1
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Lou JS, Su M, Wang J, Do HN, Miao Y, Huang XY. Distinct binding conformations of epinephrine with α- and β-adrenergic receptors. Exp Mol Med 2024:10.1038/s12276-024-01296-x. [PMID: 39218975 DOI: 10.1038/s12276-024-01296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/09/2024] [Accepted: 06/09/2024] [Indexed: 09/04/2024] Open
Abstract
Agonists targeting α2-adrenergic receptors (ARs) are used to treat diverse conditions, including hypertension, attention-deficit/hyperactivity disorder, pain, panic disorders, opioid and alcohol withdrawal symptoms, and cigarette cravings. These receptors transduce signals through heterotrimeric Gi proteins. Here, we elucidated cryo-EM structures that depict α2A-AR in complex with Gi proteins, along with the endogenous agonist epinephrine or the synthetic agonist dexmedetomidine. Molecular dynamics simulations and functional studies reinforce the results of the structural revelations. Our investigation revealed that epinephrine exhibits different conformations when engaging with α-ARs and β-ARs. Furthermore, α2A-AR and β1-AR (primarily coupled to Gs, with secondary associations to Gi) were compared and found to exhibit different interactions with Gi proteins. Notably, the stability of the epinephrine-α2A-AR-Gi complex is greater than that of the dexmedetomidine-α2A-AR-Gi complex. These findings substantiate and improve our knowledge on the intricate signaling mechanisms orchestrated by ARs and concurrently shed light on the regulation of α-ARs and β-ARs by epinephrine.
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Affiliation(s)
- Jian-Shu Lou
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Minfei Su
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Hung Nguyen Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Xin-Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.
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2
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Deng X, Cui H, Liang H, Wang X, Yu H, Wang J, Wang W, Liu D, Zhang Y, Dong E, Tang Y, Xiao H. SARS-CoV-2 spike protein acts as a β-adrenergic receptor agonist: A potential mechanism for cardiac sequelae of long COVID. J Intern Med 2024; 296:291-297. [PMID: 39073192 DOI: 10.1111/joim.20000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
BACKGROUND Currently, pathophysiological mechanisms of post-acute sequelae of coronavirus disease-19-cardiovascular syndrome (PASC-CVS) remain unknown. METHODS AND RESULTS Patients with PASC-CVS exhibited significantly higher circulating levels of severe acute respiratory syndrome-coronavirus-2 spike protein S1 than the non-PASC-CVS patients and healthy controls. Moreover, individuals with high plasma spike protein S1 concentrations exhibited elevated heart rates and normalized low frequency, suggesting cardiac β-adrenergic receptor (β-AR) hyperactivity. Microscale thermophoresis (MST) assay revealed that the spike protein bound to β1- and β2-AR, but not to D1-dopamine receptor. These interactions were blocked by β1- and β2-AR blockers. Molecular docking and MST assay of β-AR mutants revealed that the spike protein interacted with the extracellular loop 2 of both β-ARs. In cardiomyocytes, spike protein dose-dependently increased the cyclic adenosine monophosphate production with or without epinephrine, indicating its allosteric effects on β-ARs. CONCLUSION Severe acute respiratory syndrome-coronavirus-2 spike proteins act as an allosteric β-AR agonist, leading to cardiac β-AR hyperactivity, thus contributing to PASC-CVS.
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Affiliation(s)
- Xiangning Deng
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Hongtu Cui
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Hao Liang
- Drug Clinical Trial Center, Peking University Third Hospital, Beijing, China
| | - Xinyu Wang
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Haiyi Yu
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Jingjia Wang
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Wenyao Wang
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Dongyang Liu
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
- Drug Clinical Trial Center, Peking University Third Hospital, Beijing, China
| | - Youyi Zhang
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Erdan Dong
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- University of Health and Rehabilitation Sciences, Qingdao, China
| | - Yida Tang
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Han Xiao
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Haihe Laboratory of Cell Ecosystem, Beijing, China
- Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
- University of Health and Rehabilitation Sciences, Qingdao, China
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China
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3
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Fan L, Zhuang Y, Wu H, Li H, Xu Y, Wang Y, He L, Wang S, Chen Z, Cheng J, Xu HE, Wang S. Structural basis of psychedelic LSD recognition at dopamine D 1 receptor. Neuron 2024:S0896-6273(24)00494-X. [PMID: 39094559 DOI: 10.1016/j.neuron.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/11/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024]
Abstract
Understanding the kinetics of LSD in receptors and subsequent induced signaling is crucial for comprehending both the psychoactive and therapeutic effects of LSD. Despite extensive research on LSD's interactions with serotonin 2A and 2B receptors, its behavior on other targets, including dopamine receptors, has remained elusive. Here, we present cryo-EM structures of LSD/PF6142-bound dopamine D1 receptor (DRD1)-legobody complexes, accompanied by a β-arrestin-mimicking nanobody, NBA3, shedding light on the determinants of G protein coupling versus β-arrestin coupling. Structural analysis unveils a distinctive binding mode of LSD in DRD1, particularly with the ergoline moiety oriented toward TM4. Kinetic investigations uncover an exceptionally rapid dissociation rate of LSD in DRD1, attributed to the flexibility of extracellular loop 2 (ECL2). Moreover, G protein can stabilize ECL2 conformation, leading to a significant slowdown in ligand's dissociation rate. These findings establish a solid foundation for further exploration of G protein-coupled receptor (GPCR) dynamics and their relevance to signal transduction.
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Affiliation(s)
- Luyu Fan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Youwen Zhuang
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongyu Wu
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huiqiong Li
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yue Wang
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Licong He
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shishan Wang
- Laboratory of Anesthesia and Critical Care Medicine in Colleges and Universities of Shandong Province, School of Anesthesiology, Shandong Second Medical University, Weifang 261021, China
| | - Zhangcheng Chen
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; Lingang Laboratory, Shanghai 200031, China.
| | - Sheng Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
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4
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Szwabowski GL, Griffing M, Mugabe EJ, O’Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [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: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | | | | | | | | | - Daniel L. Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
| | - Abby L. Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
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5
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Abaffy T, Fu O, Harume-Nagai M, Goldenberg JM, Kenyon V, Kenakin T. Intracellular Allosteric Antagonist of the Olfactory Receptor OR51E2. Mol Pharmacol 2024; 106:21-32. [PMID: 38719475 PMCID: PMC11187688 DOI: 10.1124/molpharm.123.000843] [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: 11/09/2023] [Accepted: 04/16/2024] [Indexed: 06/20/2024] Open
Abstract
Olfactory receptors are members of class A (rhodopsin-like) family of G protein-coupled receptors (GPCRs). Their expression and function have been increasingly studied in nonolfactory tissues, and many have been identified as potential therapeutic targets. In this manuscript, we focus on the discovery of novel ligands for the olfactory receptor family 51 subfamily E2 (OR51E2). We performed an artificial intelligence-based virtual drug screen of a ∼2.2 million small molecule library. Cell-based functional assay identified compound 80 (C80) as an antagonist and inverse agonist, and detailed pharmacological analysis revealed C80 acts as a negative allosteric modulator by significantly decreasing the agonist efficacy, while having a minimal effect on receptor affinity for agonist. C80 binds to an allosteric binding site formed by a network of nine residues localized in the intracellular parts of transmembrane domains 3, 5, 6, 7, and H8, which also partially overlaps with a G protein binding site. Mutational experiments of residues involved in C80 binding uncovered the significance of the C2406.37 position in blocking the activation-related conformational change and keeping the receptor in the inactive form. Our study provides a mechanistic understanding of the negative allosteric action of C80 on agonist-ctivated OR51E2. We believe the identification of the antagonist of OR51E2 will enable a multitude of studies aiming to determine the functional role of this receptor in specific biologic processes. SIGNIFICANCE STATEMENT: OR51E2 has been implicated in various biological processes, and its antagonists that can effectively modulate its activity have therapeutic potential. Here we report the discovery of a negative allosteric modulator of OR51E2 and provide a mechanistic understanding of its action. We demonstrate that this modulator has an inhibitory effect on the efficacy of the agonist for the receptor and reveal a network of nine residues that constitute its binding pocket, which also partially overlaps with the G protein binding site.
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Affiliation(s)
- Tatjana Abaffy
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina (T.A., O.F.); Columbia Center for Human Development/Columbia Center for Stem Cell Therapies Department, Columbia University, New York (M.H.-N.); Chemistry Department, School of Math and Science at the United States Naval Academy, Annapolis, Maryland (J.M.G.); Atomwise Inc., San Francisco, California (J.M.G., V.K.); and Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (T.K.)
| | - Olivia Fu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina (T.A., O.F.); Columbia Center for Human Development/Columbia Center for Stem Cell Therapies Department, Columbia University, New York (M.H.-N.); Chemistry Department, School of Math and Science at the United States Naval Academy, Annapolis, Maryland (J.M.G.); Atomwise Inc., San Francisco, California (J.M.G., V.K.); and Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (T.K.)
| | - Maira Harume-Nagai
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina (T.A., O.F.); Columbia Center for Human Development/Columbia Center for Stem Cell Therapies Department, Columbia University, New York (M.H.-N.); Chemistry Department, School of Math and Science at the United States Naval Academy, Annapolis, Maryland (J.M.G.); Atomwise Inc., San Francisco, California (J.M.G., V.K.); and Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (T.K.)
| | - Josh M Goldenberg
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina (T.A., O.F.); Columbia Center for Human Development/Columbia Center for Stem Cell Therapies Department, Columbia University, New York (M.H.-N.); Chemistry Department, School of Math and Science at the United States Naval Academy, Annapolis, Maryland (J.M.G.); Atomwise Inc., San Francisco, California (J.M.G., V.K.); and Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (T.K.)
| | - Victor Kenyon
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina (T.A., O.F.); Columbia Center for Human Development/Columbia Center for Stem Cell Therapies Department, Columbia University, New York (M.H.-N.); Chemistry Department, School of Math and Science at the United States Naval Academy, Annapolis, Maryland (J.M.G.); Atomwise Inc., San Francisco, California (J.M.G., V.K.); and Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (T.K.)
| | - Terry Kenakin
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina (T.A., O.F.); Columbia Center for Human Development/Columbia Center for Stem Cell Therapies Department, Columbia University, New York (M.H.-N.); Chemistry Department, School of Math and Science at the United States Naval Academy, Annapolis, Maryland (J.M.G.); Atomwise Inc., San Francisco, California (J.M.G., V.K.); and Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (T.K.)
