1
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Guan L, Tan J, Qi B, Chen Y, Cao M, Zhang Q, Zou Y. Effects of an external static EF on the conformational transition of 5-HT1A receptor: A molecular dynamics simulation study. Biophys Chem 2024; 312:107283. [PMID: 38941873 DOI: 10.1016/j.bpc.2024.107283] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
The serotonin receptor subtype 1A (5-HT1AR), one of the G-protein-coupled receptor (GPCR) family, has been implicated in several neurological conditions. Understanding the activation and inactivation mechanism of 5-HT1AR at the molecular level is critical for discovering novel therapeutics in many diseases. Recently there has been a growing appreciation for the role of external electric fields (EFs) in influencing the structure and activity of biomolecules. In this study, we used molecular dynamics (MD) simulations to examine conformational features of active states of 5-HT1AR and investigate the effect of an external static EF with 0.02 V/nm applied on the active state of 5-HT1AR. Our results showed that the active state of 5-HT1AR maintained the native structure, while the EF led to structural modifications in 5-HT1AR, particularly inducing the inward movement of transmembrane helix 6 (TM6). Furthermore, it disturbed the conformational switches associated with activation in the CWxP, DRY, PIF, and NPxxY motifs, consequently predisposing an inclination towards the inactive-like conformation. We also found that the EF led to an overall increase in the dipole moment of 5-HT1AR, encompassing TM6 and pivotal amino acids. The analyses of conformational properties of TM6 showed that the changed secondary structure and decreased solvent exposure occurred upon the EF condition. The interaction of 5-HT1AR with the membrane lipid bilayer was also altered under the EF. Our findings reveal the molecular mechanism underlying the transition of 5-HT1AR conformation induced by external EFs, which offer potential novel insights into the prospect of employing structure-based EF applications for GPCRs.
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Affiliation(s)
- Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Jingwang Tan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Bote Qi
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Yukang Chen
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Meng Cao
- Department of Physical Education, College of Sport, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong 518061, PR China
| | - Qingwen Zhang
- College of Physical Education, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, PR China
| | - Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China.
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2
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Agyemang E, Gonneville AN, Tiruvadi-Krishnan S, Lamichhane R. Exploring GPCR conformational dynamics using single-molecule fluorescence. Methods 2024; 226:35-48. [PMID: 38604413 PMCID: PMC11098685 DOI: 10.1016/j.ymeth.2024.03.011] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.
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Affiliation(s)
- Eugene Agyemang
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Alyssa N Gonneville
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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3
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Matsuzaki K, Sugimoto N, Hossain S, Islam R, Sumiyoshi E, Hashimoto M, Kishi H, Shido O. Theobromine improves hyperactivity, inattention, and working memory via modulation of dopaminergic neural function in the frontal cortex of spontaneously hypertensive rats. Food Funct 2024; 15:5579-5595. [PMID: 38713055 DOI: 10.1039/d4fo00683f] [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: 05/08/2024]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a developmental disorder and dopaminergic dysfunction in the prefrontal cortex (PFC) may play a role. Our previous research indicated that theobromine (TB), a methylxanthine, enhances cognitive function in rodents via the PFC. This study investigates TB's effects on hyperactivity and cognitive function in stroke-prone spontaneously hypertensive rats (SHR), an ADHD animal model. Male SHRs (6-week old) received a diet containing 0.05% TB for 40 days, while control rats received normal diets. Age-matched male Wistar-Kyoto rats (WKY) served as genetic controls. During the TB administration period, we conducted open-field tests and Y-maze tasks to evaluate hyperactivity and cognitive function, then assessed dopamine concentrations and tyrosine hydroxylase (TH), dopamine receptor D1-5 (DRD1-5), dopamine transporter (DAT), vesicular monoamine transporter-2 (VMAT-2), synaptosome-associated protein-25 (SNAP-25), and brain-derived neurotrophic factor (BDNF) expressions in the PFC. Additionally, the binding affinity of TB for the adenosine receptors (ARs) was evaluated. Compared to WKY, SHR exhibited hyperactivity, inattention and working memory deficits. However, chronic TB administration significantly improved these ADHD-like behaviors in SHR. TB administration also normalized dopamine concentrations and expression levels of TH, DRD2, DRD4, SNAP-25, and BDNF in the PFC of SHR. No changes were observed in DRD1, DRD3, DRD5, DAT, and VMAT-2 expression between SHR and WKY rats, and TB intake had minimal effects. TB was found to have affinity binding to ARs. These results indicate that long-term TB supplementation mitigates hyperactivity, inattention and cognitive deficits in SHR by modulating dopaminergic nervous function and BDNF levels in the PFC, representing a potential adjunctive treatment for ADHD.
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Affiliation(s)
- Kentaro Matsuzaki
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
| | - Naotoshi Sugimoto
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Shahdat Hossain
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
| | - Rafiad Islam
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
- Department of Psychiatry, Yale University School of Medicine, CT, USA.
| | - Eri Sumiyoshi
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
- Department of Sports and Health Science, Faculty of Human Health Science, Matsumoto University, Matsumoto, Japan.
| | - Michio Hashimoto
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
| | - Hiroko Kishi
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
| | - Osamu Shido
- Department of Environmental Physiology, Faculty of Medicine, Shimane University, Izumo, Japan.
- Shimane Rehabilitation College, Oku-izumo, Shimane, Japan.
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Sakao K, Sho C, Miyata T, Takara K, Oda R, Hou DX. Verification of In Vitro Anticancer Activity and Bioactive Compounds in Cordyceps Militaris-Infused Sweet Potato Shochu Spirits. Molecules 2024; 29:2119. [PMID: 38731610 PMCID: PMC11085083 DOI: 10.3390/molecules29092119] [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: 04/06/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Many liqueurs, including spirits infused with botanicals, are crafted not only for their taste and flavor but also for potential medicinal benefits. However, the scientific evidence supporting their medicinal effects remains limited. This study aims to verify in vitro anticancer activity and bioactive compounds in shochu spirits infused with Cordyceps militaris, a Chinese medicine. The results revealed that a bioactive fraction was eluted from the spirit extract with 40% ethanol. The infusion time impacted the inhibitory effect of the spirit extract on the proliferation of colon cancer-derived cell line HCT-116 cells, and a 21-day infusion showed the strongest inhibitory effect. Furthermore, the spirit extract was separated into four fractions, A-D, by high-performance liquid chromatography (HPLC), and Fractions B, C, and D, but not A, exerted the effects of proliferation inhibition and apoptotic induction of HCT-116 cells and HL-60 cells. Furthermore, Fractions B, C, and D were, respectively, identified as adenosine, cordycepin, and N6-(2-hydroxyethyl)-adenosine (HEA) by comprehensive chemical analyses, including proton nuclear magnetic resonance (1H-NMR), Fourier transform infrared spectroscopy (FT-IR), and electrospray ionization mass spectrometry (ESI-MS). To better understand the bioactivity mechanisms of cordycepin and HEA, the agonist and antagonist tests of the A3 adenosine receptor (A3AR) were performed. Cell viability was suppressed by cordycepin, and HEA was restored by the A3AR antagonist MR1523, suggesting that cordycepin and HEA possibly acted as agonists to activate A3ARs to inhibit cell proliferation. Molecular docking simulations revealed that both adenosine and cordycepin bound to the same pocket site of A3ARs, while HEA exhibited a different binding pattern, supporting a possible explanation for the difference in their bioactivity. Taken together, the present study demonstrated that cordycepin and HEA were major bioactive ingredients in Cordyceps militaries-infused sweet potato shochu spirits, which contributed to the in vitro anticancer activity.
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Affiliation(s)
- Kozue Sakao
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (K.S.); (T.M.); (K.T.)
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - Cho Sho
- Kirishima Shuzo Co., Ltd., 4-28-1 Shimokawahigashi, Miyakonojo, Miyazaki 885-8588, Japan;
| | - Takeshi Miyata
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (K.S.); (T.M.); (K.T.)
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kensaku Takara
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (K.S.); (T.M.); (K.T.)
- Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Rio Oda
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - De-Xing Hou
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (K.S.); (T.M.); (K.T.)
