA
| | - Siquan Sun
- Janssen Research & Development, LLC, San Diego, California, USA
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12
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Ding T, Karlov DS, Pino-Angeles A, Tikhonova IG. Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. J Chem Inf Model 2022; 62:4736-4747. [PMID: 36178787 PMCID: PMC9554917 DOI: 10.1021/acs.jcim.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.
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Affiliation(s)
- Tianyi Ding
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Almudena Pino-Angeles
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
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13
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Zhang H, Chu G, Wang G, Yao M, Lu S, Chen T. Mechanistic Understanding of the Palmitoylation of G o Protein in the Allosteric Regulation of Adhesion Receptor GPR97. Pharmaceutics 2022; 14:pharmaceutics14091856. [PMID: 36145604 PMCID: PMC9504338 DOI: 10.3390/pharmaceutics14091856] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Adhesion G-protein-coupled receptors (aGPCRs)—a major family of GPCRs—play critical roles in the regulation of tissue development and cancer progression. The orphan receptor GPR97, activated by glucocorticoid stress hormones, is a prototypical aGPCR. Although it has been established that the palmitoylation of the C-terminal Go protein is essential for Go’s efficient engagement with the active GPR97, the detailed allosteric mechanism remains to be clarified. Hence, we performed extensive large-scale molecular dynamics (MD) simulations of the GPR97−Go complex in the presence or absence of Go palmitoylation. The conformational landscapes analyzed by Markov state models revealed that the overall conformation of GPR97 is preferred to be fully active when interacting with palmitoylated Go protein. Structural and energetic analyses indicated that the palmitoylation of Go can allosterically stabilize the critical residues in the ligand-binding pocket of GPR97 and increase the affinity of the ligand for GPR97. Furthermore, the community network analysis suggests that the palmitoylation of Go not only allosterically strengthens the internal interactions between Gαo and Gβγ, but also enhances the coupling between Go and GPR97. Our study provides mechanistic insights into the regulation of aGPCRs via post-translational modifications of the Go protein, and offers guidance for future drug design of aGPCRs.
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Affiliation(s)
- Hao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, China
| | - Guojun Chu
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Gaoming Wang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Min Yao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, China
- Correspondence: (M.Y.); (S.L.); (T.C.)
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Correspondence: (M.Y.); (S.L.); (T.C.)
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
- Correspondence: (M.Y.); (S.L.); (T.C.)
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14
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Advances in membrane mimetics and mass spectrometry for understanding membrane structure and function. Curr Opin Chem Biol 2022; 69:102157. [DOI: 10.1016/j.cbpa.2022.102157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/19/2022]
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15
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Fisher CL, Fallot LB, Wan TC, Keyes RF, Suresh RR, Rothwell AC, Gao ZG, McCorvy JD, Smith BC, Jacobson KA, Auchampach JA. Characterization of Dual-Acting A 3 Adenosine Receptor Positive Allosteric Modulators That Preferentially Enhance Adenosine-Induced Gα i3 and Gα oA Isoprotein Activation. ACS Pharmacol Transl Sci 2022; 5:625-641. [PMID: 35983277 PMCID: PMC9380209 DOI: 10.1021/acsptsci.2c00076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Indexed: 12/19/2022]
Abstract
The A3 adenosine receptor (A3AR) is a promising therapeutic target for inflammatory diseases, cancer, and chronic neuropathic pain, with agonists already in advanced clinical trials. Here we report an in-depth comparison of the pharmacological properties and structure-activity relationships of existing and expanded compound libraries of 2-substituted 1H-imidazo[4,5-c]quinolin-4-amine and 4-amino-substituted quinoline derivatives that function as A3AR positive allosteric modulators (PAMs). We also show that our lead compound from each series enhances adenosine-induced A3AR signaling preferentially toward activation of Gαi3 and GαoA isoproteins, which are coexpressed with the A3AR in immune cells and spinal cord neurons. Finally, utilizing an extracellular/intracellular chimeric A3AR approach composed of sequences from a responding (human) and a nonresponding (mouse) species, we provide evidence in support of the idea that the imidazoquinolin-4-amine class of PAMs variably interacts dually with the orthosteric ligand binding site as well as with a separate allosteric site located within the inner/intracellular regions of the receptor. This study has advanced both structural and pharmacological understanding of these two classes of A3AR PAMs, which includes leads for future pharmaceutical development.