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6
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Ding X, Chen X, Sullivan EE, Shay TF, Gradinaru V. Fast, accurate ranking of engineered proteins by target-binding propensity using structure modeling. Mol Ther 2024; 32:1687-1700. [PMID: 38582966 PMCID: PMC11184338 DOI: 10.1016/j.ymthe.2024.04.003] [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: 10/17/2023] [Revised: 02/08/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
Deep-learning-based methods for protein structure prediction have achieved unprecedented accuracy, yet their utility in the engineering of protein-based binders remains constrained due to a gap between the ability to predict the structures of candidate proteins and the ability toprioritize proteins by their potential to bind to a target. To bridge this gap, we introduce Automated Pairwise Peptide-Receptor Analysis for Screening Engineered proteins (APPRAISE), a method for predicting the target-binding propensity of engineered proteins. After generating structural models of engineered proteins competing for binding to a target using an established structure prediction tool such as AlphaFold-Multimer or ESMFold, APPRAISE performs a rapid (under 1 CPU second per model) scoring analysis that takes into account biophysical and geometrical constraints. As proof-of-concept cases, we demonstrate that APPRAISE can accurately classify receptor-dependent vs. receptor-independent adeno-associated viral vectors and diverse classes of engineered proteins such as miniproteins targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike, nanobodies targeting a G-protein-coupled receptor, and peptides that specifically bind to transferrin receptor or programmed death-ligand 1 (PD-L1). APPRAISE is accessible through a web-based notebook interface using Google Colaboratory (https://tiny.cc/APPRAISE). With its accuracy, interpretability, and generalizability, APPRAISE promises to expand the utility of protein structure prediction and accelerate protein engineering for biomedical applications.
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Affiliation(s)
- Xiaozhe Ding
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA.
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA
| | - Erin E Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA
| | - Timothy F Shay
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA.
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7
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Yin J, Gou Y, Wang Y, Ma Q, Wang R, Yu J, Zhang Y, Wang J, Li Q, Zhao X. Can the heptapeptide ASSIVSF of the β 2-adrenoceptor recognize ephedrine and pseudoephedrine epimers in a complex system? J Chromatogr A 2024; 1722:464857. [PMID: 38569445 DOI: 10.1016/j.chroma.2024.464857] [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: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Epimer separation is crucial in the field of analytical chemistry, separation science, and the pharmaceutical industry. No reported methods could separate simultaneously epimers or even isomers and remove other unwanted, co-existing, interfering substances from complex systems like herbal extracts. Herein, we prepared a heptapeptide-modified stationary phase for the separation of 1R,2S-(-)-ephedrine [(-)-Ephe] and 1S,2S-(+)-pseudoephedrine [(+)-Pse] epimers from Ephedra sinica Stapf extract and blood samples. The heptapeptide stationary phase was comprehensively characterized by scanning electron microscopy, X-ray photoelectron spectroscopy, and Fourier transform infrared spectroscopy. The separation efficiency of the heptapeptide column was compared with an affinity column packed with full-length β2-AR functionalized silica gel (β2-AR column). The binding affinity of the heptapeptide with (+)-Pse was 3-fold greater than that with (-)-Ephe. Their binding mechanisms were extensively characterized by chromatographic analysis, ultraviolet spectra, circular dichroism analysis, isothermal titration calorimetry, and molecule docking. An enhanced hydrogen bonding was clearly observed in the heptapeptide-(+)-Pse complex. Such results demonstrated that the heptapeptide can recognize (+)-Pse and (-)-Ephe epimers in a complex system. This work, we believe, was the first report to simultaneously separate epimers and remove non-specific interfering substances from complex samples. The method was potentially applicable to more challenging sample separation, such as chiral separation from complex systems.
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Affiliation(s)
- Jiatai Yin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yiheng Gou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yiheng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qingyuan Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Rui Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Yu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yajun Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
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8
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Howard MK, Hoppe N, Huang XP, Macdonald CB, Mehrota E, Grimes PR, Zahm A, Trinidad DD, English J, Coyote-Maestas W, Manglik A. Molecular basis of proton-sensing by G protein-coupled receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.590000. [PMID: 38659943 PMCID: PMC11042331 DOI: 10.1101/2024.04.17.590000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Three proton-sensing G protein-coupled receptors (GPCRs), GPR4, GPR65, and GPR68, respond to changes in extracellular pH to regulate diverse physiology and are implicated in a wide range of diseases. A central challenge in determining how protons activate these receptors is identifying the set of residues that bind protons. Here, we determine structures of each receptor to understand the spatial arrangement of putative proton sensing residues in the active state. With a newly developed deep mutational scanning approach, we determined the functional importance of every residue in proton activation for GPR68 by generating ~9,500 mutants and measuring effects on signaling and surface expression. This unbiased screen revealed that, unlike other proton-sensitive cell surface channels and receptors, no single site is critical for proton recognition in GPR68. Instead, a network of titratable residues extend from the extracellular surface to the transmembrane region and converge on canonical class A GPCR activation motifs to activate proton-sensing GPCRs. More broadly, our approach integrating structure and unbiased functional interrogation defines a new framework for understanding the rich complexity of GPCR signaling.
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Affiliation(s)
- Matthew K. Howard
- Tetrad graduate program, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA, USA
| | - Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics graduate program, University of California, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology and the National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christian B. Macdonald
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA, USA
| | - Eshan Mehrota
- Tetrad graduate program, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | | | - Adam Zahm
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Donovan D. Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, United States
| | - Justin English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, USA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, USA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
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9
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Casiraghi M, Wang H, Brennan P, Habrian C, Hubner H, Schmidt MF, Maul L, Pani B, Bahriz SM, Xu B, White E, Sunahara RK, Xiang YK, Lefkowitz RJ, Isacoff EY, Nucci N, Gmeiner P, Lerch M, Kobilka BK. Structure and dynamics determine G protein coupling specificity at a class A GPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587240. [PMID: 38586060 PMCID: PMC10996611 DOI: 10.1101/2024.03.28.587240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
G protein coupled receptors (GPCRs) exhibit varying degrees of selectivity for different G protein isoforms. Despite the abundant structures of GPCR-G protein complexes, little is known about the mechanism of G protein coupling specificity. The β2-adrenergic receptor is an example of GPCR with high selectivity for Gαs, the stimulatory G protein for adenylyl cyclase, and much weaker for the Gαi family of G proteins inhibiting adenylyl cyclase. By developing a new Gαi-biased agonist (LM189), we provide structural and biophysical evidence supporting that distinct conformations at ICL2 and TM6 are required for coupling of the different G protein subtypes Gαs and Gαi. These results deepen our understanding of G protein specificity and bias and can accelerate the design of ligands that select for preferred signaling pathways.
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10
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Cullum SA, Platt S, Dale N, Isaac OC, Wragg ES, Soave M, Veprintsev DB, Woolard J, Kilpatrick LE, Hill SJ. Mechano-sensitivity of β2-adrenoceptors enhances constitutive activation of cAMP generation that is inhibited by inverse agonists. Commun Biol 2024; 7:417. [PMID: 38580813 PMCID: PMC10997663 DOI: 10.1038/s42003-024-06128-2] [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: 09/27/2023] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
The concept of agonist-independent signalling that can be attenuated by inverse agonists is a fundamental element of the cubic ternary complex model of G protein-coupled receptor (GPCR) activation. This model shows how a GPCR can exist in two conformational states in the absence of ligands; an inactive R state and an active R* state that differ in their affinities for agonists, inverse agonists, and G-protein alpha subunits. The proportion of R* receptors that exist in the absence of agonists determines the level of constitutive receptor activity. In this study we demonstrate that mechanical stimulation can induce β2-adrenoceptor agonist-independent Gs-mediated cAMP signalling that is sensitive to inhibition by inverse agonists such as ICI-118551 and propranolol. The size of the mechano-sensitive response is dependent on the cell surface receptor expression level in HEK293G cells, is still observed in a ligand-binding deficient D113A mutant β2-adrenoceptor and can be attenuated by site-directed mutagenesis of the extracellular N-glycosylation sites on the N-terminus and second extracellular loop of the β2-adrenoceptor. Similar mechano-sensitive agonist-independent responses are observed in HEK293G cells overexpressing the A2A-adenosine receptor. These data provide new insights into how agonist-independent constitutive receptor activity can be enhanced by mechanical stimulation and regulated by inverse agonists.
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Affiliation(s)
- Sean A Cullum
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Simon Platt
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Natasha Dale
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Oliver C Isaac
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Edward S Wragg
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mark Soave
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Jeanette Woolard
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Laura E Kilpatrick
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK.
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11
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Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter JF, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nat Struct Mol Biol 2024; 31:667-677. [PMID: 38326651 PMCID: PMC11221913 DOI: 10.1038/s41594-024-01223-8] [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: 05/10/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
The orphan G protein-coupled receptor (GPCR) GPR161 plays a central role in development by suppressing Hedgehog signaling. The fundamental basis of how GPR161 is activated remains unclear. Here, we determined a cryogenic-electron microscopy structure of active human GPR161 bound to heterotrimeric Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, a sterol that binds adjacent to transmembrane helices 6 and 7 stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress Gs-mediated signaling. These mutants retain the ability to suppress GLI2 transcription factor accumulation in primary cilia, a key function of ciliary GPR161. By contrast, a protein kinase A-binding site in the GPR161 C terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the role of GPR161 function in other signaling pathways.
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Affiliation(s)
- Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Simone Harrison
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ziwei Chen
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
| | - Masha Karelina
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vivek R Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samuel P Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Philipp Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Douglas F Covey
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ron O Dror
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Alex S Evers
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
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12
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Sencanski M, Glisic S, Kubale V, Cotman M, Mavri J, Vrecl M. Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β 2-Adrenergic Receptor (β 2AR). Biomolecules 2024; 14:423. [PMID: 38672440 PMCID: PMC11048008 DOI: 10.3390/biom14040423] [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: 02/27/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
This study assessed the suitability of the complementarity-determining region 2 (CDR2) of the nanobody (Nb) as a template for the derivation of nanobody-derived peptides (NDPs) targeting active-state β2-adrenergic receptor (β2AR) conformation. Sequences of conformationally selective Nbs favoring the agonist-occupied β2AR were initially analyzed by the informational spectrum method (ISM). The derived NDPs in complex with β2AR were subjected to protein-peptide docking, molecular dynamics (MD) simulations, and metadynamics-based free-energy binding calculations. Computational analyses identified a 25-amino-acid-long CDR2-NDP of Nb71, designated P4, which exhibited the following binding free-energy for the formation of the β2AR:P4 complex (ΔG = -6.8 ± 0.8 kcal/mol or a Ki = 16.5 μM at 310 K) and mapped the β2AR:P4 amino acid interaction network. In vitro characterization showed that P4 (i) can cross the plasma membrane, (ii) reduces the maximum isoproterenol-induced cAMP level by approximately 40% and the isoproterenol potency by up to 20-fold at micromolar concentration, (iii) has a very low affinity to interact with unstimulated β2AR in the cAMP assay, and (iv) cannot reduce the efficacy and potency of the isoproterenol-mediated β2AR/β-arrestin-2 interaction in the BRET2-based recruitment assay. In summary, the CDR2-NDP, P4, binds preferentially to agonist-activated β2AR and disrupts Gαs-mediated signaling.