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
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5
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Thakur N, Ray AP, Jin B, Afsharian NP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane mimetic-dependence of GPCR energy landscapes. Structure 2024; 32:523-535.e5. [PMID: 38401537 PMCID: PMC11069452 DOI: 10.1016/j.str.2024.01.013] [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: 10/16/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
We leveraged variable-temperature 19F-NMR spectroscopy to compare the conformational equilibria of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), across a range of temperatures ranging from lower temperatures typically employed in 19F-NMR experiments to physiological temperature. A2AAR complexes with partial agonists and full agonists showed large increases in the population of a fully active conformation with increasing temperature. NMR data measured at physiological temperature were more in line with functional data. This was pronounced for complexes with partial agonists, where the population of active A2AAR was nearly undetectable at lower temperature but became evident at physiological temperature. Temperature-dependent behavior of complexes with either full or partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. Cellular signaling experiments correlated with the temperature-dependent conformational equilibria of A2AAR in lipid nanodiscs but not in some detergents, underscoring the importance of the membrane environment in studies of GPCR function.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | | | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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6
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Wang L, Zhang J, Zhang W, Zheng M, Guo H, Pan X, Li W, Yang B, Ding L. The inhibitory effect of adenosine on tumor adaptive immunity and intervention strategies. Acta Pharm Sin B 2024; 14:1951-1964. [PMID: 38799637 PMCID: PMC11119508 DOI: 10.1016/j.apsb.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/02/2023] [Accepted: 11/14/2023] [Indexed: 05/29/2024] Open
Abstract
Adenosine (Ado) is significantly elevated in the tumor microenvironment (TME) compared to normal tissues. It binds to adenosine receptors (AdoRs), suppressing tumor antigen presentation and immune cell activation, thereby inhibiting tumor adaptive immunity. Ado downregulates major histocompatibility complex II (MHC II) and co-stimulatory factors on dendritic cells (DCs) and macrophages, inhibiting antigen presentation. It suppresses anti-tumor cytokine secretion and T cell activation by disrupting T cell receptor (TCR) binding and signal transduction. Ado also inhibits chemokine secretion and KCa3.1 channel activity, impeding effector T cell trafficking and infiltration into the tumor site. Furthermore, Ado diminishes T cell cytotoxicity against tumor cells by promoting immune-suppressive cytokine secretion, upregulating immune checkpoint proteins, and enhancing immune-suppressive cell activity. Reducing Ado production in the TME can significantly enhance anti-tumor immune responses and improve the efficacy of other immunotherapies. Preclinical and clinical development of inhibitors targeting Ado generation or AdoRs is underway. Therefore, this article will summarize and analyze the inhibitory effects and molecular mechanisms of Ado on tumor adaptive immunity, as well as provide an overview of the latest advancements in targeting Ado pathways in anti-tumor immune responses.
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Affiliation(s)
- Longsheng Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenxin Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingming Zheng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongjie Guo
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaohui Pan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Ling Ding
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China
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7
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Zhao J, Elgeti M, O'Brien ES, Sár CP, Ei Daibani A, Heng J, Sun X, White E, Che T, Hubbell WL, Kobilka BK, Chen C. Ligand efficacy modulates conformational dynamics of the µ-opioid receptor. Nature 2024; 629:474-480. [PMID: 38600384 PMCID: PMC11078757 DOI: 10.1038/s41586-024-07295-2] [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: 11/30/2022] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
The µ-opioid receptor (µOR) is an important target for pain management1 and molecular understanding of drug action on µOR will facilitate the development of better therapeutics. Here we show, using double electron-electron resonance and single-molecule fluorescence resonance energy transfer, how ligand-specific conformational changes of µOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several conformations of the cytoplasmic face of the receptor that interconvert on different timescales, including a pre-activated conformation that is capable of G-protein binding, and a fully activated conformation that markedly reduces GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of Gi.
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Affiliation(s)
- Jiawei Zhao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Drug Discovery, University of Leipzig Medical Center, Leipzig, Germany.
| | - Evan S O'Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecília P Sár
- Institute of Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, University of Pécs, Pécs, Hungary
| | - Amal Ei Daibani
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Jie Heng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaoou Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Elizabeth White
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tao Che
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Chunlai Chen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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8
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Weng Y, Yang X, Zhang Q, Chen Y, Xu Y, Zhu C, Xie Q, Wang Y, Yang H, Liu M, Lu W, Song G. Structural insight into the dual-antagonistic mechanism of AB928 on adenosine A 2 receptors. SCIENCE CHINA. LIFE SCIENCES 2024; 67:986-995. [PMID: 38319473 DOI: 10.1007/s11427-023-2459-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 02/07/2024]
Abstract
The adenosine subfamily G protein-coupled receptors A2AR and A2BR have been identified as promising cancer immunotherapy candidates. One of the A2AR/A2BR dual antagonists, AB928, has progressed to a phase II clinical trial to treat rectal cancer. However, the precise mechanism underlying its dual-antagonistic properties remains elusive. Herein, we report crystal structures of the A2AR complexed with AB928 and a selective A2AR antagonist 2-118. The structures revealed a common binding mode on A2AR, wherein the ligands established extensive interactions with residues from the orthosteric and secondary pockets. In contrast, the cAMP assay and A2AR and A2BR molecular dynamics simulations indicated that the ligands adopted distinct binding modes on A2BR. Detailed analysis of their chemical structures suggested that AB928 readily adapted to the A2BR pocket, while 2-118 did not due to intrinsic differences. This disparity potentially accounted for the difference in inhibitory efficacy between A2BR and A2AR. This study serves as a valuable structural template for the future development of selective or dual inhibitors targeting A2AR/A2BR for cancer therapy.
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Affiliation(s)
- Yuan Weng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xinyu Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qiansen Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Ying Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yueming Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chenyu Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Huaiyu Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Gaojie Song
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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9
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Bi M, Wang X, Wang J, Xu J, Sun W, Adediwura VA, Miao Y, Cheng Y, Ye L. Structure and function of an intermediate GPCR-Gαβγ complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587841. [PMID: 38617296 PMCID: PMC11014534 DOI: 10.1101/2024.04.02.587841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Unraveling the signaling roles of intermediate complexes is pivotal for G protein-coupled receptor (GPCR) drug development. Despite hundreds of GPCR-Gαβγ structures, these snapshots primarily capture the fully activated end-state complex. Consequently, a comprehensive understanding of the conformational transitions during GPCR activation and the roles of intermediate GPCR-G protein complexes in signaling remain elusive. Guided by a conformational landscape profiled by 19 F quantitative NMR ( 19 F-qNMR) and Molecular Dynamics (MD) simulations, we resolved the structure of an unliganded GPCR-G protein intermediate complex by blocking its transition to the fully activated end-state complex. More importantly, we presented direct evidence that the intermediate GPCR-Gαsβγ complex initiates a rate-limited nucleotide exchange without progressing to the fully activated end-state complex, thereby bridging a significant gap in our understanding the complexity of GPCR signaling. Understanding the roles of individual conformational states and their complexes in signaling efficacy and bias will help us to design drugs that discriminately target a disease-related conformation.
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10
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Cai H, Guo S, Xu Y, Sun J, Li J, Xia Z, Jiang Y, Xie X, Xu HE. Cryo-EM structures of adenosine receptor A 3AR bound to selective agonists. Nat Commun 2024; 15:3252. [PMID: 38627384 PMCID: PMC11021478 DOI: 10.1038/s41467-024-47207-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
The adenosine A3 receptor (A3AR), a key member of the G protein-coupled receptor family, is a promising therapeutic target for inflammatory and cancerous conditions. The selective A3AR agonists, CF101 and CF102, are clinically significant, yet their recognition mechanisms remained elusive. Here we report the cryogenic electron microscopy structures of the full-length human A3AR bound to CF101 and CF102 with heterotrimeric Gi protein in complex at 3.3-3.2 Å resolution. These agonists reside in the orthosteric pocket, forming conserved interactions via their adenine moieties, while their 3-iodobenzyl groups exhibit distinct orientations. Functional assays reveal the critical role of extracellular loop 3 in A3AR's ligand selectivity and receptor activation. Key mutations, including His3.37, Ser5.42, and Ser6.52, in a unique sub-pocket of A3AR, significantly impact receptor activation. Comparative analysis with the inactive A2AAR structure highlights a conserved receptor activation mechanism. Our findings provide comprehensive insights into the molecular recognition and signaling of A3AR, paving the way for designing subtype-selective adenosine receptor ligands.
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Affiliation(s)
- Hongmin Cai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Shimeng Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jun Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junrui Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhikan Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yi Jiang
- Lingang Laboratory, Shanghai, China
| | - Xin Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research, Institute for Drug Discovery, Yantai, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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11
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Wang M, Wu Z, Wang J, Weng G, Kang Y, Pan P, Li D, Deng Y, Yao X, Bing Z, Hsieh CY, Hou T. Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. J Chem Inf Model 2024; 64:1213-1228. [PMID: 38302422 DOI: 10.1021/acs.jcim.3c01964] [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: 02/03/2024]
Abstract
Deep learning-based de novo molecular design has recently gained significant attention. While numerous DL-based generative models have been successfully developed for designing novel compounds, the majority of the generated molecules lack sufficiently novel scaffolds or high drug-like profiles. The aforementioned issues may not be fully captured by commonly used metrics for the assessment of molecular generative models, such as novelty, diversity, and quantitative estimation of the drug-likeness score. To address these limitations, we proposed a genetic algorithm-guided generative model called GARel (genetic algorithm-based receptor-ligand interaction generator), a novel framework for training a DL-based generative model to produce drug-like molecules with novel scaffolds. To efficiently train the GARel model, we utilized dense net to update the parameters based on molecules with novel scaffolds and drug-like features. To demonstrate the capability of the GARel model, we used it to design inhibitors for three targets: AA2AR, EGFR, and SARS-Cov2. The results indicate that GARel-generated molecules feature more diverse and novel scaffolds and possess more desirable physicochemical properties and favorable docking scores. Compared with other generative models, GARel makes significant progress in balancing novelty and drug-likeness, providing a promising direction for the further development of DL-based de novo design methodology with potential impacts on drug discovery.