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Affiliation(s)
- Courtney L. Fisher
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Lucas B. Fallot
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
- Department of Biochemistry & Molecular Biology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814, United States
- Department of Chemistry & Life Science, United States Military Academy, 646 Swift Road, West Point, New York 10996, United States
| | - Tina C. Wan
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Robert F. Keyes
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - R. Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Amy C. Rothwell
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - John D. McCorvy
- Department of Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Brian C. Smith
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - John A. Auchampach
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
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16
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Tian R, Yin J, Yao Q, Wang T, Chen J, Liang Q, Li Q, Zhao X. Development of an Allostery Responsive Chromatographic Method for Screening Potential Allosteric Modulator of Beta2-adrenoceptor from a Natural Product-Derived DNA-Encoded Chemical Library. Anal Chem 2022; 94:9048-9057. [PMID: 35695812 DOI: 10.1021/acs.analchem.2c01210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allosteric ligands are promising drugs owing to their remote regulations of the orthosteric ligand signaling pathway. There are few allosteric ligands due to the lack of handy and efficacious method for the screening. Herein, we developed an affinity chromatographic method for allosteric ligand screening by immobilizing purified beta2 adrenoceptor (β2-AR) onto macroporous silica gel by a two-point tethering method. The method relies on the occupation of the orthosteric site by an antagonist and the chelation of N-terminal His-tag of the receptor and Ni2+ coated on the gel. The immobilized β2-AR demonstrated the greatest allosteric responsive feature when Cmpd-15 (0.25 μM) was included in the mobile phase. Under the same conditions, the association constants of three agonists (salbutamol, terbutaline, and tulobuterol) reduced to 47%, 19%, and 27% compared with the data without the inclusion of Cmpd-15 in the mobile phase. APF was screened as a potential allosteric modulator of β2-AR by applying the immobilized receptor in a natural product-derived DNA-encoded chemical library (DEL). Relying on these results, we reasoned that the current method has potential in screening allosteric ligands of the receptor. We expect that it is applicable for the discovery of new allosteric binding sites of a target protein and screening allosteric modulators of the other receptors from complex samples.
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Affiliation(s)
- Rui Tian
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jiatai Yin
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Qingqing Yao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Taotao Wang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jiahuan Chen
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Qi Liang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Qian Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
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17
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Wang L, Zhang W, Shao Y, Zhang D, Guo G, Wang X. Analytical methods for obtaining binding parameters of drug–protein interactions: A review. Anal Chim Acta 2022; 1219:340012. [DOI: 10.1016/j.aca.2022.340012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
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18
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Casadó-Anguera V, Casadó V. Unmasking allosteric binding sites: Novel targets for GPCR drug discovery. Expert Opin Drug Discov 2022; 17:897-923. [PMID: 35649692 DOI: 10.1080/17460441.2022.2085684] [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] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Unexpected non-apparent and hidden allosteric binding sites are non-classical and non-apparent allosteric centers in 3-D X-ray protein structures until orthosteric or allosteric ligands bind to them. The orthosteric center of one protomer that modulates binding centers of the other protomers within an oligomer is also an unexpected allosteric site. Furthermore, another partner protein can also produce these effects, acting as an unexpected allosteric modulator. AREAS COVERED This review summarizes both classical and non-classical allosterism. The authors focus on G protein-coupled receptor (GPCR) oligomers as a paradigm of allosteric molecules. Moreover, they show several examples of unexpected allosteric sites such as hidden allosteric sites in a protomer that appear after the interaction with other molecules and the allosterism exerted between orthosteric sites within GPCR oligomer, emphasizing on the allosteric modulations that can occur between binding sites. EXPERT OPINION The study of these new non-classical allosteric sites will expand the diversity of allosteric control on the function of orthosteric sites within proteins, whether GPCRs or other receptors, enzymes or transporters. Moreover, the design of new drugs targeting these hidden allosteric sites or already known orthosteric sites acting as allosteric sites in protein homo- or hetero-oligomers will increase the therapeutic potential of allosterism.