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Affiliation(s)
- Milan Sencanski
- Laboratory for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, National Institute of Serbia, University of Belgrade, 11000 Belgrade, Serbia;
| | - Sanja Glisic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, National Institute of Serbia, University of Belgrade, 11000 Belgrade, Serbia;
| | - Valentina Kubale
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (V.K.); (M.C.)
| | - Marko Cotman
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (V.K.); (M.C.)
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Milka Vrecl
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (V.K.); (M.C.)
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13
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Determinants of Neutral Antagonism and Inverse Agonism in the β 2-Adrenergic Receptor. J Chem Inf Model 2024; 64:2045-2057. [PMID: 38447156 DOI: 10.1021/acs.jcim.3c01763] [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: 03/08/2024]
Abstract
Free-energy profiles for the activation/deactivation of the β2-adrenergic receptor (ADRB2) with neutral antagonist and inverse agonist ligands have been determined with well-tempered multiple-walker (MW) metadynamics simulations. The inverse agonists carazolol and ICI118551 clearly favor single inactive conformational minima in both the binary and ternary ligand-receptor-G-protein complexes, in accord with the inverse-agonist activity of the ligands. The behavior of neutral antagonists is more complex, as they seem also to affect the recruitment of the G-protein. The results are analyzed in terms of the conformational states of the well-known microswitches that have been proposed as indicators of receptor activity.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04107 Leipzig, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, United Kingdom
- Swiss Bioinformatics Institute, CH1206 Geneva, Switzerland
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
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14
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Costanzi S, Stahr LG, Trivellin G, Stratakis CA. GPR101: Modeling a constitutively active receptor linked to X-linked acrogigantism. J Mol Graph Model 2024; 127:108676. [PMID: 38006624 PMCID: PMC10843723 DOI: 10.1016/j.jmgm.2023.108676] [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: 06/05/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023]
Abstract
GPR101 is a G protein-coupled receptor (GPCR) implicated in a rare form of genetic gigantism known as X-linked acrogigantism, or X-LAG. In particular, X-LAG patients harbor microduplications in the long arm of the X-chromosome that invariably include the GPR101 gene. Duplications of the GPR101 gene lead to the formation of a new chromatin domain that causes over-expression of the receptor in the pituitary tumors of the patients. Notably, GPR101 is a constitutively active receptor, which stimulates cells to produce the second messenger cyclic AMP (cAMP) in the absence of ligands. Moreover, GPR101 was recently reported to constitutively activate not only the cAMP pathway via Gs, but also other G protein subunits (Gq/11 and G12/13). Hence, chemicals that block the constitutive activity of GPR101, known as inverse agonists, have the potential to be useful for the development of pharmacological tools for the treatment of X-LAG. In this study, we provide structural insights into the putative structure of GPR101 based on in-house built homology models, as well as third party models based on the machine learning methods AlphaFold and AlphaFold-Multistate. Moreover, we report a molecular dynamics study, meant to further probe the constitutive activity of GPR101. Finally, we provide a structural comparison with the closest GPCRs, which suggests that GPR101 does not share their natural ligands. While this manuscript was under review, cryo-electron microscopy structures of GPR101 were reported. These structures are expected to enable computer-aided ligand discovery efforts targeting GPR101.
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Affiliation(s)
- Stefano Costanzi
- American University, Department of Chemistry, Washington, DC, USA.
| | - Lea G Stahr
- American University, Department of Chemistry, Washington, DC, USA
| | - Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
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15
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Miller WE, O'Connor CM. CMV-encoded GPCRs in infection, disease, and pathogenesis. Adv Virus Res 2024; 118:1-75. [PMID: 38461029 DOI: 10.1016/bs.aivir.2024.01.001] [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] [Indexed: 03/11/2024]
Abstract
G protein coupled receptors (GPCRs) are seven-transmembrane domain proteins that modulate cellular processes in response to external stimuli. These receptors represent the largest family of membrane proteins, and in mammals, their signaling regulates important physiological functions, such as vision, taste, and olfaction. Many organisms, including yeast, slime molds, and viruses encode GPCRs. Cytomegaloviruses (CMVs) are large, betaherpesviruses, that encode viral GPCRs (vGPCRs). Human CMV (HCMV) encodes four vGPCRs, including UL33, UL78, US27, and US28. Each of these vGPCRs, as well as their rodent and primate orthologues, have been investigated for their contributions to viral infection and disease. Herein, we discuss how the CMV vGPCRs function during lytic and latent infection, as well as our understanding of how they impact viral pathogenesis.
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Affiliation(s)
- William E Miller
- Department of Molecular and Cellular Bioscience, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Christine M O'Connor
- Infection Biology, Sheikha Fatima bint Mubarak Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States.
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16
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Jayakody T, Inoue A, Kannan S, Nakamura G, Kawakami K, Mendis K, Nguyen TB, Li J, Herr DR, Verma CS, Dawe GS. Mechanisms of biased agonism by Gα i/o-biased stapled peptide agonists of the relaxin-3 receptor. Sci Signal 2024; 17:eabl5880. [PMID: 38349968 DOI: 10.1126/scisignal.abl5880] [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: 07/22/2021] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
The neuropeptide relaxin-3 is composed of an A chain and a B chain held together by disulfide bonds, and it modulates functions such as anxiety and food intake by binding to and activating its cognate receptor RXFP3, mainly through the B chain. Biased ligands of RXFP3 would help to determine the molecular mechanisms underlying the activation of G proteins and β-arrestins downstream of RXFP3 that lead to such diverse functions. We showed that the i, i+4 stapled relaxin-3 B chains, 14s18 and d(1-7)14s18, were Gαi/o-biased agonists of RXFP3. These peptides did not induce recruitment of β-arrestin1/2 to RXFP3 by GPCR kinases (GRKs), in contrast to relaxin-3, which enabled the GRK2/3-mediated recruitment of β-arrestin1/2 to RXFP3. Relaxin-3 and the previously reported peptide 4 (an i, i+4 stapled relaxin-3 B chain) did not exhibit biased signaling. The staple linker of peptide 4 and parts of both the A chain and B chain of relaxin-3 interacted with extracellular loop 3 (ECL3) of RXFP3, moving it away from the binding pocket, suggesting that unbiased ligands promote a more open conformation of RXFP3. These findings highlight roles for the A chain and the N-terminal residues of the B chain of relaxin-3 in inducing conformational changes in RXFP3, which will help in designing selective biased ligands with improved therapeutic efficacy.
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Affiliation(s)
- Tharindunee Jayakody
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | | | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Krishan Mendis
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Thanh-Binh Nguyen
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jianguo Li
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 6 Science Drive 4, Singapore 117558
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Gavin S Dawe
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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17
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Faivre N, Verollet C, Dumas F. The chemokine receptor CCR5: multi-faceted hook for HIV-1. Retrovirology 2024; 21:2. [PMID: 38263120 PMCID: PMC10807162 DOI: 10.1186/s12977-024-00634-1] [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: 09/27/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
Chemokines are cytokines whose primary role is cellular activation and stimulation of leukocyte migration. They perform their various functions by interacting with G protein-coupled cell surface receptors (GPCRs) and are involved in the regulation of many biological processes such as apoptosis, proliferation, angiogenesis, hematopoiesis or organogenesis. They contribute to the maintenance of the homeostasis of lymphocytes and coordinate the function of the immune system. However, chemokines and their receptors are sometimes hijacked by some pathogens to infect the host organism. For a given chemokine receptor, there is a wide structural, organizational and conformational diversity. In this review, we describe the evidence for structural variety reported for the chemokine receptor CCR5, how this variability can be exploited by HIV-1 to infect its target cells and what therapeutic solutions are currently being developed to overcome this problem.
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Affiliation(s)
- Natacha Faivre
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Christel Verollet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Fabrice Dumas
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France.
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18
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Mullin M, McClory J, Haynes W, Grace J, Robertson N, van Heeke G. Applications and challenges in designing VHH-based bispecific antibodies: leveraging machine learning solutions. MAbs 2024; 16:2341443. [PMID: 38666503 PMCID: PMC11057648 DOI: 10.1080/19420862.2024.2341443] [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: 09/22/2023] [Accepted: 04/05/2024] [Indexed: 05/01/2024] Open
Abstract
The development of bispecific antibodies that bind at least two different targets relies on bringing together multiple binding domains with different binding properties and biophysical characteristics to produce a drug-like therapeutic. These building blocks play an important role in the overall quality of the molecule and can influence many important aspects from potency and specificity to stability and half-life. Single-domain antibodies, particularly camelid-derived variable heavy domain of heavy chain (VHH) antibodies, are becoming an increasingly popular choice for bispecific construction due to their single-domain modularity, favorable biophysical properties, and potential to work in multiple antibody formats. Here, we review the use of VHH domains as building blocks in the construction of multispecific antibodies and the challenges in creating optimized molecules. In addition to exploring traditional approaches to VHH development, we review the integration of machine learning techniques at various stages of the process. Specifically, the utilization of machine learning for structural prediction, lead identification, lead optimization, and humanization of VHH antibodies.
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19
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Heydenreich FM, Marti-Solano M, Sandhu M, Kobilka BK, Bouvier M, Babu MM. Molecular determinants of ligand efficacy and potency in GPCR signaling. Science 2023; 382:eadh1859. [PMID: 38127743 PMCID: PMC7615523 DOI: 10.1126/science.adh1859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) bind to extracellular ligands and drugs and modulate intracellular responses through conformational changes. Despite their importance as drug targets, the molecular origins of pharmacological properties such as efficacy (maximum signaling response) and potency (the ligand concentration at half-maximal response) remain poorly understood for any ligand-receptor-signaling system. We used the prototypical adrenaline-β2 adrenergic receptor-G protein system to reveal how specific receptor residues decode and translate the information encoded in a ligand to mediate a signaling response. We present a data science framework to integrate pharmacological and structural data to uncover structural changes and allosteric networks relevant for ligand pharmacology. These methods can be tailored to study any ligand-receptor-signaling system, and the principles open possibilities for designing orthosteric and allosteric compounds with defined signaling properties.