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Affiliation(s)
- Mingyang Wang
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
- CarbonSilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang ,China
| | - Zhengjian Wu
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
- School of Computer Science, Wuhan University, Wuhan 430072, Hubei ,China
| | - Jike Wang
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
- CarbonSilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang ,China
| | - Gaoqi Weng
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Yu Kang
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Peichen Pan
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Dan Li
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Yafeng Deng
- CarbonSilicon AI Technology Co., Ltd., Hangzhou 310018, Zhejiang ,China
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery Macau Institute for Applied Research in Medicine and Health State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Zhitong Bing
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
| | - Chang-Yu Hsieh
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
| | - Tingjun Hou
- College of Pharmaceutical Sciences and Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang ,China
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12
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Stampelou M, Ladds G, Kolocouris A. Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A 3 Receptor. J Phys Chem B 2024; 128:914-936. [PMID: 38236582 DOI: 10.1021/acs.jpcb.3c05986] [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: 01/19/2024]
Abstract
A structure-based drug design pipeline that considers both thermodynamic and kinetic binding data of ligands against a receptor will enable the computational design of improved drug molecules. For unresolved GPCR-ligand complexes, a workflow that can apply both thermodynamic and kinetic binding data in combination with alpha-fold (AF)-derived or other homology models and experimentally resolved binding modes of relevant ligands in GPCR-homologs needs to be tested. Here, as test case, we studied a congeneric set of ligands that bind to a structurally unresolved G protein-coupled receptor (GPCR), the inactive human adenosine A3 receptor (hA3R). We tested three available homology models from which two have been generated from experimental structures of hA1R or hA2AR and one model was a multistate alphafold 2 (AF2)-derived model. We applied alchemical calculations with thermodynamic integration coupled with molecular dynamics (TI/MD) simulations to calculate the experimental relative binding free energies and residence time (τ)-random accelerated MD (τ-RAMD) simulations to calculate the relative residence times (RTs) for antagonists. While the TI/MD calculations produced, for the three homology models, good Pearson correlation coefficients, correspondingly, r = 0.74, 0.62, and 0.67 and mean unsigned error (mue) values of 0.94, 1.31, and 0.81 kcal mol-1, the τ-RAMD method showed r = 0.92 and 0.52 for the first two models but failed to produce accurate results for the multistate AF2-derived model. With subsequent optimization of the AF2-derived model by reorientation of the side chain of R1735.34 located in the extracellular loop 2 (EL2) that blocked ligand's unbinding, the computational model showed r = 0.84 for kinetic data and improved performance for thermodynamic data (r = 0.81, mue = 0.56 kcal mol-1). Overall, after refining the multistate AF2 model with physics-based tools, we were able to show a strong correlation between predicted and experimental ligand relative residence times and affinities, achieving a level of accuracy comparable to an experimental structure. The computational workflow used can be applied to other receptors, helping to rank candidate drugs in a congeneric series and enabling the prioritization of leads with stronger binding affinities and longer residence times.
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Affiliation(s)
- Margarita Stampelou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
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13
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Chauhan A, Singh J, Sangwan N, Avti PK. Mechanistic insights into sodium ion-mediated ligand binding affinity and modulation of 5-HT2B GPCR activity: implications for drug discovery and development. J Recept Signal Transduct Res 2024; 44:8-18. [PMID: 38529713 DOI: 10.1080/10799893.2024.2332886] [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: 10/26/2023] [Accepted: 03/02/2024] [Indexed: 03/27/2024]
Abstract
PURPOSE The G-protein coupled receptor (GPCR) family, implicated in neurological disorders and drug targets, includes the sensitive serotonin receptor subtype, 5-HT2B. The influence of sodium ions on ligand binding at the receptor's allosteric region is being increasingly studied for its impact on receptor structure. METHODS High-throughput virtual screening of three libraries, specifically the Asinex-GPCR library, which contains 8,532 compounds and FDA-approved (2466 compounds) and investigational compounds (2731)) against the modeled receptor [4IB4-5HT2BRM] using the standard agonist/antagonist (Ergotamine/Methysergide), as previously selected from our studies based on ADMET profiling, and further on basis of binding free energy a single compound - dihydroergotamine is chosen. RESULTS This compound displayed strong interactions with the conserved active site. Ions influence ligand binding, with stronger interactions (3-H-bonds and 1-π-bond around 3.35 Å) observed when an agonist and ions are present. Ions entry is guided by conserved motifs in helices III, IV, and VII, which regulate the receptor. Dihydroergotamine, the selected drug, showed binding variance based on ions presence/absence, affecting amino acid residues in these motifs. DCCM and PCA confirmed the stabilization of ligands, with a greater correlation (∼46.6%-PC1) observed with ions. Dihydroergotamine-modified interaction sites within the receptor necessary for activation, serving as a potential 5HT2BRM agonist. RDF analysis showed the sodium ions density around the active site during dihydroergotamine binding. CONCLUSION Our study provides insights into sodium ion mobility's role in controlling ligand binding affinity in 5HT2BR, offering therapeutic development insights.
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Affiliation(s)
- Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Namrata Sangwan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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14
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McIntire WE, Purdy MD, Leonhardt SA, Kucharska I, Hanson MA, Poulos S, Garrison JC, Linden J, Yeager M. G protein β 4 as a structural determinant of enhanced nucleotide exchange in the A 2AAR-Gs complex. RESEARCH SQUARE 2024:rs.3.rs-3814988. [PMID: 38343806 PMCID: PMC10854301 DOI: 10.21203/rs.3.rs-3814988/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Adenosine A2A receptors (A2AAR) evoke pleiotropic intracellular signaling events via activation of the stimulatory heterotrimeric G protein, Gs. Here, we used cryoEM to solve the agonist-bound structure of A2AAR in a complex with full-length Gs α and Gβ4γ2 (A2AAR-Gs α:β4γ2). The orthosteric binding site of A2AAR-Gs α:β4γ2 was similar to other structures of agonist-bound A2AAR, with or without Gs. Unexpectedly, the solvent accessible surface area within the interior of the complex was substantially larger for the complex with Gβ4 versus the closest analog, A2AAR-miniGs α:β1γ2. Consequently, there are fewer interactions between the switch II in Gs α and the Gβ4 torus. In reconstitution experiments Gβ4γ2 displayed a ten-fold higher efficiency over Gβ1γ2 in catalyzing A2AAR dependent GTPγS binding to Gs α. We propose that the less constrained switch II in A2AAR-Gs α:β4γ2 accounts for this increased efficiency. These results suggest that Gβ4 functions as a positive allosteric enhancer versus Gβ1.
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Affiliation(s)
- William E. McIntire
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Michael D. Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
- Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Susan A. Leonhardt
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Iga Kucharska
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Michael A. Hanson
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Sandra Poulos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
| | - James C. Garrison
- Department of Pharmacology, University of Virginia Health System, Charlottesville, VA 22903 Virginia 22908, USA
| | - Joel Linden
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
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15
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Raïch I, Lillo J, Ferreiro-Vera C, Sánchez de Medina V, Navarro G, Franco R. Cannabidiol at Nanomolar Concentrations Negatively Affects Signaling through the Adenosine A 2A Receptor. Int J Mol Sci 2023; 24:17500. [PMID: 38139329 PMCID: PMC10744210 DOI: 10.3390/ijms242417500] [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: 10/28/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cannabidiol (CBD) is a phytocannabinoid with potential as a therapy for a variety of diseases. CBD may act via cannabinoid receptors but also via other G-protein-coupled receptors (GPCRs), including the adenosine A2A receptor. Homogenous binding and signaling assays in Chinese hamster ovary (CHO) cells expressing the human version of the A2A receptor were performed to address the effect of CBD on receptor functionality. CBD was not able to compete for the binding of a SCH 442416 derivative labeled with a red emitting fluorescent probe that is a selective antagonist that binds to the orthosteric site of the receptor. However, CBD reduced the effect of the selective A2A receptor agonist, CGS 21680, on Gs-coupling and on the activation of the mitogen activated kinase signaling pathway. It is suggested that CBD is a negative allosteric modulator of the A2A receptor.
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Affiliation(s)
- Iu Raïch
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08028 Barcelona, Spain; (I.R.); (G.N.)
- CiberNed, Network Center for Neurodegenerative Diseases, Spanish National Health Institute Carlos III, 28029 Madrid, Spain;
| | - Jaume Lillo
- CiberNed, Network Center for Neurodegenerative Diseases, Spanish National Health Institute Carlos III, 28029 Madrid, Spain;
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | | | | | - Gemma Navarro
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08028 Barcelona, Spain; (I.R.); (G.N.)