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Affiliation(s)
- Verònica Casadó-Anguera
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, and Institute of Biomedicine of the Universitat de Barcelona, Barcelona, Spain.,Laboratory of Neuropharmacology-Neurophar, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Vicent Casadó
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, and Institute of Biomedicine of the Universitat de Barcelona, Barcelona, Spain
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19
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Cong X, Zhang X, Liang X, He X, Tang Y, Zheng X, Lu S, Zhang J, Chen T. Delineating the conformational landscape and intrinsic properties of the angiotensin II type 2 receptor using a computational study. Comput Struct Biotechnol J 2022; 20:2268-2279. [PMID: 35615027 PMCID: PMC9117689 DOI: 10.1016/j.csbj.2022.05.012] [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: 03/09/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/22/2022] Open
Abstract
As a key regulator for the renin-angiotensin system, a class A G protein-coupled receptor (GPCR), AngII type 2 receptor (AT2R), plays a pivotal role in the homeostasis of the cardiovascular system. Compared with other GPCRs, AT2R has a unique antagonist-bound conformation and its mechanism is still an enigma. Here, we applied combined dynamic and evolutional approaches to investigate the conformational space and intrinsic properties of AT2R. With molecular dynamic simulations, Markov State Models, and statistics coupled analysis, we captured the conformational landscape of AT2R and identified its uniquity from both dynamical and evolutional viewpoints. A cryptic pocket was also discovered in the intermediate state during conformation transitions. These findings offer a deeper understanding of the AT2R mechanism at an atomic level and provide hints for the design of novel AT2R modulators.
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Affiliation(s)
- Xiaoliang Cong
- Department of Cardiology, Shanghai Changzheng Hospital, the Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xiaogang Zhang
- Department of Cardiology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
| | - Xin Liang
- Department of Cardiology, Shanghai Changzheng Hospital, the Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xinheng He
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yehua Tang
- Department of Cardiology, Shanghai Changzheng Hospital, the Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xing Zheng
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Corresponding authors.
| | - Jiayou Zhang
- Department of Cardiology, Shanghai Changzheng Hospital, the Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
- Corresponding authors.
| | - Ting Chen
- Department of Cardiology, Shanghai Changzheng Hospital, the Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
- Corresponding authors.
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20
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G protein–coupled receptor 21 in macrophages: An in vitro study. Eur J Pharmacol 2022; 926:175018. [DOI: 10.1016/j.ejphar.2022.175018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022]
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21
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Abstract
SignificanceThe allosteric modulators, which bind to nonorthosteric sites to enhance the signaling activities of G-protein-coupled receptors (GPCRs), are new candidates for GPCR-targeting drugs. Our solution NMR analyses of the μ-opioid receptor (MOR) revealed that the MOR activity was determined by a conformational equilibrium between three conformations. Interestingly, an allosteric modulator shifted the equilibrium toward a conformation with the highest activity to a level that cannot be reached by orthosteric ligands alone, leading to the increased activity of MOR. Our NMR analyses also identified the binding site of the allosteric modulator, including the residues contributing to the regulation of the equilibrium. These findings provide insights into the rational developments of novel allosteric modulators.
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22
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High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol 2022; 5:360. [PMID: 35422073 PMCID: PMC9010423 DOI: 10.1038/s42003-022-03233-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia. Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.