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Affiliation(s)
- Franziska M. Heydenreich
- Department of Molecular and Cellular Physiology, Stanford University
School of Medicine, Stanford, CA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biochemistry and Molecular Medicine, Institute for
Research in Immunology and Cancer, Université de Montréal, Montreal,
QC, Canada
| | - Maria Marti-Solano
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Pharmacology, University of Cambridge, Cambridge,
UK
| | - Manbir Sandhu
- Department of Pharmacology, University of Cambridge, Cambridge,
UK
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University
School of Medicine, Stanford, CA, USA
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for
Research in Immunology and Cancer, Université de Montréal, Montreal,
QC, Canada
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Structural Biology and Center of Excellence for
Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN,
USA
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20
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Tureček F. Covalent crosslinking in gas-phase biomolecular ions. An account and perspective. Phys Chem Chem Phys 2023; 25:32292-32304. [PMID: 37990588 DOI: 10.1039/d3cp04879a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Photochemical crosslinking in gas-phase ion complexes has been introduced as a method to study biomolecular structures and dynamics. Emphasis has been on carbene-based crosslinking induced by photodissociation of diazirine-tagged ions. The features that characterize gas-phase crosslinking include (1) complex formation in electrospray droplets that allows for library-type screening; (2) well defined stoichiometry of the complexes due to mass-selective isolation; (3) facile reaction monitoring and yield determination, and (4) post-crosslinking structure analysis by tandem mass spectrometry that has been combined with hydrogen-deuterium exchange, UV-vis action spectroscopy, and ion mobility measurements. In this account, examples are given of peptide-peptide, peptide-nucleotide, and peptide-ligand crosslinking that chiefly used carbene-based reactions. The pros and cons of gas-phase crosslinking are discussed. Nitrile-imine based crosslinking in gas-phase ions is introduced as a promising new approach to ion structure analysis that offers high efficiency and has the potential for wide ranging applications.
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Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, WA 98195-1700, USA.
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21
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Mitrovic D, Chen Y, Marciniak A, Delemotte L. Coevolution-Driven Method for Efficiently Simulating Conformational Changes in Proteins Reveals Molecular Details of Ligand Effects in the β2AR Receptor. J Phys Chem B 2023; 127:9891-9904. [PMID: 37947090 PMCID: PMC10683026 DOI: 10.1021/acs.jpcb.3c04897] [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: 07/20/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
With the advent of AI-powered structure prediction, the scientific community is inching closer to solving protein folding. An unresolved enigma, however, is to accurately, reliably, and deterministically predict alternative conformational states that are crucial for the function of, e.g., transporters, receptors, or ion channels where conformational cycling is innately coupled to protein function. Accurately discovering and exploring all conformational states of membrane proteins has been challenging due to the need to retain atomistic detail while enhancing the sampling along interesting degrees of freedom. The challenges include but are not limited to finding which degrees of freedom are relevant, how to accelerate the sampling along them, and then quantifying the populations of each micro- and macrostate. In this work, we present a methodology that finds relevant degrees of freedom by combining evolution and physics through machine learning and apply it to the conformational sampling of the β2 adrenergic receptor. In addition to predicting new conformations that are beyond the training set, we have computed free energy surfaces associated with the protein's conformational landscape. We then show that the methodology is able to quantitatively predict the effect of an array of ligands on the β2 adrenergic receptor activation through the discovery of new metastable states not present in the training set. Lastly, we also stake out the structural determinants of activation and inactivation pathway signaling through different ligands and compare them to functional experiments to validate our methodology and potentially gain further insights into the activation mechanism of the β2 adrenergic receptor.
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Affiliation(s)
- Darko Mitrovic
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Yue Chen
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Antoni Marciniak
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
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22
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Liccardo F, Morstein J, Lin TY, Pampel J, Shokat KM, Irannejad R. Selective activation of intracellular β1AR using a spatially restricted antagonist. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568314. [PMID: 38045405 PMCID: PMC10690298 DOI: 10.1101/2023.11.22.568314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
G-protein-coupled receptors (GPCRs) regulate several physiological and pathological processes and represent the target of approximately 30% of FDA-approved drugs. GPCR-mediated signaling was thought to occur exclusively at the plasma membrane. However, recent studies have unveiled their presence and function at subcellular membrane compartments. There is a growing interest in studying compartmentalized signaling of GPCRs. This requires development of novel tools to separate GPCRs signaling at the plasma membrane from the ones initiated at intracellular compartments. We took advantage of the structural and pharmacological information available for β1-adrenergic receptor (β1AR), an exemplary GPCR that functions at subcellular compartments, and rationally designed spatially restricted antagonists. We generated a cell impermeable β1AR antagonist by conjugating a suitable pharmacophore to a sulfonate-containing fluorophore. This cell-impermeable antagonist only inhibited β1AR on the plasma membrane. In contrast, a cell permeable β1AR agonist containing a non-sulfonated fluorophore, efficiently inhibited both the plasma membrane and Golgi pools of β1ARs. Furthermore, the cell impermeable antagonist selectively inhibited the phosphorylation of downstream effectors of PKA proximal to the plasma membrane in adult cardiomyocytes while β1AR intracellular pool remained active. Our tools offer promising avenues for investigating compartmentalized β1AR signaling in various context, potentially advancing our understanding of β1AR-mediated cellular responses in health and disease. They also offer a general strategy to study compartmentalized signaling for other GPCRs in various biological systems.
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23
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Castañeda-Leautaud AC, Vidal-Limon A, Aguila SA. Molecular dynamics and free energy calculations of clozapine bound to D2 and H1 receptors reveal a cardiometabolic mitigated derivative. J Biomol Struct Dyn 2023; 41:9313-9325. [PMID: 36416566 DOI: 10.1080/07391102.2022.2148748] [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: 05/24/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022]
Abstract
Most atypical antipsychotics derive from a high dropout of drug treatments due to adverse cardiometabolic side effects. These side effects are caused, in part, by the H1 receptor blockade. The current work sought a clozapine derivative with a reduced affinity for the H1 receptor while maintaining its therapeutic effect linked to D2 receptor binding. Explicit molecular dynamics simulations and end-point free energy calculations of clozapine in complex with the D2 and H1 receptors embedded in cholesterol-rich lipid bilayers were performed to analyze the intermolecular interactions and address the relevance of clozapine-functional groups. Based on that, free energy perturbation calculations were performed to measure the change in free energy of clozapine structural modifications. Our results indicate the best clozapine derivative is the iodine atom substitution for chlorine. The latter is mainly due to electrostatic interaction loss for the H1 receptor, while the halogen orientation out of the D2 active site reduces the impact on the affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alma C Castañeda-Leautaud
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
- Nanosciences, Center for Scientific Research and Higher Education of Ensenada, Ensenada, B.C., Mexico
| | - Abraham Vidal-Limon
- Instituto de Ecología A.C. (INECOL). Red de Estudios Moleculares Avanzados, Xalapa, Veracruz, México
| | - Sergio A Aguila
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
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24
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Activation/Deactivation Free-Energy Profiles for the β 2-Adrenergic Receptor: Ligand Modes of Action. J Chem Inf Model 2023; 63:6332-6343. [PMID: 37824365 DOI: 10.1021/acs.jcim.3c00805] [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: 10/14/2023]
Abstract
We use enhanced-sampling simulations with an effective collective variable to study the activation of the β2-adrenergic receptor in the presence of ligands with different efficacy. The free-energy profiles are computed for the ligand-free (apo) receptor and binary (apo-receptor + G-protein α-subunit and receptor + ligand) and ternary complexes. The results are not only compatible with available experiments but also allow unprecedented structural insight into the nature of GPCR conformations along the activation pathway and their role in the activation mechanism. In particular, the simulations reveal an unexpected mode of action of partial agonists such as salmeterol and salbutamol that arises already in the binary complex without the G-protein. Specific differences in the polar interactions with residues in TM5, which are required to stabilize an optimal TM6 conformation that facilitates G-protein binding and receptor activation, play a major role in differentiating them from full agonists.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04109 Leipzig, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, United Kingdom
- Swiss Bioinformatics Institute, CH1206 Geneva, Switzerland
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
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25
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Miller RM, Sescil J, Sarcinella MC, Bailey RC, Wang W. Accessible and Generalizable in Vitro Luminescence Assay for Detecting GPCR Activation. ACS MEASUREMENT SCIENCE AU 2023; 3:337-343. [PMID: 37868356 PMCID: PMC10588934 DOI: 10.1021/acsmeasuresciau.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/20/2023] [Indexed: 10/24/2023]
Abstract
G protein-coupled receptors (GPCRs) serve critical physiological roles as the most abundant family of receptors. Here, we describe the design of a generalizable and cell lysate-based method that leverages the interaction between an agonist-activated GPCR and a conformation-specific binder to reconstitute split nanoluciferase (NanoLuc) in vitro. This tool, In vitro GPCR split NanoLuc ligand Triggered Reporter (IGNiTR), has broad applications. We have demonstrated IGNiTR's use with three Gs-coupled GPCRs, two Gi-coupled GPCRs and three classes of conformation-specific binders: nanobodies, miniG proteins, and G protein peptidomimetics. As an in vitro method, IGNiTR enables the use of synthetic G protein peptidomimetics and provides easily scalable and portable reagents for characterizing GPCRs and ligands. We tested three diverse applications of IGNiTR: (1) proof-of-concept GPCR ligand screening using dopamine receptor D1 IGNiTR; (2) detection of opioids for point-of-care testing; and (3) characterizing GPCR functionality during Nanodisc-based reconstitution processes. Due to IGNiTR's unique advantages and the convenience of its cell lysate-based format, this tool will find extensive applications in GPCR ligand detection, screening, and GPCR characterization.
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Affiliation(s)
- Ruby M. Miller
- Life Sciences
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Sescil
- Life Sciences
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Marina C. Sarcinella
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan C. Bailey
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wenjing Wang
- Life Sciences
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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26
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Gavryushov S, Bashilov A, Cherashev-Tumanov KV, Kuzmich NN, Burykina TI, Izotov BN. Interaction of Synthetic Cannabinoid Receptor Agonists with Cannabinoid Receptor I: Insights into Activation Molecular Mechanism. Int J Mol Sci 2023; 24:14874. [PMID: 37834323 PMCID: PMC10574015 DOI: 10.3390/ijms241914874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Synthetic cannabinoid receptor agonists (SCRAs) have become a wide group of new psychoactive substances since the 2010s. For the last few years, the X-ray structures of the complexes of cannabinoid receptor I (CB1) with SCRAs as well as the complexes of CB1 with its antagonist have been published. Based on those data, SCRA-CB1 interactions are analyzed in detail, using molecular modeling and molecular dynamics simulations. The molecular mechanism of the conformational transformation of the transmembrane domain of CB1 caused by its interaction with SCRA is studied. These conformational changes allosterically modulate the CB1-Gi complex, providing activation of the Gi protein. Based on the X-ray-determined structures of the CB1-ligand complexes, a stable apo conformation of inactive CB1 with a relatively low potential barrier of receptor activation was modeled. For that model, molecular dynamic simulations of SCRA binding to CB1 led to the active state of CB1, which allowed us to explore the key features of this activation and the molecular mechanism of the receptor's structural transformation. The simulated CB1 activation is in accordance with the previously published experimental data for the activation at protein mutations or structural changes of ligands. The key feature of the suggested activation mechanism is the determination of the stiff core of the CB1 transmembrane domain and the statement that the entire conformational transformation of the receptor to the active state is caused by a shift of alpha helix TM7 relative to this core. The shift itself is caused by protein-ligand interactions. It was verified via steered molecular dynamics simulations of the X-ray-determined structures of the inactive receptor, which resulted in the active conformation of CB1 irrespective of the placement of agonist ligand in the receptor's active site.