- CiberNed, Network Center for Neurodegenerative Diseases, Spanish National Health Institute Carlos III, 28029 Madrid, Spain;
- Institute of Neurosciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Rafael Franco
- CiberNed, Network Center for Neurodegenerative Diseases, Spanish National Health Institute Carlos III, 28029 Madrid, Spain;
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
- School of Chemistry, Universitat de Barcelona, 08028 Barcelona, Spain
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16
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Vázquez-Cuevas FG, Reyna-Jeldes M, Velázquez-Miranda E, Coddou C. Transactivation of receptor tyrosine kinases by purinergic P2Y and adenosine receptors. Purinergic Signal 2023; 19:613-621. [PMID: 36529846 PMCID: PMC10754767 DOI: 10.1007/s11302-022-09913-y] [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: 09/20/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Transactivation of receptor tyrosine kinases (RTK) is a crosstalk mechanism exhibited by G-protein-coupled receptors (GPCR) to activate signaling pathways classically associated with growth factors. The discovery of RTK transactivation was a breakthrough in signal transduction that contributed to developing current concepts in intracellular signaling. RTK transactivation links GPCR signaling to important cellular processes, such as cell proliferation and differentiation, and explains the functional diversity of these receptors. Purinergic (P2Y and adenosine) receptors belong to class A of GPCR; in the present work, we systematically review the experimental evidence showing that purinergic receptors have the ability to transactivate RTK in multiple tissues and physiopathological conditions resulting in the modulation of cellular physiology. Of particular relevance, the crosstalk between purinergic receptors and epidermal growth factor receptor is a redundant pathway that participates in multiple pathophysiological processes. Specific and detailed knowledge of purinergic receptor-regulated pathways advances our understanding of the complexity of GPCR signal transduction and opens the way for pharmacologic intervention in the pathological context.
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Affiliation(s)
- F G Vázquez-Cuevas
- Departamento de Neurobiología Celular Y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla # 3001, Juriquilla, Querétaro, 76230, México.
| | - M Reyna-Jeldes
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Larrondo 1281, Coquimbo, 1781421, Chile
- Millennium Nucleus for the Study of Pain (MiNuSPain), Santiago, 8331150, Chile
- Núcleo Para El Estudio del Cáncer a Nivel Básico, Aplicado Y Clínico, Universidad Católica del Norte, Larrondo 1281, Coquimbo , 1781421, Chile
| | - E Velázquez-Miranda
- Departamento de Neurobiología Celular Y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla # 3001, Juriquilla, Querétaro, 76230, México
| | - C Coddou
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Larrondo 1281, Coquimbo, 1781421, Chile.
- Millennium Nucleus for the Study of Pain (MiNuSPain), Santiago, 8331150, Chile.
- Núcleo Para El Estudio del Cáncer a Nivel Básico, Aplicado Y Clínico, Universidad Católica del Norte, Larrondo 1281, Coquimbo , 1781421, Chile.
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17
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Wei S, Pour NG, Tiruvadi-Krishnan S, Ray AP, Thakur N, Eddy MT, Lamichhane R. Single-molecule visualization of human A 2A adenosine receptor activation by a G protein and constitutively activating mutations. Commun Biol 2023; 6:1218. [PMID: 38036689 PMCID: PMC10689853 DOI: 10.1038/s42003-023-05603-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Mutations that constitutively activate G protein-coupled receptors (GPCRs), known as constitutively activating mutations (CAMs), modify cell signaling and interfere with drugs, resulting in diseases with limited treatment options. We utilize fluorescence imaging at the single-molecule level to visualize the dynamic process of CAM-mediated activation of the human A2A adenosine receptor (A2AAR) in real time. We observe an active-state population for all CAMs without agonist stimulation. Importantly, activating mutations significantly increase the population of an intermediate state crucial for receptor activation, notably distinct from the addition of a partner G protein. Activation kinetics show that while CAMs increase the frequency of transitions to the intermediate state, mutations altering sodium sensitivity increase transitions away from it. These findings indicate changes in GPCR function caused by mutations may be predicted based on whether they favor or disfavor formation of an intermediate state, providing a framework for designing receptors with altered functions or therapies that target intermediate states.
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Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Arka Prabha Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA.
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18
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Ramos-Gonzalez N, Paul B, Majumdar S. IUPHAR themed review: Opioid efficacy, bias, and selectivity. Pharmacol Res 2023; 197:106961. [PMID: 37844653 DOI: 10.1016/j.phrs.2023.106961] [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] [Received: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
Drugs acting at the opioid receptor family are clinically used to treat chronic and acute pain, though they represent the second line of treatment behind GABA analogs, antidepressants and SSRI's. Within the opioid family mu and kappa opioid receptor are commonly targeted. However, activation of the mu opioid receptor has side effects of constipation, tolerance, dependence, euphoria, and respiratory depression; activation of the kappa opioid receptor leads to dysphoria and sedation. The side effects of mu opioid receptor activation have led to mu receptor drugs being widely abused with great overdose risk. For these reasons, newer safer opioid analgesics are in high demand. For many years a focus within the opioid field was finding drugs that activated the G protein pathway at mu opioid receptor, without activating the β-arrestin pathway, known as biased agonism. Recent advances have shown that this may not be the way forward to develop safer analgesics at mu opioid receptor, though there is still some promise at the kappa opioid receptor. Here we discuss recent novel approaches to develop safer opioid drugs including efficacy vs bias and fine-tuning receptor activation by targeting sub-pockets in the orthosteric site, we explore recent works on the structural basis of bias, and we put forward the suggestion that Gα subtype selectivity may be an exciting new area of interest.
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Affiliation(s)
- Nokomis Ramos-Gonzalez
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, Saint Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, USA
| | - Barnali Paul
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, Saint Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, USA
| | - Susruta Majumdar
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, Saint Louis, MO, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, MO, USA.
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19
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Garcia PJB, Huang SKH, De Castro-Cruz KA, Leron RB, Tsai PW. In Silico Neuroprotective Effects of Specific Rheum palmatum Metabolites on Parkinson's Disease Targets. Int J Mol Sci 2023; 24:13929. [PMID: 37762232 PMCID: PMC10530814 DOI: 10.3390/ijms241813929] [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: 07/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Parkinson's disease (PD) is one of the large-scale health issues detrimental to human quality of life, and current treatments are only focused on neuroprotection and easing symptoms. This study evaluated in silico binding activity and estimated the stability of major metabolites in the roots of R. palmatum (RP) with main protein targets in Parkinson's disease and their ADMET properties. The major metabolites of RP were subjected to molecular docking and QSAR with α-synuclein, monoamine oxidase isoform B, catechol o-methyltransferase, and A2A adenosine receptor. From this, emodin had the greatest binding activity with Parkinson's disease targets. The chemical stability of the selected compounds was estimated using density functional theory analyses. The docked compounds showed good stability for inhibitory action compared to dopamine and levodopa. According to their structure-activity relationship, aloe-emodin, chrysophanol, emodin, and rhein exhibited good inhibitory activity to specific targets. Finally, mediocre pharmacokinetic properties were observed due to unexceptional blood-brain barrier penetration and safety profile. It was revealed that the major metabolites of RP may have good neuroprotective activity as an additional hit for PD drug development. Also, an association between redox-mediating and activities with PD-relevant protein targets was observed, potentially opening discussion on electrochemical mechanisms with biological functions.
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Affiliation(s)
- Patrick Jay B. Garcia
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines; (P.J.B.G.); (K.A.D.C.-C.); (R.B.L.)
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines
| | - Steven Kuan-Hua Huang
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan;
- Division of Urology, Department of Surgery, Chi Mei Medical Center, Tainan 711, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Kathlia A. De Castro-Cruz
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines; (P.J.B.G.); (K.A.D.C.-C.); (R.B.L.)
| | - Rhoda B. Leron
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines; (P.J.B.G.); (K.A.D.C.-C.); (R.B.L.)
| | - Po-Wei Tsai
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan;
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20
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Jacobson KA, Suresh RR, Oliva P. A 2A adenosine receptor agonists, antagonists, inverse agonists and partial agonists. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2023; 170:1-27. [PMID: 37741687 PMCID: PMC10775762 DOI: 10.1016/bs.irn.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2023]
Abstract
The Gs-coupled A2A adenosine receptor (A2AAR) has been explored extensively as a pharmaceutical target, which has led to numerous clinical trials. However, only one selective A2AAR agonist (regadenoson, Lexiscan) and one selective A2AAR antagonist (istradefylline, Nouriast) have been approved by the FDA, as a pharmacological agent for myocardial perfusion imaging (MPI) and as a cotherapy for Parkinson's disease (PD), respectively. Adenosine is widely used in MPI, as Adenoscan. Despite numerous unsuccessful clinical trials, medicinal chemical activity around A2AAR ligands has accelerated recently, particularly through structure-based drug design. New drug-like A2AAR antagonists for PD and cancer immunotherapy have been identified, and many clinical trials have ensued. For example, imaradenant (AZD4635), a compound that was designed computationally, based on A2AAR X-ray structures and biophysical mapping. Mixed A2AAR/A2BAR antagonists are also hopeful for cancer treatment. A2AAR antagonists may also have potential as neuroprotective agents for treatment of Alzheimer's disease.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States.