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23
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Egyed A, Kiss DJ, Keserű GM. The Impact of the Secondary Binding Pocket on the Pharmacology of Class A GPCRs. Front Pharmacol 2022; 13:847788. [PMID: 35355719 PMCID: PMC8959758 DOI: 10.3389/fphar.2022.847788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are considered important therapeutic targets due to their pathophysiological significance and pharmacological relevance. Class A receptors represent the largest group of GPCRs that gives the highest number of validated drug targets. Endogenous ligands bind to the orthosteric binding pocket (OBP) embedded in the intrahelical space of the receptor. During the last 10 years, however, it has been turned out that in many receptors there is secondary binding pocket (SBP) located in the extracellular vestibule that is much less conserved. In some cases, it serves as a stable allosteric site harbouring allosteric ligands that modulate the pharmacology of orthosteric binders. In other cases it is used by bitopic compounds occupying both the OBP and SBP. In these terms, SBP binding moieties might influence the pharmacology of the bitopic ligands. Together with others, our research group showed that SBP binders contribute significantly to the affinity, selectivity, functional activity, functional selectivity and binding kinetics of bitopic ligands. Based on these observations we developed a structure-based protocol for designing bitopic compounds with desired pharmacological profile.
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Affiliation(s)
- Attila Egyed
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dóra Judit Kiss
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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24
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Drug-Targeted Genomes: Mutability of Ion Channels and GPCRs. Biomedicines 2022; 10:biomedicines10030594. [PMID: 35327396 PMCID: PMC8945769 DOI: 10.3390/biomedicines10030594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Mutations of ion channels and G-protein-coupled receptors (GPCRs) are not uncommon and can lead to cardiovascular diseases. Given previously reported multiple factors associated with high mutation rates, we sorted the relative mutability of multiple human genes by (i) proximity to telomeres and/or (ii) high adenine and thymine (A+T) content. We extracted genomic information using the genome data viewer and examined the mutability of 118 ion channel and 143 GPCR genes based on their association with factors (i) and (ii). We then assessed these two factors with 31 genes encoding ion channels or GPCRs that are targeted by the United States Food and Drug Administration (FDA)-approved drugs. Out of the 118 ion channel genes studied, 80 met either factor (i) or (ii), resulting in a 68% match. In contrast, a 78% match was found for the 143 GPCR genes. We also found that the GPCR genes (n = 20) targeted by FDA-approved drugs have a relatively lower mutability than those genes encoding ion channels (n = 11), where targeted genes encoding GPCRs were shorter in length. The result of this study suggests that the use of matching rate analysis on factor-druggable genome is feasible to systematically compare the relative mutability of GPCRs and ion channels. The analysis on chromosomes by two factors identified a unique characteristic of GPCRs, which have a significant relationship between their nucleotide sizes and proximity to telomeres, unlike most genetic loci susceptible to human diseases.
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25
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Zha J, Li M, Kong R, Lu S, Zhang J. Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques. J Mol Biol 2022; 434:167481. [DOI: 10.1016/j.jmb.2022.167481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/17/2022]
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26
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Wang Y, Li M, Liang W, Shi X, Fan J, Kong R, Liu Y, Zhang J, Chen T, Lu S. Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor. Comput Struct Biotechnol J 2022; 20:628-639. [PMID: 35140883 PMCID: PMC8801358 DOI: 10.1016/j.csbj.2022.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/09/2023] Open
Abstract
Class B G protein-coupled receptors (GPCRs) are important targets in the treatment of metabolic syndrome and diabetes. Although multiple structures of class B GPCRs-G protein complexes have been elucidated, the detailed activation mechanism of the receptors remains unclear. Here, we combine Gaussian accelerated molecular dynamics simulations and Markov state models (MSM) to investigate the activation mechanism of a canonical class B GPCR, human glucagon receptor-GCGR, including the negative allosteric modulator-bound inactive state, the agonist glucagon-bound active state, and both glucagon- and Gs-bound fully active state. The free-energy landscapes of GCGR show the conformational ensemble consisting of three activation-associated states: inactive, active, and fully active. The structural analysis indicates the high dynamics of GCGR upon glucagon binding with both active and inactive conformations in the ensemble. Significantly, the H8 and TM6 exhibits distinct features from the inactive to the active states. The additional simulations demonstrate the role of H8 in the recruitment of Gs. Gs binding presents a crucial function of stabilizing the glucagon binding site and MSM highlights the absolute requirement of Gs to help the GCGR reach the fully active state. Together, our results reveal the detailed activation mechanism of GCGR from the view of conformational dynamics.