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Affiliation(s)
- Sergei Gavryushov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow 119991, Russia
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 2-4 Bolshaya Pirogovskaya Str., Moscow 119991, Russia; (A.B.); (K.V.C.-T.); (T.I.B.); (B.N.I.)
| | - Anton Bashilov
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 2-4 Bolshaya Pirogovskaya Str., Moscow 119991, Russia; (A.B.); (K.V.C.-T.); (T.I.B.); (B.N.I.)
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russia
| | - Konstantin V. Cherashev-Tumanov
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 2-4 Bolshaya Pirogovskaya Str., Moscow 119991, Russia; (A.B.); (K.V.C.-T.); (T.I.B.); (B.N.I.)
| | - Nikolay N. Kuzmich
- The Maurice and Vivienne Wohl Institute for Drug Discovery, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Tatyana I. Burykina
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 2-4 Bolshaya Pirogovskaya Str., Moscow 119991, Russia; (A.B.); (K.V.C.-T.); (T.I.B.); (B.N.I.)
| | - Boris N. Izotov
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 2-4 Bolshaya Pirogovskaya Str., Moscow 119991, Russia; (A.B.); (K.V.C.-T.); (T.I.B.); (B.N.I.)
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27
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Zilberg G, Parpounas AK, Warren AL, Yang S, Wacker D. Molecular Basis of Human Trace Amine-Associated Receptor 1 Activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556555. [PMID: 37986760 PMCID: PMC10659437 DOI: 10.1101/2023.09.06.556555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The human trace amine-associated receptor 1 (hTAAR1, hTA1) is a key regulator of monoaminergic neurotransmission and the actions of psychostimulants. Despite preclinical research demonstrating its tractability as a drug target, its molecular mechanisms of activation remain unclear. Moreover, poorly understood pharmacological differences between rodent and human TA1 complicate the translation of findings from preclinical disease models into novel pharmacotherapies. To elucidate hTA1's mechanisms on the molecular scale and investigate the underpinnings of its divergent pharmacology from rodent orthologs, we herein report the structure of the human TA1 receptor in complex with a Gαs heterotrimer. Our structure reveals shared structural elements with other TAARs, as well as with its closest monoaminergic ortholog, the serotonin receptor 5-HT4R. We further find that a single mutation dramatically shifts the selectivity of hTA1 towards that of its rodent orthologs, and report on the effects of substituting residues to those found in serotonin and dopamine receptors. Strikingly, we also discover that the atypical antipsychotic medication and pan-monoaminergic antagonist asenapine potently and efficaciously activates hTA1. Together our studies provide detailed insight into hTA1 structure and function, contrast its molecular pharmacology with that of related receptors, and uncover off-target activities of monoaminergic drugs at hTA1.
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Affiliation(s)
- Gregory Zilberg
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Alexandra K. Parpounas
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Audrey L. Warren
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Shifan Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daniel Wacker
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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28
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Lee KH, Manning JJ, Javitch J, Shi L. A Novel "Activation Switch" Motif Common to All Aminergic Receptors. J Chem Inf Model 2023; 63:5001-5017. [PMID: 37540602 PMCID: PMC10695015 DOI: 10.1021/acs.jcim.3c00732] [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] [Indexed: 08/06/2023]
Abstract
Aminergic receptors are G protein-coupled receptors (GPCRs) that transduce signals from small endogenous biogenic amines to regulate intracellular signaling pathways. Agonist binding in the ligand binding pocket on the extracellular side opens and prepares a cavity on the intracellular face of the receptors to interact with and activate G proteins and β-arrestins. Here, by reviewing and analyzing all available aminergic receptor structures, we seek to identify activation-related conformational changes that are independent of the specific scaffold of the bound agonist, which we define as "activation conformational changes" (ACCs). While some common intracellular ACCs have been well-documented, identifying common extracellular ACCs, including those in the ligand binding pocket, is complicated by local adjustments to different ligand scaffolds. Our analysis shows no common ACCs at the extracellular ends of the transmembrane helices. Furthermore, the restricted access to the ligand binding pocket identified previously in some receptors is not universal. Notably, the Trp6.48 toggle switch and the Pro5.50-Ile3.40-Phe6.44 (PIF) motif at the bottom of the ligand binding pocket have previously been proposed to mediate the conformational consequences of ligand binding to the intracellular side of the receptors. Our analysis shows that common ACCs in the ligand binding pocket are associated with the PIF motif and nearby residues, including Trp6.48, but fails to support a shared rotamer toggle associated with activation. However, we identify two common rearrangements between the extracellular and middle subsegments, and propose a novel "activation switch" motif common to all aminergic receptors. This motif includes the middle subsegments of transmembrane helices 3, 5, and 6 and integrates both the PIF motif and Trp6.48.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jamie J. Manning
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jonathan Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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29
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Zhang X, Guseinov AA, Jenkins L, Li K, Tikhonova IG, Milligan G, Zhang C. Structural basis for the ligand recognition and signaling of free fatty acid receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.553924. [PMID: 37662198 PMCID: PMC10473637 DOI: 10.1101/2023.08.20.553924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Free fatty acid receptors 1-4 (FFA1-4) are class A G protein-coupled receptors (GPCRs). FFA1-3 share substantial sequence similarity whereas FFA4 is unrelated. Despite this FFA1 and FFA4 are activated by the same range of long chain fatty acids (LCFAs) whilst FFA2 and FFA3 are instead activated by short chain fatty acids (SCFAs) generated by the intestinal microbiota. Each of FFA1, 2 and 4 are promising targets for novel drug development in metabolic and inflammatory conditions. To gain insights into the basis of ligand interactions with, and molecular mechanisms underlying activation of, FFAs by LCFAs and SCFAs, we determined the active structures of FFA1 and FFA4 bound to the polyunsaturated LCFA docosahexaenoic acid (DHA), FFA4 bound to the synthetic agonist TUG-891, as well as SCFA butyrate-bound FFA2, each complexed with an engineered heterotrimeric Gq protein (miniGq), by cryo-electron microscopy. Together with computational simulations and mutagenesis studies, we elucidated the similarities and differences in the binding modes of fatty acid ligands with varying chain lengths to their respective GPCRs. Our findings unveil distinct mechanisms of receptor activation and G protein coupling. We anticipate that these outcomes will facilitate structure-based drug development and underpin future research to understand allosteric modulation and biased signaling of this group of GPCRs.
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Affiliation(s)
- Xuan Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261, USA
| | - Abdul-Akim Guseinov
- School of Pharmacy, Medical Biology Centre, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Laura Jenkins
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Kunpeng Li
- Cryo-EM core facility, Case Western Reserve University, OH44106, USA
| | - Irina G. Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Graeme Milligan
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261, USA
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30
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Våbenø J, Oliva-Santiago M, Jørgensen AS, Karlshøj S, Rosenkilde MM. Identification of a Salt Bridge That Is Functionally Important for Chemokine Receptor CXCR1 but not CXCR2. ACS Pharmacol Transl Sci 2023; 6:1120-1128. [PMID: 37588755 PMCID: PMC10425996 DOI: 10.1021/acsptsci.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 08/18/2023]
Abstract
CXC chemokine receptors 1 (CXCR1) and 2 (CXCR2) have high sequence similarity and overlapping chemokine ligand profiles. Residue positions 3.32 and 7.39 are critical for signal transduction in the related CXCR4, and in these positions CXCR1 and CXCR2 contain oppositely charged residues (Lys3.32 and Glu7.39). Experimental and computed receptor structures reveal the possible formation of a salt bridge between transmembrane (TM) helices 3 and 7 via these two residues. To investigate the functional importance of Lys1173.32 and Glu2917.39 in CXCR1, along with the flanking Glu1183.33, we performed a signaling study on 16 CXCR1 mutants using two different CXCL8 isoforms. While single Ala-mutation (K1173.32A, E2917.39A) and charge reversal (K1173.32E, E2917.39K) resulted in nonfunctional receptors, double (K1173.32E-E2917.39K) and triple (K1173.32E-E1183.33A-E2917.39K) mutants rescued CXCR1 function. In contrast, the corresponding mutations did not affect the CXCR2 function to the same extent. Our findings show that the Lys3.32-Glu7.39 salt bridge between TM3 and -7 is functionally important for CXCR1 but not for CXCR2, meaning that signal transduction for these highly homologous receptors is not conserved.
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Affiliation(s)
- Jon Våbenø
- Helgeland
Hospital Trust, Prestmarkveien
1, 8800 Sandnessjøen, Norway
| | - Marta Oliva-Santiago
- Laboratory
for Molecular Pharmacology, Department of Biomedical Sciences, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Astrid S. Jørgensen
- Laboratory
for Molecular Pharmacology, Department of Biomedical Sciences, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Stefanie Karlshøj
- Laboratory
for Molecular Pharmacology, Department of Biomedical Sciences, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Mette M. Rosenkilde
- Laboratory
for Molecular Pharmacology, Department of Biomedical Sciences, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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31
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Su M, Wang J, Xiang G, Do HN, Levitz J, Miao Y, Huang XY. Structural basis of agonist specificity of α 1A-adrenergic receptor. Nat Commun 2023; 14:4819. [PMID: 37563160 PMCID: PMC10415349 DOI: 10.1038/s41467-023-40524-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
α1-adrenergic receptors (α1-ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists for all α1 subtypes has limited our understanding of the physiological roles of different α1-AR subtypes, and led to the stagnancy in agonist-based drug development for these receptors. Here we report cryo-EM structures of α1A-AR in complex with heterotrimeric G-proteins and either the endogenous common agonist epinephrine or the α1A-AR-specific synthetic agonist A61603. These structures provide molecular insights into the mechanisms underlying the discrimination between α1A-AR and α1B-AR by A61603. Guided by the structures and corresponding molecular dynamics simulations, we engineer α1A-AR mutants that are not responsive to A61603, and α1B-AR mutants that can be potently activated by A61603. Together, these findings advance our understanding of the agonist specificity for α1-ARs at the molecular level, opening the possibility of rational design of subtype-specific agonists.