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Paola Oliva
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
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21
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Merugu SK, Krishnan K VBR, Kumar K R, Ansari SA, Ansari IA, Bollikolla HB. Synthesis, Anticancer Evaluation and in Silico Studies of 1,4-Dihydropyridines. Chem Biodivers 2023; 20:e202201158. [PMID: 37400965 DOI: 10.1002/cbdv.202201158] [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: 12/06/2022] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
An efficient 1,4-dihydropyridine synthesis under mild conditions has been developed. Numerous substrates were tested, with yields of 1,4-dihydropridines ranging from good to excellent and a wide range of functional group tolerance. A549, HT-29, and HepG2 cancer cells were used to investigate the anticancer efficacy of each of the produced compounds. Additionally, in-silico docking studies were conducted to understand the structure-based features of the anticancer mechanism with the cancer medication target of Adenosine A2A receptor as well as the molecular level interactions of the compounds.
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Affiliation(s)
- Santha Kumari Merugu
- Department of Chemistry, Acharya Nagarjuna University, NNagar, Guntur, 522510, AP-, India
- Department of Chemistry, Government Degree college, Rajhamundry, 533524, AP-, India
| | - V B R Krishnan K
- Department of Chemistry, Acharya Nagarjuna University, NNagar, Guntur, 522510, AP-, India
| | - Ravi Kumar K
- Department of Pharmaceutical Chemistry and Phytochemistry, Nirmala College of Pharmacy, Atmakur, Mangalagiri, Guntur, 522302, AP-, India
| | - Siddique Akber Ansari
- Department of Pharmaceutical chemistry, College of Pharmacy, King Saud University, PO Box.2457, Riyadh, 11451, Saudi Arabia
| | - Irfan Aamer Ansari
- Department of Drug Science & Technology, University of Turin, 10124, Turin, Italy
| | - Hari Babu Bollikolla
- Department of Chemistry, Acharya Nagarjuna University, NNagar, Guntur, 522510, AP-, India
- Department of Nanotechnology, Acharya Nagarjuna University, NNagar, Guntur, 522510, AP, India
- Department of Chemistry, Andhra Kesari University, Ongole, Prakasam Dist, 523 001, AP-, India
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22
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Leonhardt SA, Purdy MD, Grover JR, Yang Z, Poulos S, McIntire WE, Tatham EA, Erramilli SK, Nosol K, Lai KK, Ding S, Lu M, Uchil PD, Finzi A, Rein A, Kossiakoff AA, Mothes W, Yeager M. Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry. Nat Commun 2023; 14:4368. [PMID: 37474505 PMCID: PMC10359404 DOI: 10.1038/s41467-023-39262-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.
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Grants
- P01 AI150471 NIAID NIH HHS
- P41 GM103311 NIGMS NIH HHS
- G20 RR031199 NCRR NIH HHS
- R01 GM117372 NIGMS NIH HHS
- U54 AI170856 NIAID NIH HHS
- S10 OD018149 NIH HHS
- U24 GM129539 NIGMS NIH HHS
- S10 RR025067 NCRR NIH HHS
- This work was supported by the National Institutes of Health (NIH) grants P50 AI15046 and U54 AI170856-01 (M.Y., W.M. and A.K.K.), R01 AI154092 (M.Y.), R01 GM117372 (A.A.K.) and P01 AI150471 (W.M.)., by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, and in part by the NIH Intramural AIDS Targeted Antiviral Program. S.D. and A.F. were supported by the CIHR grant 352417 and a Canada Research Chair. Some molecular graphics and analyses were performed with the University of California, San Francisco Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by the National Institute of General Medical Sciences Grant P41 GM103311).
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Affiliation(s)
- Susan A Leonhardt
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael D Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ziwei Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sandra Poulos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - William E McIntire
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elizabeth A Tatham
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kamil Nosol
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA.
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA.
- Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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23
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Ray AP, Thakur N, Pour NG, Eddy MT. Dual mechanisms of cholesterol-GPCR interactions that depend on membrane phospholipid composition. Structure 2023; 31:836-847.e6. [PMID: 37236187 PMCID: PMC10330489 DOI: 10.1016/j.str.2023.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/25/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023]
Abstract
Cholesterol is a critical component of mammalian cell membranes and an allosteric modulator of G protein-coupled receptors (GPCRs), but divergent views exist on the mechanisms by which cholesterol influences receptor functions. Leveraging the benefits of lipid nanodiscs, i.e., quantitative control of lipid composition, we observe distinct impacts of cholesterol in the presence and absence of anionic phospholipids on the function-related conformational dynamics of the human A2A adenosine receptor (A2AAR). Direct receptor-cholesterol interactions drive activation of agonist-bound A2AAR in membranes containing zwitterionic phospholipids. Intriguingly, the presence of anionic lipids attenuates cholesterol's impact through direct interactions with the receptor, highlighting a more complex role for cholesterol that depends on membrane phospholipid composition. Targeted amino acid replacements at two frequently predicted cholesterol interaction sites showed distinct impacts of cholesterol at different receptor locations, demonstrating the ability to delineate different roles of cholesterol in modulating receptor signaling and maintaining receptor structural integrity.
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Affiliation(s)
- Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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24
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [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: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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25
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Zhang J, Feng D, Cheng J, Wüthrich K. Adenosine A 2A Receptor (A 2AAR) Ligand Screening Using the 19F-NMR Probe FPPA. J Am Chem Soc 2023. [PMID: 37276462 DOI: 10.1021/jacs.3c04218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The binding affinity of G protein-coupled receptor (GPCR) ligands is customarily measured by radio-ligand competition experiments. As an alternative approach, 19F nuclear magnetic resonance spectroscopy (19F-NMR) is used for the screening of small-molecule lead compounds in drug discovery; the two methods are complementary in that the measurements are performed with widely different experimental conditions. Here, we used the structure of the A2A adenosine receptor (A2AAR) complex with V-2006 (3-(4-amino-3-methylbenzyl)-7-(furan-2-yl)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine) as the basis for the design of a fluorine-containing probe molecule, FPPA (4-(furan-2-yl)-7-(4-(trifluoromethyl)benzyl)-7H-pyrrolo[2,3-d]pyramidin-2-amine), for binding studies with A2AAR. A protocol of experimental conditions for drug screening and measurements of drug binding affinities using 1D 19F-NMR observation of FPPA is validated with studies of known A2AAR ligands. 19F-NMR with FPPA is thus found to be a robust approach for the discovery of ligands with new core structures, which will expand the libraries of A2AAR-targeting drug candidates.
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Affiliation(s)
- Jinfeng Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Dandan Feng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- Department of Integrated Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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26
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Matricon P, Nguyen AT, Vo DD, Baltos JA, Jaiteh M, Luttens A, Kampen S, Christopoulos A, Kihlberg J, May LT, Carlsson J. Structure-based virtual screening discovers potent and selective adenosine A 1 receptor antagonists. Eur J Med Chem 2023; 257:115419. [PMID: 37301076 DOI: 10.1016/j.ejmech.2023.115419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023]
Abstract
Development of subtype-selective leads is essential in drug discovery campaigns targeting G protein-coupled receptors (GPCRs). Herein, a structure-based virtual screening approach to rationally design subtype-selective ligands was applied to the A1 and A2A adenosine receptors (A1R and A2AR). Crystal structures of these closely related subtypes revealed a non-conserved subpocket in the binding sites that could be exploited to identify A1R selective ligands. A library of 4.6 million compounds was screened computationally against both receptors using molecular docking and 20 A1R selective ligands were predicted. Of these, seven antagonized the A1R with micromolar activities and several compounds displayed slight selectivity for this subtype. Twenty-seven analogs of two discovered scaffolds were designed, resulting in antagonists with nanomolar potency and up to 76-fold A1R-selectivity. Our results show the potential of structure-based virtual screening to guide discovery and optimization of subtype-selective ligands, which could facilitate the development of safer drugs.
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Affiliation(s)
- Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Anh Tn Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Duc Duy Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Andreas Luttens
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Lauren Therese May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
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27
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Zhao J, Elgeti M, O’Brien ES, Sár CP, EI Daibani A, Heng J, Sun X, Che T, Hubbell WL, Kobilka BK, Chen C. Conformational dynamics of the μ-opioid receptor determine ligand intrinsic efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538657. [PMID: 37163120 PMCID: PMC10168371 DOI: 10.1101/2023.04.28.538657] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The μ-opioid receptor (μOR) is an important target for pain management and the molecular understanding of drug action will facilitate the development of better therapeutics. Here we show, using double electron-electron resonance (DEER) and single-molecule fluorescence resonance energy transfer (smFRET), how ligand-specific conformational changes of the μOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several cytoplasmic receptor conformations interconverting on different timescales, including a pre-activated receptor conformation which is capable of G protein binding, and a fully activated conformation which dramatically lowers GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of G protein Gi.