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Affiliation(s)
- Ying Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Wenqi Liang
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xinchao Shi
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200023, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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27
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Fan J, Liu Y, Kong R, Ni D, Yu Z, Lu S, Zhang J. Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. J Med Chem 2021; 64:17728-17743. [PMID: 34878270 DOI: 10.1021/acs.jmedchem.1c01695] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a fundamental and extensive mechanism of intramolecular signal transmission. Allosteric drugs possess several unique pharmacological advantages over traditional orthosteric drugs, including greater selectivity, better physicochemical properties, and lower off-target toxicity. However, owing to the complexity of allosteric regulation, experimental approaches for the development of allosteric modulators are traditionally serendipitous. Recently, the reversed allosteric communication theory has been proposed, providing a feasible tool for the unbiased detection of allosteric sites. Herein, we review the latest research on the reversed allosteric communication effect using the examples of sirtuin 6, epidermal growth factor receptor, 3-phosphoinositide-dependent protein kinase 1, and Related to A and C kinases (RAC) serine/threonine protein kinase B and recapitulate the methodologies of reversed allosteric communication strategy. The novel reversed allosteric communication strategy greatly expands the horizon of allosteric site identification and allosteric mechanism exploration and is expected to accelerate an end-to-end framework for drug discovery.
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Affiliation(s)
- Jigang Fan
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Zhiyuan Innovative Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Shaoyong Lu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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28
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Liu L, Fan Z, Rovira X, Xue L, Roux S, Brabet I, Xin M, Pin JP, Rondard P, Liu J. Allosteric ligands control the activation of a class C GPCR heterodimer by acting at the transmembrane interface. eLife 2021; 10:70188. [PMID: 34866572 PMCID: PMC8700296 DOI: 10.7554/elife.70188] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 12/02/2021] [Indexed: 01/02/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are among the most promising drug targets. They often form homo- and heterodimers with allosteric cross-talk between receptor entities, which contributes to fine-tuning of transmembrane signaling. Specifically controlling the activity of GPCR dimers with ligands is a good approach to clarify their physiological roles and validate them as drug targets. Here, we examined the mode of action of positive allosteric modulators (PAMs) that bind at the interface of the transmembrane domains of the heterodimeric GABAB receptor. Our site-directed mutagenesis results show that mutations of this interface impact the function of the three PAMs tested. The data support the inference that they act at the active interface between both transmembrane domains, the binding site involving residues of the TM6s of the GABAB1 and the GABAB2 subunit. Importantly, the agonist activity of these PAMs involves a key region in the central core of the GABAB2 transmembrane domain, which also controls the constitutive activity of the GABAB receptor. This region corresponds to the sodium ion binding site in class A GPCRs that controls the basal state of the receptors. Overall, these data reveal the possibility of developing allosteric compounds able to specifically modulate the activity of GPCR homo- and heterodimers by acting at their transmembrane interface.