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Affiliation(s)
- Minfei Su
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Guoqing Xiang
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
- Department of Psychiatry, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Hung Nguyen Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
- Department of Psychiatry, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA.
| | - Xin-Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.
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32
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Zupancic JM, Smith MD, Trzeciakiewicz H, Skinner ME, Ferris SP, Makowski EK, Lucas MJ, McArthur N, Kane RS, Paulson HL, Tessier PM. Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates. Front Immunol 2023; 14:1164080. [PMID: 37622125 PMCID: PMC10445546 DOI: 10.3389/fimmu.2023.1164080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/15/2023] [Indexed: 08/26/2023] Open
Abstract
Single-domain antibodies, also known as nanobodies, are broadly important for studying the structure and conformational states of several classes of proteins, including membrane proteins, enzymes, and amyloidogenic proteins. Conformational nanobodies specific for aggregated conformations of amyloidogenic proteins are particularly needed to better target and study aggregates associated with a growing class of associated diseases, especially neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. However, there are few reported nanobodies with both conformational and sequence specificity for amyloid aggregates, especially for large and complex proteins such as the tau protein associated with Alzheimer's disease, due to difficulties in selecting nanobodies that bind to complex aggregated proteins. Here, we report the selection of conformational nanobodies that selectively recognize aggregated (fibrillar) tau relative to soluble (monomeric) tau. Notably, we demonstrate that these nanobodies can be directly isolated from immune libraries using quantitative flow cytometric sorting of yeast-displayed libraries against tau aggregates conjugated to quantum dots, and this process eliminates the need for secondary nanobody screening. The isolated nanobodies demonstrate conformational specificity for tau aggregates in brain samples from both a transgenic mouse model and human tauopathies. We expect that our facile approach will be broadly useful for isolating conformational nanobodies against diverse amyloid aggregates and other complex antigens.
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Affiliation(s)
- Jennifer M. Zupancic
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States
| | - Matthew D. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States
| | - Hanna Trzeciakiewicz
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, United States
| | - Mary E. Skinner
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Sean P. Ferris
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Emily K. Makowski
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Michael J. Lucas
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Nikki McArthur
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ravi S. Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Henry L. Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
- Protein Folding Disease Initiative, University of Michigan, Ann Arbor, MI, United States
- Michigan Alzheimer’s Disease Center, University of Michigan, Ann Arbor, MI, United States
| | - Peter M. Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, United States
- Protein Folding Disease Initiative, University of Michigan, Ann Arbor, MI, United States
- Michigan Alzheimer’s Disease Center, University of Michigan, Ann Arbor, MI, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
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33
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Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC. The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. Nat Chem Biol 2023; 19:1013-1021. [PMID: 37081311 PMCID: PMC10530065 DOI: 10.1038/s41589-023-01321-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
The relaxin family peptide receptor 1 (RXFP1) is the receptor for relaxin-2, an important regulator of reproductive and cardiovascular physiology. RXFP1 is a multi-domain G protein-coupled receptor (GPCR) with an ectodomain consisting of a low-density lipoprotein receptor class A (LDLa) module and leucine-rich repeats. The mechanism of RXFP1 signal transduction is clearly distinct from that of other GPCRs, but remains very poorly understood. In the present study, we determine the cryo-electron microscopy structure of active-state human RXFP1, bound to a single-chain version of the endogenous agonist relaxin-2 and the heterotrimeric Gs protein. Evolutionary coupling analysis and structure-guided functional experiments reveal that RXFP1 signals through a mechanism of autoinhibition. Our results explain how an unusual GPCR family functions, providing a path to rational drug development targeting the relaxin receptors.
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Affiliation(s)
- Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James Osei-Owusu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly P Brock
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xinyue Liu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Julian Mintseris
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiaojing Cong
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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34
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Mafi A, Kim SK, Goddard WA. The dynamics of agonist-β 2-adrenergic receptor activation induced by binding of GDP-bound Gs protein. Nat Chem 2023:10.1038/s41557-023-01238-6. [PMID: 37349378 DOI: 10.1038/s41557-023-01238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 05/12/2023] [Indexed: 06/24/2023]
Abstract
There is considerable uncertainty about the mechanism by which the β2-adrenergic receptor (β2AR) is activated. Here we use molecular metadynamics computations to predict the mechanism by which an agonist induces the activation of the β2AR and its cognate Gs protein. We found that binding agonist alone to the inactive β2AR does not break the ionic lock and hence does not drive the β2AR towards the activated conformation. However, we found that attaching the inactive Gs protein to the agonist-bound inactive β2AR (containing the ionic lock) leads to partial insertion of Gαs-α5 into the core of β2AR, which breaks the ionic lock, leading to activation of the Gs protein coupled to β2AR. Upon activation, the Gαs protein undergoes a remarkable opening of the GDP binding pocket, making the GDP available for exchange or release. Concomitantly, Gαs-α5 undergoes a remarkable expansion in the β2AR cytoplasmic region after the ionic lock is broken, inducing TM6 to displace outward by ~5 Å from TM3.
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Affiliation(s)
- Amirhossein Mafi
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - William A Goddard
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA.
- California Institute of Technology, Pasadena, CA, USA.
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35
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Toyoda Y, Zhu A, Kong F, Shan S, Zhao J, Wang N, Sun X, Zhang L, Yan C, Kobilka BK, Liu X. Structural basis of α 1A-adrenergic receptor activation and recognition by an extracellular nanobody. Nat Commun 2023; 14:3655. [PMID: 37339967 DOI: 10.1038/s41467-023-39310-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
The α1A-adrenergic receptor (α1AAR) belongs to the family of G protein-coupled receptors that respond to adrenaline and noradrenaline. α1AAR is involved in smooth muscle contraction and cognitive function. Here, we present three cryo-electron microscopy structures of human α1AAR bound to the endogenous agonist noradrenaline, its selective agonist oxymetazoline, and the antagonist tamsulosin, with resolutions range from 2.9 Å to 3.5 Å. Our active and inactive α1AAR structures reveal the activation mechanism and distinct ligand binding modes for noradrenaline compared with other adrenergic receptor subtypes. In addition, we identified a nanobody that preferentially binds to the extracellular vestibule of α1AAR when bound to the selective agonist oxymetazoline. These results should facilitate the design of more selective therapeutic drugs targeting both orthosteric and allosteric sites in this receptor family.
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Affiliation(s)
- Yosuke Toyoda
- School of Medicine, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, 606-8501, Japan.
| | - Angqi Zhu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fang Kong
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Sisi Shan
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Tsinghua University, Beijing, 100084, China
| | - Jiawei Zhao
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Nan Wang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaoou Sun
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Linqi Zhang
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Tsinghua University, Beijing, 100084, China
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Xiangyu Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
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36
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Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife 2023; 12:83477. [PMID: 37248726 DOI: 10.7554/elife.83477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4 muscarinic acetylcholine receptor (M4 mAChR) is a validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. In this study, we rigorously quantified the affinity, efficacy, and magnitude of modulation of two different positive allosteric modulators, LY2033298 (LY298) and VU0467154 (VU154), combined with the endogenous agonist acetylcholine (ACh) or the high-affinity agonist iperoxo (Ipx), at the human M4 mAChR. By determining the cryo-electron microscopy structures of the M4 mAChR, bound to a cognate Gi1 protein and in complex with ACh, Ipx, LY298-Ipx, and VU154-Ipx, and applying molecular dynamics simulations, we determine key molecular mechanisms underlying allosteric pharmacology. In addition to delineating the contribution of spatially distinct binding sites on observed pharmacology, our findings also revealed a vital role for orthosteric and allosteric ligand-receptor-transducer complex stability, mediated by conformational dynamics between these sites, in the ultimate determination of affinity, efficacy, cooperativity, probe dependence, and species variability. There results provide a holistic framework for further GPCR mechanistic studies and can aid in the discovery and design of future allosteric drugs.
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Affiliation(s)
- Ziva Vuckovic
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jesse I Mobbs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Mahmuda Yeasmin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Vindhya Nawaratne
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Emma T van der Westhuizen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Elham Khajehali
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Craig W Lindsley
- Department of Pharmacology, Warren Center for Neuroscience Drug Discovery and Department of Chemistry, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, United States
| | - Andrew Tobin
- The Centre for Translational Pharmacology, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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37
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Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter J, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.540554. [PMID: 37292845 PMCID: PMC10245861 DOI: 10.1101/2023.05.23.540554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The orphan G protein-coupled receptor (GPCR) GPR161 is enriched in primary cilia, where it plays a central role in suppressing Hedgehog signaling1. GPR161 mutations lead to developmental defects and cancers2,3,4. The fundamental basis of how GPR161 is activated, including potential endogenous activators and pathway-relevant signal transducers, remains unclear. To elucidate GPR161 function, we determined a cryogenic-electron microscopy structure of active GPR161 bound to the heterotrimeric G protein complex Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, we identify a sterol that binds to a conserved extrahelical site adjacent to transmembrane helices 6 and 7 and stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress cAMP pathway activation. Surprisingly, these mutants retain the ability to suppress GLI2 transcription factor accumulation in cilia, a key function of ciliary GPR161 in Hedgehog pathway suppression. By contrast, a protein kinase A-binding site in the GPR161 C-terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how unique structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the broader role of GPR161 function in other signaling pathways.