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Affiliation(s)
- Jiawei Zhao
- Tsinghua-Peaking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University; Beijing, 100084, China
| | - Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California; Los Angeles, Los Angeles, CA 90095, USA
| | - Evan S. O’Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine; Stanford, CA 94305, USA
| | - Cecília P. Sár
- Institute of Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, University of Pécs; Szigeti st. 12, H-7624 Pécs, Hungary
| | - Amal EI Daibani
- Department of Anesthesiology, Washington University School of Medicine; Saint Louis, MO 63110, USA
| | - Jie Heng
- Tsinghua-Peaking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University; Beijing, 100084, China
| | - Xiaoou Sun
- Tsinghua-Peaking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University; Beijing, 100084, China
| | - Tao Che
- Department of Anesthesiology, Washington University School of Medicine; Saint Louis, MO 63110, USA
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California; Los Angeles, Los Angeles, CA 90095, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine; Stanford, CA 94305, USA
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University; Beijing, 100084, China
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28
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Maslov I, Volkov O, Khorn P, Orekhov P, Gusach A, Kuzmichev P, Gerasimov A, Luginina A, Coucke Q, Bogorodskiy A, Gordeliy V, Wanninger S, Barth A, Mishin A, Hofkens J, Cherezov V, Gensch T, Hendrix J, Borshchevskiy V. Sub-millisecond conformational dynamics of the A 2A adenosine receptor revealed by single-molecule FRET. Commun Biol 2023; 6:362. [PMID: 37012383 PMCID: PMC10070357 DOI: 10.1038/s42003-023-04727-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
The complex pharmacology of G-protein-coupled receptors (GPCRs) is defined by their multi-state conformational dynamics. Single-molecule Förster Resonance Energy Transfer (smFRET) is well suited to quantify dynamics for individual protein molecules; however, its application to GPCRs is challenging. Therefore, smFRET has been limited to studies of inter-receptor interactions in cellular membranes and receptors in detergent environments. Here, we performed smFRET experiments on functionally active human A2A adenosine receptor (A2AAR) molecules embedded in freely diffusing lipid nanodiscs to study their intramolecular conformational dynamics. We propose a dynamic model of A2AAR activation that involves a slow (>2 ms) exchange between the active-like and inactive-like conformations in both apo and antagonist-bound A2AAR, explaining the receptor's constitutive activity. For the agonist-bound A2AAR, we detected faster (390 ± 80 µs) ligand efficacy-dependent dynamics. Our work establishes a general smFRET platform for GPCR investigations that can potentially be used for drug screening and/or mechanism-of-action studies.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | | | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Anastasiia Gusach
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Andrey Gerasimov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Vyatka State University, Kirov, Russia
| | - Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Quinten Coucke
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Simon Wanninger
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, HZ, Delft, The Netherlands
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium.
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium.
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
- Joint Institute for Nuclear Research, Dubna, Russian Federation.
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29
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Ye H, Zhao J, Xu X, Zhang D, Shen H, Wang S. Role of adenosine A2a receptor in cancers and autoimmune diseases. Immun Inflamm Dis 2023; 11:e826. [PMID: 37102661 PMCID: PMC10091380 DOI: 10.1002/iid3.826] [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: 08/23/2022] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 04/28/2023] Open
Abstract
Adenosine receptors are P1 class of purinergic receptors that belong to G protein-coupled receptors. There are 4 subtypes of adenosine receptors, namely A1, A2A, A2B, and A3. A2AR has a high affinity for the ligand adenosine. Under pathological conditions or external stimuli, ATP is sequentially hydrolyzed to adenosine by CD39 and CD73. The combination of adenosine and A2AR can increase the concentration of cAMP and activate a series of downstream signaling pathways, and further playing the role of immunosuppression and promotion of tumor invasion. A2AR is expressed to some extent on various immune cells, where it is abnormally expressed on immune cells in cancers and autoimmune diseases. A2AR expression also correlates with disease progression. Inhibitors and agonists of A2AR may be potential new strategies for treatment of cancers and autoimmune diseases. We herein briefly reviewed the expression and distribution of A2AR, adenosine/A2AR signaling pathway, expression, and potential as a therapeutic target.
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Affiliation(s)
- Hongling Ye
- Department of Clinical Laboratory Medicine, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, P.R. China
| | - Junqi Zhao
- Department of Clinical Laboratory Medicine, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, P.R. China
| | - Xuejing Xu
- Department of Clinical Laboratory Medicine, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, P.R. China
| | - Dagan Zhang
- Department of Clinical Laboratory Medicine, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, P.R. China
| | - Han Shen
- Department of Clinical Laboratory Medicine, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, P.R. China
| | - Sen Wang
- Department of Clinical Laboratory Medicine, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, P.R. China
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30
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Yang Y, Kang HJ, Gao R, Wang J, Han GW, DiBerto JF, Wu L, Tong J, Qu L, Wu Y, Pileski R, Li X, Zhang XC, Zhao S, Kenakin T, Wang Q, Stevens RC, Peng W, Roth BL, Rao Z, Liu ZJ. Structural insights into the human niacin receptor HCA2-G i signalling complex. Nat Commun 2023; 14:1692. [PMID: 36973264 PMCID: PMC10043007 DOI: 10.1038/s41467-023-37177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The hydroxycarboxylic acid receptor 2 (HCA2) agonist niacin has been used as treatment for dyslipidemia for several decades albeit with skin flushing as a common side-effect in treated individuals. Extensive efforts have been made to identify HCA2 targeting lipid lowering agents with fewer adverse effects, despite little being known about the molecular basis of HCA2 mediated signalling. Here, we report the cryo-electron microscopy structure of the HCA2-Gi signalling complex with the potent agonist MK-6892, along with crystal structures of HCA2 in inactive state. These structures, together with comprehensive pharmacological analysis, reveal the ligand binding mode and activation and signalling mechanisms of HCA2. This study elucidates the structural determinants essential for HCA2 mediated signalling and provides insights into ligand discovery for HCA2 and related receptors.
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Affiliation(s)
- Yang Yang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hye Jin Kang
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Ruogu Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Wang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Jiahui Tong
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Qu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Ryan Pileski
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
- Department of Obstetrics and Gynecology, Duke University, Durham, NC, USA
| | - Xuemei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Terry Kenakin
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
| | - Quan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | | | - Wei Peng
- Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, 510320, China.
| | - Bryan L Roth
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA.
| | - Zihe Rao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
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31
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Martynowycz MW, Shiriaeva A, Clabbers MTB, Nicolas WJ, Weaver SJ, Hattne J, Gonen T. A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Nat Commun 2023; 14:1086. [PMID: 36841804 PMCID: PMC9968316 DOI: 10.1038/s41467-023-36733-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Crystallizing G protein-coupled receptors (GPCRs) in lipidic cubic phase (LCP) often yields crystals suited for the cryogenic electron microscopy (cryoEM) method microcrystal electron diffraction (MicroED). However, sample preparation is challenging. Embedded crystals cannot be targeted topologically. Here, we use an integrated fluorescence light microscope (iFLM) inside of a focused ion beam and scanning electron microscope (FIB-SEM) to identify fluorescently labeled GPCR crystals. Crystals are targeted using the iFLM and LCP is milled using a plasma focused ion beam (pFIB). The optimal ion source for preparing biological lamellae is identified using standard crystals of proteinase K. Lamellae prepared using either argon or xenon produced the highest quality data and structures. MicroED data are collected from the milled lamellae and the structures are determined. This study outlines a robust approach to identify and mill membrane protein crystals for MicroED and demonstrates plasma ion-beam milling is a powerful tool for preparing biological lamellae.
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Affiliation(s)
- Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Anna Shiriaeva
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - William J Nicolas
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sara J Weaver
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA. .,Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
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32
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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic phospholipids control mechanisms of GPCR-G protein recognition. Nat Commun 2023; 14:794. [PMID: 36781870 PMCID: PMC9925817 DOI: 10.1038/s41467-023-36425-z] [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: 08/10/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we explore the impact of anionic lipids on the function-related conformational equilibria of the human A2A adenosine receptor (A2AAR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids prime the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeds through a less favorable induced fit mechanism. In computational models, anionic lipids mimic interactions between a G protein and positively charged residues in A2AAR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly alters the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA.
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33
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Tzortzini E, Corey RA, Kolocouris A. Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:928-949. [PMID: 36637988 DOI: 10.1021/acs.jcim.2c01181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and the A1 adenosine receptor (A1R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP2)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A1R, three binding sites, and for the inactive A1R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A2AR and A1R. The stability of the identified binding sites to A1R or A2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A2AR have shallow binding free energy minima compared to the related binding sites in A1R, suggesting a stronger binding for cholesterol to A1R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A1R and A2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A1R (i.e., generally higher association rates) compared to A2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A2AR and A1R. Taken together, binding sites of active A1R may be considered as promising allosteric targets.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
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34
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Cornut D, Soulié M, Moreno A, Boussambe GNM, Damian M, Igonet S, Guillet P, Banères JL, Durand G. Non-ionic cholesterol-based additives for the stabilization of membrane proteins. Biochimie 2023; 205:27-39. [PMID: 36586567 DOI: 10.1016/j.biochi.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
We report herein the synthesis of two non-ionic amphiphiles with a cholesterol hydrophobic moiety that can be used as chemical additives for biochemical studies of membrane proteins. They were designed to show a high similarity with the planar steroid core of cholesterol and small-to-medium polar head groups attached at the C3 position of ring-A on the sterol skeleton. The two Chol-Tris and Chol-DG have a Tris-hydroxymethyl and a branched diglucose polar head group, respectively, which provide them sufficient water solubility when mixed with the "gold standard" detergent n-Dodecyl-β-D-Maltoside (DDM). The colloidal properties of these mixed micelles were investigated by means of surface tension (SFT) measurements and dynamic light scattering (DLS) experiments and showed the formation of globular micelles of about 8 nm in diameter with a critical micellar concentration of 0.20 mM for DDM:Chol-DG and 0.22 mM for DDM:Chol-Tris. We showed that mixed micelles do not alter the extraction potency of a G-protein coupled receptor (GPCR): the human adenosine A2A receptor (A2AR). The thermostabilizing effect of the mixed micelles was confirmed on two GPCRs, A2AR and the growth hormone secretagogue receptor (GHSR). Finally, these two mixed micelles were found suitable for the purification of an active form of A2AR which remained able to bind two ligands of different class i.e. the specific agonist CGS-21680 and the specific inverse agonist ZM-241385. This suggests that Chol-Tris and Chol-DG may be used as a non-ionic alternative to the cholesteryl hemisuccinate (CHS) stabilizing agent.