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Affiliation(s)
- Lei Liu
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Zhiran Fan
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xavier Rovira
- MCS, Laboratory of Medicinal Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Li Xue
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Salomé Roux
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Isabelle Brabet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Mingxia Xin
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Jianfeng Liu
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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29
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Cholesterol-dependent endocytosis of GPCRs: implications in pathophysiology and therapeutics. Biophys Rev 2021; 13:1007-1017. [DOI: 10.1007/s12551-021-00878-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022] Open
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30
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Ni D, Chai Z, Wang Y, Li M, Yu Z, Liu Y, Lu S, Zhang J. Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Duan Ni
- College of Pharmacy Ningxia Medical University Yinchuan China
- The Charles Perkins Centre University of Sydney Sydney New South Wales Australia
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital Second Military Medical University Shanghai China
| | - Ying Wang
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Mingyu Li
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
| | | | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Shaoyong Lu
- College of Pharmacy Ningxia Medical University Yinchuan China
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jian Zhang
- College of Pharmacy Ningxia Medical University Yinchuan China
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
- School of Pharmaceutical Sciences Zhengzhou University Zhengzhou China
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31
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Reinmuth L, Hsiao CC, Hamann J, Rosenkilde M, Mackrill J. Multiple Targets for Oxysterols in Their Regulation of the Immune System. Cells 2021; 10:cells10082078. [PMID: 34440846 PMCID: PMC8391951 DOI: 10.3390/cells10082078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Oxysterols, or cholesterol oxidation products, are naturally occurring lipids which regulate the physiology of cells, including those of the immune system. In contrast to effects that are mediated through nuclear receptors or by epigenetic mechanism, which take tens of minutes to occur, changes in the activities of cell-surface receptors caused by oxysterols can be extremely rapid, often taking place within subsecond timescales. Such cell-surface receptor effects of oxysterols allow for the regulation of fast cellular processes, such as motility, secretion and endocytosis. These cellular processes play critical roles in both the innate and adaptive immune systems. This review will survey the two broad classes of cell-surface receptors for oxysterols (G-protein coupled receptors (GPCRs) and ion channels), the mechanisms by which cholesterol oxidation products act on them, and their presence and functions in the different cell types of the immune system. Overall, this review will highlight the potential of oxysterols, synthetic derivatives and their receptors for physiological and therapeutic modulation of the immune system.
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Affiliation(s)
- Lisa Reinmuth
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark;
| | - Cheng-Chih Hsiao
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands; (C.-C.H.); (J.H.)
- Neuroimmunology Research Group, The Netherlands Institute for Neuroscience, 1105BA Amsterdam, The Netherlands
| | - Jörg Hamann
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands; (C.-C.H.); (J.H.)
- Neuroimmunology Research Group, The Netherlands Institute for Neuroscience, 1105BA Amsterdam, The Netherlands
| | - Mette Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark;
- Correspondence: (M.R.); (J.M.); Tel.: +353-(0)21-490-1400 (J.M.)
| | - John Mackrill
- Department of Physiology, School of Medicine, BioSciences Institute, University College Cork, College Road, Cork T12 YT20, Ireland
- Correspondence: (M.R.); (J.M.); Tel.: +353-(0)21-490-1400 (J.M.)
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32
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Villemure E, Terrett JA, Larouche-Gauthier R, Déry M, Chen H, Reese RM, Shields SD, Chen J, Magnuson S, Volgraf M. A Retrospective Look at the Impact of Binding Site Environment on the Optimization of TRPA1 Antagonists. ACS Med Chem Lett 2021; 12:1230-1237. [PMID: 34413952 DOI: 10.1021/acsmedchemlett.1c00305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022] Open
Abstract
Transient receptor potential ankyrin 1 (TRPA1) antagonists have generated broad interest in the pharmaceutical industry for the treatment of both pain and asthma. Over the past decade, multiple antagonist classes have been reported in the literature with a wide range of structural diversity. Our own work has focused on the development of proline sulfonamide and hypoxanthine-based antagonists, two antagonist classes with distinct physicochemical properties and pharmacokinetic (PK) trends. Late in our discovery program, cryogenic electron microscopy (cryoEM) studies revealed two different antagonist binding sites: a membrane-exposed proline sulfonamide transmembrane site and an intracellular hypoxanthine site near the membrane interface. A retrospective look at the discovery program reveals how the different binding sites, and their location relative to the cell membrane, influenced the optimization trajectories and overall drug profiles of each antagonist class.