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Affiliation(s)
- Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Simone Harrison
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ziwei Chen
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Taylor Institute for Innovative Psychiatric Research, St. Louis, MO 63110, USA
| | - Masha Karelina
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vivek R. Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samuel P. Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Philipp Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck; Tyrolean Cancer Research Institute (TKFI), Innsbruck 6020, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
| | - Douglas F. Covey
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Taylor Institute for Innovative Psychiatric Research, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck 6020, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck; Tyrolean Cancer Research Institute (TKFI), Innsbruck 6020, Austria
| | - Debora S. Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeremy Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158
| | - Ron O. Dror
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Alex S. Evers
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Taylor Institute for Innovative Psychiatric Research, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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38
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Di Rienzo L, Miotto M, Milanetti E, Ruocco G. Computational structural-based GPCR optimization for user-defined ligand: Implications for the development of biosensors. Comput Struct Biotechnol J 2023; 21:3002-3009. [PMID: 37249971 PMCID: PMC10220229 DOI: 10.1016/j.csbj.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
Organisms have developed effective mechanisms to sense the external environment. Human-designed biosensors exploit this natural optimization, where different biological machinery have been adapted to detect the presence of user-defined molecules. Specifically, the pheromone pathway in the model organism Saccharomyces cerevisiae represents a suitable candidate as a synthetic signaling system. Indeed, it expresses just one G-Protein Coupled Receptor (GPCR), Ste2, able to recognize pheromone and initiate the expression of pheromone-dependent genes. To date, the standard procedure to engineer this system relies on the substitution of the yeast GPCR with another one and on the modification of the yeast G-protein to bind the inserted receptor. Here, we propose an innovative computational procedure, based on geometrical and chemical optimization of protein binding pockets, to select the amino acid substitutions required to make the native yeast GPCR able to recognize a user-defined ligand. This procedure would allow the yeast to recognize a wide range of ligands, without a-priori knowledge about a GPCR recognizing them or the corresponding G protein. We used Monte Carlo simulations to design on Ste2 a binding pocket able to recognize epinephrine, selected as a test ligand. We validated Ste2 mutants via molecular docking and molecular dynamics. We verified that the amino acid substitutions we identified make Ste2 able to accommodate and remain firmly bound to epinephrine. Our results indicate that we sampled efficiently the huge space of possible mutants, proposing such a strategy as a promising starting point for the development of a new kind of S.cerevisiae-based biosensors.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Mattia Miotto
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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39
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Sano FK, Akasaka H, Shihoya W, Nureki O. Cryo-EM structure of the endothelin-1-ET B-G i complex. eLife 2023; 12:85821. [PMID: 37096326 PMCID: PMC10129325 DOI: 10.7554/elife.85821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/23/2023] [Indexed: 04/26/2023] Open
Abstract
The endothelin ETB receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ETB signaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle. Consequently, ETB agonists are expected to be drugs for neuroprotection and improved anti-tumor drug delivery. Here, we report the cryo-electron microscopy structure of the endothelin-1-ETB-Gi complex at 2.8 Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ETB receptor structures revealed how endothelin-1 activates the ETB receptor. The NPxxY motif, essential for G-protein activation, is not conserved in ETB, resulting in a unique structural change upon G-protein activation. Compared with other GPCR-G-protein complexes, ETB binds Gi in the shallowest position, further expanding the diversity of G-protein binding modes. This structural information will facilitate the elucidation of G-protein activation and the rational design of ETB agonists.
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Affiliation(s)
- Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Akasaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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40
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Xu X, Shonberg J, Kaindl J, Clark MJ, Stößel A, Maul L, Mayer D, Hübner H, Hirata K, Venkatakrishnan AJ, Dror RO, Kobilka BK, Sunahara RK, Liu X, Gmeiner P. Constrained catecholamines gain β 2AR selectivity through allosteric effects on pocket dynamics. Nat Commun 2023; 14:2138. [PMID: 37059717 PMCID: PMC10104803 DOI: 10.1038/s41467-023-37808-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
G protein-coupled receptors (GPCRs) within the same subfamily often share high homology in their orthosteric pocket and therefore pose challenges to drug development. The amino acids that form the orthosteric binding pocket for epinephrine and norepinephrine in the β1 and β2 adrenergic receptors (β1AR and β2AR) are identical. Here, to examine the effect of conformational restriction on ligand binding kinetics, we synthesized a constrained form of epinephrine. Surprisingly, the constrained epinephrine exhibits over 100-fold selectivity for the β2AR over the β1AR. We provide evidence that the selectivity may be due to reduced ligand flexibility that enhances the association rate for the β2AR, as well as a less stable binding pocket for constrained epinephrine in the β1AR. The differences in the amino acid sequence of the extracellular vestibule of the β1AR allosterically alter the shape and stability of the binding pocket, resulting in a marked difference in affinity compared to the β2AR. These studies suggest that for receptors containing identical binding pocket residues, the binding selectivity may be influenced in an allosteric manner by surrounding residues, like those of the extracellular loops (ECLs) that form the vestibule. Exploiting these allosteric influences may facilitate the development of more subtype-selective ligands for GPCRs.
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Affiliation(s)
- Xinyu Xu
- State Key laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Jeremy Shonberg
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Jonas Kaindl
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Mary J Clark
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Anne Stößel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Luis Maul
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Daniel Mayer
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo, 679-5148, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - A J Venkatakrishnan
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California, 92093, USA.
| | - Xiangyu Liu
- State Key laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China.
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany.
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41
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Heng J, Hu Y, Pérez-Hernández G, Inoue A, Zhao J, Ma X, Sun X, Kawakami K, Ikuta T, Ding J, Yang Y, Zhang L, Peng S, Niu X, Li H, Guixà-González R, Jin C, Hildebrand PW, Chen C, Kobilka BK. Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor. Nat Commun 2023; 14:2005. [PMID: 37037825 PMCID: PMC10085991 DOI: 10.1038/s41467-023-37233-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
Advances in structural biology have provided important mechanistic insights into signaling by the transmembrane core of G-protein coupled receptors (GPCRs); however, much less is known about intrinsically disordered regions such as the carboxyl terminus (CT), which is highly flexible and not visible in GPCR structures. The β2 adrenergic receptor's (β2AR) 71 amino acid CT is a substrate for GPCR kinases and binds β-arrestins to regulate signaling. Here we show that the β2AR CT directly inhibits basal and agonist-stimulated signaling in cell lines lacking β-arrestins. Combining single-molecule fluorescence resonance energy transfer (FRET), NMR spectroscopy, and molecular dynamics simulations, we reveal that the negatively charged β2AR-CT serves as an autoinhibitory factor via interacting with the positively charged cytoplasmic surface of the receptor to limit access to G-proteins. The stability of this interaction is influenced by agonists and allosteric modulators, emphasizing that the CT plays important role in allosterically regulating GPCR activation.
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Affiliation(s)
- Jie Heng
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
| | - Guillermo Pérez-Hernández
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Charitéplatz 1, 10117, Berlin, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Jiawei Zhao
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiuyan Ma
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xiaoou Sun
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Tatsuya Ikuta
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yujie Yang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lujia Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Sijia Peng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hongwei Li
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232, Villigen, PSI, Switzerland
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peter W Hildebrand
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Medical Physics and Biophysics, University Leipzig, 04107, Leipzig, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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42
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Maciag M, Plazinski W, Pulawski W, Kolinski M, Jozwiak K, Plazinska A. A comprehensive pharmacological analysis of fenoterol and its derivatives to unravel the role of β 2-adrenergic receptor in zebrafish. Biomed Pharmacother 2023; 160:114355. [PMID: 36739761 DOI: 10.1016/j.biopha.2023.114355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
β-adrenergic receptors (βARs) belong to a key molecular targets that regulate the most important processes occurring in the human organism. Although over the last decades a zebrafish model has been developed as a model complementary to rodents in biomedical research, the role of β2AR in regulation of pathological and toxicological effects remains to elucidate. Therefore, the study aimed to clarify the role of β2AR with a particular emphasis on the distinct role of subtypes A and B of zebrafish β2AR. As model compounds selective β2AR agonists - (R,R)-fenoterol ((R,R)-Fen) and its new derivatives: (R,R)-4'-methoxyfenoterol ((R,R)-MFen) and (R,R)-4'-methoxy-1-naphtylfenoterol ((R,R)-MNFen) - were tested. We described dose-dependent changes observed after fenoterols exposure in terms of general toxicity, cardiotoxicity and neurobehavioural responses. Subsequently, to better characterise the role of β2-adrenergic stimulation in zebrafish, we have performed a series of molecular docking simulations. Our results indicate that (R,R)-Fen displays the highest affinity for subtype A of zebrafish β2AR and β2AAR might be involved in pigment depletion. (R,R)-MFen shows the lowest affinity for zebrafish β2ARs out of the tested fenoterols and this might be associated with its cardiotoxic and anxiogenic effects. (R,R)-MNFen displays the highest affinity for subtype B of zebrafish β2AR and modulation of this receptor might be associated with the development of malformations, increases locomotor activity and induces a negative chronotropic effect. Taken together, the presented data offer insights into the functional responses of the zebrafish β2ARs confirming their intraspecies conservation, and support the translation of the zebrafish model in pharmacological and toxicological research.
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Affiliation(s)
- Monika Maciag
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland; Independent Laboratory of Behavioral Studies, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland.
| | - Wojciech Plazinski
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland; Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 8 Niezapominajek Street, 30-239 Cracow, Poland
| | - Wojciech Pulawski
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, e Pawinskiego Street, 02-106 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, e Pawinskiego Street, 02-106 Warsaw, Poland
| | - Krzysztof Jozwiak
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland
| | - Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland.
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43
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Shpakov AO. Allosteric Regulation of G-Protein-Coupled Receptors: From Diversity of Molecular Mechanisms to Multiple Allosteric Sites and Their Ligands. Int J Mol Sci 2023; 24:6187. [PMID: 37047169 PMCID: PMC10094638 DOI: 10.3390/ijms24076187] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Allosteric regulation is critical for the functioning of G protein-coupled receptors (GPCRs) and their signaling pathways. Endogenous allosteric regulators of GPCRs are simple ions, various biomolecules, and protein components of GPCR signaling (G proteins and β-arrestins). The stability and functional activity of GPCR complexes is also due to multicenter allosteric interactions between protomers. The complexity of allosteric effects caused by numerous regulators differing in structure, availability, and mechanisms of action predetermines the multiplicity and different topology of allosteric sites in GPCRs. These sites can be localized in extracellular loops; inside the transmembrane tunnel and in its upper and lower vestibules; in cytoplasmic loops; and on the outer, membrane-contacting surface of the transmembrane domain. They are involved in the regulation of basal and orthosteric agonist-stimulated receptor activity, biased agonism, GPCR-complex formation, and endocytosis. They are targets for a large number of synthetic allosteric regulators and modulators, including those constructed using molecular docking. The review is devoted to the principles and mechanisms of GPCRs allosteric regulation, the multiplicity of allosteric sites and their topology, and the endogenous and synthetic allosteric regulators, including autoantibodies and pepducins. The allosteric regulation of chemokine receptors, proteinase-activated receptors, thyroid-stimulating and luteinizing hormone receptors, and beta-adrenergic receptors are described in more detail.