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Affiliation(s)
- Damien Cornut
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM & Avignon Université, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France; CHEM2STAB, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France
| | - Marine Soulié
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM & Avignon Université, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France; CHEM2STAB, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France
| | | | - Gildas Nyame Mendendy Boussambe
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM & Avignon Université, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France; CHEM2STAB, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM, 1919 route de Mende, 34293, Montpellier, Cedex 5, France
| | | | - Pierre Guillet
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM & Avignon Université, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France; CHEM2STAB, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM, 1919 route de Mende, 34293, Montpellier, Cedex 5, France
| | - Grégory Durand
- Institut des Biomolécules Max Mousseron UMR 5247 UM-CNRS-ENSCM & Avignon Université, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France; CHEM2STAB, 301 rue Baruch de Spinoza, 84916, Avignon, Cedex 9, France.
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35
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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic Phospholipids Control Mechanisms of GPCR-G Protein Recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523010. [PMID: 36711594 PMCID: PMC9882065 DOI: 10.1101/2023.01.11.523010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we visualized the impact of anionic lipids on the function-related conformational equilibria of the human A 2A adenosine receptor (A 2A AR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids primed the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeded through a less favorable induced fit mechanism. In computational models, anionic lipids mimicked interactions between a G protein and positively charged residues in A 2A AR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly altered the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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36
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Abstract
GPR21 is a class-A orphan G protein-coupled receptor (GPCR) and a potential therapeutic target for type 2 diabetes and other metabolic disorders. This receptor shows high basal activity in coupling to multiple G proteins in the absence of any known endogenous agonist or synthetic ligand. Here, we present the structures of ligand-free human GPR21 bound to heterotrimeric miniGs and miniG15 proteins, respectively. We identified an agonist-like motif in extracellular loop 2 (ECL2) that occupies the orthosteric pocket and promotes receptor activation. A side pocket that may be employed as a new ligand binding site was also uncovered. Remarkably, G protein binding is accommodated by a flexible cytoplasmic portion of transmembrane helix 6 (TM6) which adopts little or undetectable outward movement. These findings will enable the design of modulators for GPR21 for understanding its signal transduction and exploring opportunity for deorphanization.
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37
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Han R, Yoon H, Yoo J, Lee Y. Systematic analyses of the sequence conservation and ligand interaction patterns of purinergic P1 and P2Y receptors provide a structural basis for receptor selectivity. Comput Struct Biotechnol J 2023; 21:889-898. [PMID: 36698973 PMCID: PMC9860165 DOI: 10.1016/j.csbj.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023] Open
Abstract
Purinergic receptors are membrane proteins that regulate numerous cellular functions by catalyzing reactions involving purine nucleotides or nucleosides. Among the three receptor families, i.e., P1, P2X, and P2Y, the P1 and P2Y receptors share common structural features of class A GPCR. Comprehensive sequence and structural analysis revealed that the P1 and P2Y receptors belong to two distinct groups. They exhibit different ligand-binding site features that can distinguish between specific activators. These specific amino acid residues in the binding cavity may be involved in the selectivity and unique pharmacological behavior of each subtype. In this study, we conducted a structure-based analysis of purinergic P1 and P2Y receptors to identify their evolutionary signature and obtain structural insights into ligand recognition and selectivity. The structural features of the P1 and P2Y receptor classes were compared based on sequence conservation and ligand interaction patterns. Orthologous protein sequences were collected for the P1 and P2Y receptors, and sequence conservation was calculated based on Shannon entropy to identify highly conserved residues. To analyze the ligand interaction patterns, we performed docking studies on the P1 and P2Y receptors using known ligand information extracted from the ChEMBL database. We analyzed how the conserved residues are related to ligand-binding sites and how the key interacting residues differ between P1 and P2Y receptors, or between agonists and antagonists. We extracted new similarities and differences between the receptor subtypes, and the results can be used for designing new ligands by predicting hotspot residues that are important for functional selectivity.
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38
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Wang X, Stephen Chan HC, Yuan S. Modeling of Olfactory Receptors. Methods Mol Biol 2023; 2627:183-193. [PMID: 36959448 DOI: 10.1007/978-1-0716-2974-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Olfactory receptors (ORs) form the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date. Homology modeling has become a popular strategy to propose plausible OR models, in order to study the structure-function relationships of the receptors and to aid the discovery and development of ligands capable of modulating receptor activity. In this chapter, we provide a general guideline for OR structure construction, including the collection of candidate templates, structure-based sequence alignment, 3D structure construction, ligand docking, and molecular dynamic simulation.
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Affiliation(s)
- Xueying Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - H C Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China.
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39
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Chen Y, Zhang J, Weng Y, Xu Y, Lu W, Liu W, Liu M, Hua T, Song G. Cryo-EM structure of the human adenosine A 2B receptor-G s signaling complex. SCIENCE ADVANCES 2022; 8:eadd3709. [PMID: 36563137 PMCID: PMC9788782 DOI: 10.1126/sciadv.add3709] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/22/2022] [Indexed: 06/03/2023]
Abstract
The human adenosine A2B receptor (A2BR) is a class A G protein-coupled receptor that is involved in several major physiological and pathological processes throughout the body. A2BR recognizes its ligands adenosine and NECA with relatively low affinity, but the detailed mechanism for its ligand recognition and signaling is still elusive. Here, we present two structures determined by cryo-electron microscopy of A2BR bound to its agonists NECA and BAY60-6583, each coupled to an engineered Gs protein. The structures reveal conserved orthosteric binding pockets with subtle differences, whereas the selectivity or specificity can mainly be attributed to regions extended from the orthosteric pocket. We also found that BAY60-6583 occupies a secondary pocket, where residues V2506.51 and N2737.36 were two key determinants for its selectivity against A2BR. This study offers a better understanding of ligand selectivity for the adenosine receptor family and provides a structural template for further development of A2BR ligands for related diseases.
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Affiliation(s)
- Ying Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jinyi Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuan Weng
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yueming Xu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiqiang Lu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gaojie Song
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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40
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Ferré G, Anazia K, Silva LO, Thakur N, Ray AP, Eddy MT. Global insights into the fine tuning of human A 2AAR conformational dynamics in a ternary complex with an engineered G protein viewed by NMR. Cell Rep 2022; 41:111844. [PMID: 36543140 PMCID: PMC9832913 DOI: 10.1016/j.celrep.2022.111844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptor (GPCR) conformational plasticity enables formation of ternary signaling complexes with intracellular proteins in response to binding extracellular ligands. We investigate the dynamic process of GPCR complex formation in solution with the human A2A adenosine receptor (A2AAR) and an engineered Gs protein, mini-Gs. 2D nuclear magnetic resonance (NMR) data with uniform stable isotope-labeled A2AAR enabled a global comparison of A2AAR conformations between complexes with an agonist and mini-Gs and with an agonist alone. The two conformations are similar and show subtle differences at the receptor intracellular surface, supporting a model whereby agonist binding alone is sufficient to populate a conformation resembling the active state. However, an A2AAR "hot spot" connecting the extracellular ligand-binding pocket to the intracellular surface is observed to be highly dynamic in the ternary complex, suggesting a mechanism for allosteric connection between the bound G protein and the drug-binding pocket involving structural plasticity of the "toggle switch" tryptophan.