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Affiliation(s)
- Elisia Villemure
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jack A. Terrett
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Martin Déry
- Paraza Pharma, Inc. 2525 Avenue Marie-Curie, Montréal, Québec H4S 2E1, Canada
| | - Huifen Chen
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Rebecca M. Reese
- Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shannon D. Shields
- Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jun Chen
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven Magnuson
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthew Volgraf
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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33
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Ligand binding at the protein-lipid interface: strategic considerations for drug design. Nat Rev Drug Discov 2021; 20:710-722. [PMID: 34257432 DOI: 10.1038/s41573-021-00240-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Many drug targets are embedded within the phospholipid bilayer of cellular membranes, including G protein-coupled receptors, ion channels, transporters and membrane-bound enzymes. Increasing evidence from biophysical and structural studies suggests that many small-molecule drugs commonly associate with these targets at binding sites at the protein-phospholipid interface. Without a direct path from bulk solvent to a binding site, a drug must first partition in the phospholipid membrane before interacting with the protein target. This membrane access mechanism necessarily affects the interpretation of potency data, structure-activity relationships, pharmacokinetics and physicochemical properties for drugs that target these sites. With an increasing number of small-molecule intramembrane binding sites revealed through X-ray crystallography and cryogenic electron microscopy, we suggest that ligand-lipid interactions likely play a larger role in small-molecule drug action than commonly appreciated. This Perspective introduces key concepts and drug design considerations to aid discovery teams operating within this target space, and discusses challenges and future opportunities in the field.
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34
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Kumar GA, Sarkar P, Stepniewski TM, Jafurulla M, Singh SP, Selent J, Chattopadhyay A. A molecular sensor for cholesterol in the human serotonin 1A receptor. SCIENCE ADVANCES 2021; 7:7/30/eabh2922. [PMID: 34301606 PMCID: PMC8302130 DOI: 10.1126/sciadv.abh2922] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/09/2021] [Indexed: 05/10/2023]
Abstract
The function of several G protein-coupled receptors (GPCRs) exhibits cholesterol sensitivity. Cholesterol sensitivity of GPCRs could be attributed to specific sequence and structural features, such as the cholesterol recognition/interaction amino acid consensus (CRAC) motif, that facilitate their cholesterol-receptor interaction. In this work, we explored the molecular basis of cholesterol sensitivity exhibited by the serotonin1A receptor, the most studied GPCR in the context of cholesterol sensitivity, by generating mutants of key residues in CRAC motifs in transmembrane helix 2 (TM2) and TM5 of the receptor. Our results show that a lysine residue (K101) in one of the CRAC motifs is crucial for sensing altered membrane cholesterol levels. Insights from all-atom molecular dynamics simulations showed that cholesterol-sensitive functional states of the serotonin1A receptor are associated with reduced conformational dynamics of extracellular loops of the receptor. These results constitute one of the first reports on the molecular mechanism underlying cholesterol sensitivity of GPCRs.
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Affiliation(s)
- G Aditya Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Md Jafurulla
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Shishu Pal Singh
- National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bengaluru 560 065, India
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain.
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35
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Ma N, Nivedha AK, Vaidehi N. Allosteric communication regulates ligand-specific GPCR activity. FEBS J 2021; 288:2502-2512. [PMID: 33738925 PMCID: PMC9805801 DOI: 10.1111/febs.15826] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 01/11/2023]
Abstract
G protein-coupled receptors (GPCRs) are membrane-bound proteins that are ubiquitously expressed in many cell types and take part in mediating multiple signaling pathways. GPCRs are dynamic proteins and exist in an equilibrium between an ensemble of conformational states such as inactive and fully active states. This dynamic nature of GPCRs is one of the factors that confers their basal activity even in the absence of any ligand-mediated activation. Ligands selectively bind and stabilize a subset of the conformations from the ensemble leading to a shift in the equilibrium toward the inactive or the active state depending on the nature of the ligand. This ligand-selective effect is achieved through allosteric communication between the ligand binding site and G protein or β-arrestin coupling site. Similarly, the G protein coupling to the receptor exerts the allosteric effect on the ligand binding region leading to increased binding affinity for agonists and decreased affinity for antagonists or inverse agonists. In this review, we enumerate the current state of our understanding of the mechanism of allosteric communication in GPCRs with a specific focus on the critical role of computational methods in delineating the residues involved in allosteric communication. Analyzing allosteric communication mechanism using molecular dynamics simulations has revealed (a) a structurally conserved mechanism of allosteric communication that regulates the G protein coupling, (b) a rational structure-based approach to designing selective ligands, and (c) an approach to designing allosteric GPCR mutants that are either ligand and G protein or β-arrestin selective.
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Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Anita K. Nivedha
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010,to whom correspondence should be addressed:
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