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Affiliation(s)
- Alexander O Shpakov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia
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44
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Han Y, Dawson JRD, DeMarco KR, Rouen KC, Bekker S, Yarov-Yarovoy V, Clancy CE, Xiang YK, Vorobyov I. Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein. Proc Natl Acad Sci U S A 2023; 120:e2215916120. [PMID: 36853938 PMCID: PMC10013855 DOI: 10.1073/pnas.2215916120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest group of membrane receptors for transmembrane signal transduction. Ligand-induced activation of GPCRs triggers G protein activation followed by various signaling cascades. Understanding the structural and energetic determinants of ligand binding to GPCRs and GPCRs to G proteins is crucial to the design of pharmacological treatments targeting specific conformations of these proteins to precisely control their signaling properties. In this study, we focused on interactions of a prototypical GPCR, beta-2 adrenergic receptor (β2AR), with its endogenous agonist, norepinephrine (NE), and the stimulatory G protein (Gs). Using molecular dynamics (MD) simulations, we demonstrated the stabilization of cationic NE, NE(+), binding to β2AR by Gs protein recruitment, in line with experimental observations. We also captured the partial dissociation of the ligand from β2AR and the conformational interconversions of Gs between closed and open conformations in the NE(+)-β2AR-Gs ternary complex while it is still bound to the receptor. The variation of NE(+) binding poses was found to alter Gs α subunit (Gsα) conformational transitions. Our simulations showed that the interdomain movement and the stacking of Gsα α1 and α5 helices are significant for increasing the distance between the Gsα and β2AR, which may indicate a partial dissociation of Gsα The distance increase commences when Gsα is predominantly in an open state and can be triggered by the intracellular loop 3 (ICL3) of β2AR interacting with Gsα, causing conformational changes of the α5 helix. Our results help explain molecular mechanisms of ligand and GPCR-mediated modulation of G protein activation.
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Affiliation(s)
- Yanxiao Han
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - John R. D. Dawson
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - Kyle C. Rouen
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Science and Engineering, American River College, Sacramento, CA95841
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA95616
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
| | - Yang K. Xiang
- Department of Pharmacology, University of California, Davis, CA95616
- VA Northern California Health Care System, Mather, CA95655
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
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45
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Sadler F, Ma N, Ritt M, Sharma Y, Vaidehi N, Sivaramakrishnan S. Autoregulation of GPCR signalling through the third intracellular loop. Nature 2023; 615:734-741. [PMID: 36890236 PMCID: PMC10033409 DOI: 10.1038/s41586-023-05789-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/03/2023] [Indexed: 03/10/2023]
Abstract
The third intracellular loop (ICL3) of the G protein-coupled receptor (GPCR) fold is important for the signal transduction process downstream of receptor activation1-3. Despite this, the lack of a defined structure of ICL3, combined with its high sequence divergence among GPCRs, complicates characterization of its involvement in receptor signalling4. Previous studies focusing on the β2 adrenergic receptor (β2AR) suggest that ICL3 is involved in the structural process of receptor activation and signalling5-7. Here we derive mechanistic insights into the role of ICL3 in β2AR signalling, observing that ICL3 autoregulates receptor activity through a dynamic conformational equilibrium between states that block or expose the receptor's G protein-binding site. We demonstrate the importance of this equilibrium for receptor pharmacology, showing that G protein-mimetic effectors bias the exposed states of ICL3 to allosterically activate the receptor. Our findings additionally reveal that ICL3 tunes signalling specificity by inhibiting receptor coupling to G protein subtypes that weakly couple to the receptor. Despite the sequence diversity of ICL3, we demonstrate that this negative G protein-selection mechanism through ICL3 extends to GPCRs across the superfamily, expanding the range of known mechanisms by which receptors mediate G protein subtype selective signalling. Furthermore, our collective findings suggest ICL3 as an allosteric site for receptor- and signalling pathway-specific ligands.
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Affiliation(s)
- Fredrik Sadler
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ning Ma
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Michael Ritt
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Yatharth Sharma
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Nagarajan Vaidehi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Sivaraj Sivaramakrishnan
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
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46
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Billesbølle CB, de March CA, van der Velden WJC, Ma N, Tewari J, Del Torrent CL, Li L, Faust B, Vaidehi N, Matsunami H, Manglik A. Structural basis of odorant recognition by a human odorant receptor. Nature 2023; 615:742-749. [PMID: 36922591 PMCID: PMC10580732 DOI: 10.1038/s41586-023-05798-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
Our sense of smell enables us to navigate a vast space of chemically diverse odour molecules. This task is accomplished by the combinatorial activation of approximately 400 odorant G protein-coupled receptors encoded in the human genome1-3. How odorants are recognized by odorant receptors remains unclear. Here we provide mechanistic insight into how an odorant binds to a human odorant receptor. Using cryo-electron microscopy, we determined the structure of the active human odorant receptor OR51E2 bound to the fatty acid propionate. Propionate is bound within an occluded pocket in OR51E2 and makes specific contacts critical to receptor activation. Mutation of the odorant-binding pocket in OR51E2 alters the recognition spectrum for fatty acids of varying chain length, suggesting that odorant selectivity is controlled by tight packing interactions between an odorant and an odorant receptor. Molecular dynamics simulations demonstrate that propionate-induced conformational changes in extracellular loop 3 activate OR51E2. Together, our studies provide a high-resolution view of chemical recognition of an odorant by a vertebrate odorant receptor, providing insight into how this large family of G protein-coupled receptors enables our olfactory sense.
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Affiliation(s)
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Institut de Chimie des Substances Naturelles, UPR2301 CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Wijnand J C van der Velden
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Jeevan Tewari
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Claudia Llinas Del Torrent
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, Bellaterra, Barcelona, Spain
| | - Linus Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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47
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Biophysical investigations of class A GPCRs. Biochimie 2023; 205:86-94. [PMID: 36220484 DOI: 10.1016/j.biochi.2022.10.001] [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: 05/11/2022] [Revised: 08/29/2022] [Accepted: 10/04/2022] [Indexed: 11/23/2022]
Abstract
G protein-coupled receptors (GPCRs) play a central role in cellular communication, converting external stimuli into intracellular responses. GPCRs bind a very broad panel of ligands, such as hormones, neurotransmitters, peptides and lipids. Ligand binding triggers a series of receptor conformational rearrangements, enabling the coupling to intracellular partners and the activation of signaling cascades. The major breakthrough in GPCRs structural biology of the past decade has considerably advanced our understanding of GPCR activation. However, structural information cannot fully explain the molecular details of GPCRs pharmacology. Biophysical investigations reveal that GPCRs are very dynamic proteins, capable of exploring a wide range of conformational states. Binding to ligands of various pharmacological classes, as well as intracellular effectors and allosteric modulators, can shift the equilibrium between these states and the kinetic of interconversions among the different conformers. Investigation of GPCR dynamic interplay is therefore important to better understand the complex pharmacology and signaling profile of these receptors.
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48
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Jiang C, He X, Wang Y, Chen CJ, Othman Y, Hao Y, Yuan J, Xie XQ, Feng Z. Molecular Modeling Study of a Receptor-Orthosteric Ligand-Allosteric Modulator Signaling Complex. ACS Chem Neurosci 2023; 14:418-434. [PMID: 36692197 PMCID: PMC10032570 DOI: 10.1021/acschemneuro.2c00554] [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: 09/12/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Allosteric modulators (AMs) are considered as a perpetual hotspot in research for their higher selectivity and various effects on orthosteric ligands (OL). They are classified in terms of their functionalities as positive, negative, or silent allosteric modulators (PAM, NAM, or SAM, respectively). In the present work, 11 pairs of three-dimensional (3D) structures of receptor-orthosteric ligand and receptor-orthosteric ligand-allosteric modulator complexes have been collected for the studies, including three different systems: GPCR, enzyme, and ion channel. Molecular dynamics (MD) simulations are applied to quantify the dynamic interactions in both the orthosteric and allosteric binding pockets and the structural fluctuation of the involved proteins. Our results showed that MD simulations of moderately large molecules or peptides undergo insignificant changes compared to crystal structure results. Furthermore, we also studied the conformational changes of receptors that bound with PAM and NAM, as well as the different allosteric binding sites in a receptor. There should be no preference for the position of the allosteric binding pocket after comparing the allosteric binding pockets of these three systems. Finally, we aligned four distinct β2 adrenoceptor structures and three N-methyl-d-aspartate receptor (NMDAR) structures to investigate conformational changes. In the β2 adrenoceptor systems, the aligned results revealed that transmembrane (TM) helices 1, 5, and 6 gradually increased outward movement from an enhanced inactive state to an improved active state. TM6 endured the most significant conformational changes (around 11 Å). For NMDAR, the bottom section of NMDAR's ligand-binding domain (LBD) experienced an upward and outward shift during the gradually activating process. In conclusion, our research provides insight into receptor-orthosteric ligand-allosteric modulator studies and the design and development of allosteric modulator drugs using MD simulation.
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Affiliation(s)
- Chen Jiang
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Xibing He
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Yuanqiang Wang
- School
of Pharmacy and Bioengineering, Chongqing
University of Technology, Chongqing400054, China
- Chongqing
Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing400054, China
- Chongqing
Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing400054, China
| | - Chih-Jung Chen
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Yasmin Othman
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Yixuan Hao
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Jiayi Yuan
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Xiang-Qun Xie
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Zhiwei Feng
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, Pharmacometrics & System Pharmacology (PSP) PharmacoAnalytics,
School of Pharmacy; National Center of Excellence for Computational
Drug Abuse Research; Drug Discovery Institute; Departments of Computational
Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15261, United States
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49
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Kang H, Park C, Choi YK, Bae J, Kwon S, Kim J, Choi C, Seok C, Im W, Choi HJ. Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling. Structure 2023; 31:44-57.e6. [PMID: 36525977 DOI: 10.1016/j.str.2022.11.010] [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: 10/26/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Neuropeptide Y (NPY) and its receptors are expressed in various human tissues including the brain where they regulate appetite and emotion. Upon NPY stimulation, the neuropeptide Y1 and Y2 receptors (Y1R and Y2R, respectively) activate GI signaling, but their physiological responses to food intake are different. In addition, deletion of the two N-terminal amino acids of peptide YY (PYY(3-36)), the endogenous form found in circulation, can stimulate Y2R but not Y1R, suggesting that Y1R and Y2R may have distinct ligand-binding modes. Here, we report the cryo-electron microscopy structures of the PYY(3-36)‒Y2R‒Gi and NPY‒Y2R‒Gi complexes. Using cell-based assays, molecular dynamics simulations, and structural analysis, we revealed the molecular basis of the exclusive binding of PYY(3-36) to Y2R. Furthermore, we demonstrated that Y2R favors G protein signaling over β-arrestin signaling upon activation, whereas Y1R does not show a preference between these two pathways.
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Affiliation(s)
- Hyunook Kang
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaehee Park
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Jungnam Bae
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sohee Kwon
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinuk Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulwon Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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50
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Mordalski S, Kościółek T. Homology Modeling of the G Protein-Coupled Receptors. Methods Mol Biol 2023; 2627:167-181. [PMID: 36959447 DOI: 10.1007/978-1-0716-2974-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
G protein-coupled receptors (GPCRs) are therapeutically important family of membrane proteins. Despite growing number of experimental structures available for GPCRs, homology modeling remains a relevant method for studying these receptors and for discovering new ligands for them. Here we describe the state-of-the-art methods for modeling GPCRs, starting from template selection, through fine-tuning sequence alignment to model refinement.
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Affiliation(s)
- Stefan Mordalski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland.
| | - Tomasz Kościółek
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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