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Affiliation(s)
- Guillaume Ferré
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA,Present address: Institut de Pharmacologie et Biologie Structurale; Université de Toulouse, CNRS, Université Paul Sabatier; Toulouse 31000, France
| | - Kara Anazia
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Larissa O. Silva
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Naveen Thakur
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Arka P. Ray
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA,Lead contact,Correspondence:
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41
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Muzychka LV, Verves EV, Yaremchuk IO, Zinchenko AM, Shishkina SV, Semenyuta IV, Hodyna DM, Metelytsia LO, Kovalishyn V, Smolii OB. Synthesis, QSAR modeling, and molecular docking of novel fused 7-deazaxanthine derivatives as adenosine A 2A receptor antagonists. Chem Biol Drug Des 2022; 100:1025-1032. [PMID: 34651417 DOI: 10.1111/cbdd.13975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/21/2021] [Accepted: 10/10/2021] [Indexed: 01/25/2023]
Abstract
Predictive QSAR models for the search of new adenosine A2A receptor antagonists were developed by using OCHEM platform. The predictive ability of the regression models has coefficient of determination q2 = 0.65-0.71 with cross-validation and independent test set. The inhibition activities of novel fused 7-deazaxanthine compounds were predicted by the developed QSAR models. A preparative method for the synthesis of pyrimido[5',4':4,5]pyrrolo[1,2-a][1,4]diazepine derivatives was developed, and 11 new adenosine A2A receptor antagonists were obtained. Preliminary investigations into the toxicology of fused 7-deazaxanthine compounds toward commonly used model organism to assess toxicity invertebrate cladoceran D. magna were also described.
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Affiliation(s)
- Liubov V Muzychka
- Department of Chemistry of Natural Compounds, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Evgenii V Verves
- Department of Chemistry of Natural Compounds, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine.,Enamine Ltd, Kyiv, Ukraine
| | - Iryna O Yaremchuk
- Department of Chemistry of Natural Compounds, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Anna M Zinchenko
- Department of Chemistry of Natural Compounds, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Svitlana V Shishkina
- Department of X-ray Diffraction Studies and Quantum Chemistry, STC "Institute for Single Crystals", NAS of Ukraine, Kharkiv, Ukraine
| | - Ivan V Semenyuta
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Diana M Hodyna
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Larysa O Metelytsia
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Vasyl Kovalishyn
- Department of Medical and Biological Researches, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Oleg B Smolii
- Department of Chemistry of Natural Compounds, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
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42
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Stäubert C, Wozniak M, Dupuis N, Laschet C, Pillaiyar T, Hanson J. Superconserved receptors expressed in the brain: Expression, function, motifs and evolution of an orphan receptor family. Pharmacol Ther 2022; 240:108217. [PMID: 35644261 DOI: 10.1016/j.pharmthera.2022.108217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/14/2022]
Abstract
GPR27, GPR85 and GPR173 constitute a small family of G protein-coupled receptors (GPCR) that share the distinctive characteristics of being highly conserved throughout vertebrate evolution and predominantly expressed in the brain. Accordingly, they have been coined as "Superconserved Receptors Expressed in the Brain" (SREB), although their expression profile is more complex than what was originally thought. SREBs have no known validated endogenous ligands and are thus labeled as "orphan" receptors. The investigation of this particular category of uncharacterized receptors holds great promise both in terms of physiology and drug development. In the largest GPCR family, the Rhodopsin-like or Class A, around 100 receptors are considered orphans. Because GPCRs are the most successful source of drug targets, the discovery of a novel function or ligand most likely will lead to significant breakthroughs for the discovery of innovative therapies. The high level of conservation is one of the characteristic features of the SREBs. We propose herein a detailed analysis of the putative evolutionary origin of this family. We highlight the properties that distinguish SREBs from other rhodopsin-like GPCRs. We present the current evidence for these receptors downstream signaling pathways and functions. We discuss the pharmacological challenge for the identification of natural or synthetic ligands of orphan receptors like SREBs. The different SREB-related scientific questions are presented with a highlight on what should be addressed in the near future, including the confirmation of published evidence and their validation as drug targets. In particular, we discuss in which pathological conditions these receptors may be of great relevance to solve unmet medical needs.
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Affiliation(s)
- Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Nadine Dupuis
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Céline Laschet
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium; Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines, University of Liège, Liège, Belgium.
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43
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Nucleoside transporters and immunosuppressive adenosine signaling in the tumor microenvironment: Potential therapeutic opportunities. Pharmacol Ther 2022; 240:108300. [PMID: 36283452 DOI: 10.1016/j.pharmthera.2022.108300] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
Adenosine compartmentalization has a profound impact on immune cell function by regulating adenosine localization and, therefore, extracellular signaling capabilities, which suppresses immune cell function in the tumor microenvironment. Nucleoside transporters, responsible for the translocation and cellular compartmentalization of hydrophilic adenosine, represent an understudied yet crucial component of adenosine disposition in the tumor microenvironment. In this review article, we will summarize what is known regarding nucleoside transporter's function within the purinome in relation to currently devised points of intervention (i.e., ectonucleotidases, adenosine receptors) for cancer immunotherapy, alterations in nucleoside transporter expression reported in cancer, and potential avenues for targeting of nucleoside transporters for the desired modulation of adenosine compartmentalization and action. Further, we put forward that nucleoside transporters are an unexplored therapeutic opportunity, and modulation of nucleoside transport processes could attenuate the pathogenic buildup of immunosuppressive adenosine in solid tumors, particularly those enriched with nucleoside transport proteins.
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44
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Qian Y, Wang J, Yang L, Liu Y, Wang L, Liu W, Lin Y, Yang H, Ma L, Ye S, Wu S, Qiao A. Activation and signaling mechanism revealed by GPR119-G s complex structures. Nat Commun 2022; 13:7033. [PMID: 36396650 PMCID: PMC9671963 DOI: 10.1038/s41467-022-34696-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
Agonists selectively targeting cannabinoid receptor-like G-protein-coupled receptor (GPCR) GPR119 hold promise for treating metabolic disorders while avoiding unwanted side effects. Here we present the cryo-electron microscopy (cryo-EM) structures of the human GPR119-Gs signaling complexes bound to AR231453 and MBX-2982, two representative agonists reported for GPR119. The structures reveal a one-amino acid shift of the conserved proline residue of TM5 that forms an outward bulge, opening up a hydrophobic cavity between TM4 and TM5 at the middle of the membrane for its endogenous ligands-monounsaturated lipid metabolites. In addition, we observed a salt bridge between ICL1 of GPR119 and Gβs. Disruption of the salt bridge eliminates the cAMP production of GPR119, indicating an important role of Gβs in GPR119-mediated signaling. Our structures, together with mutagenesis studies, illustrate the conserved binding mode of the chemically different agonists, and provide insights into the conformational changes in receptor activation and G protein coupling.
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Affiliation(s)
- Yuxia Qian
- grid.33763.320000 0004 1761 2484Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P. R. China
| | - Jiening Wang
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei China
| | - Linlin Yang
- grid.207374.50000 0001 2189 3846Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanru Liu
- grid.33763.320000 0004 1761 2484Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P. R. China
| | - Lina Wang
- grid.207374.50000 0001 2189 3846Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Wei Liu
- grid.33763.320000 0004 1761 2484Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P. R. China
| | - Yun Lin
- grid.33763.320000 0004 1761 2484Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P. R. China
| | - Hong Yang
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei China
| | - Lixin Ma
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei China
| | - Sheng Ye
- grid.33763.320000 0004 1761 2484Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P. R. China ,grid.13402.340000 0004 1759 700XLife Sciences Institute, Zhejiang University, Hangzhou, Zhejiang China
| | - Shan Wu
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei China
| | - Anna Qiao
- grid.33763.320000 0004 1761 2484Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P. R. China
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45
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Stampelou M, Suchankova A, Tzortzini E, Dhingra L, Barkan K, Lougiakis N, Marakos P, Pouli N, Ladds G, Kolocouris A. Dual A1/A3 Adenosine Receptor Antagonists: Binding Kinetics and Structure-Activity Relationship Studies Using Mutagenesis and Alchemical Binding Free Energy Calculations. J Med Chem 2022; 65:13305-13327. [PMID: 36173355 DOI: 10.1021/acs.jmedchem.2c01123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drugs targeting adenosine receptors (AR) can provide treatment for diseases. We report the identification of 7-(phenylamino)-pyrazolo[3,4-c]pyridines L2-L10, A15, and A17 as low-micromolar to low-nanomolar A1R/A3R dual antagonists, with 3-phenyl-5-cyano-7-(trimethoxyphenylamino)-pyrazolo[3,4-c]pyridine (A17) displaying the highest affinity at both receptors with a long residence time of binding, as determined using a NanoBRET-based assay. Two binding orientations of A17 produce stable complexes inside the orthosteric binding area of A1R in molecular dynamics (MD) simulations, and we selected the most plausible orientation based on the agreement with alanine mutagenesis supported by affinity experiments. Interestingly, for drug design purposes, the mutation of L2506.51 to alanine increased the binding affinity of A17 at A1R. We explored the structure-activity relationships against A1R using alchemical binding free energy calculations with the thermodynamic integration coupled with the MD simulation (TI/MD) method, applied on the whole G-protein-coupled receptor-membrane system, which showed a good agreement (r = 0.73) between calculated and experimental relative binding free energies.
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Affiliation(s)
- Margarita Stampelou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Anna Suchankova
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Lakshiv Dhingra
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Kerry Barkan
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Nikolaos Lougiakis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Panagiotis Marakos
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Nicole Pouli
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
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46
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Akhunzada MJ, Yoon HJ, Deb I, Braka A, Wu S. Bell-Evans model and steered molecular dynamics in uncovering the dissociation kinetics of ligands targeting G-protein-coupled receptors. Sci Rep 2022; 12:15972. [PMID: 36153364 PMCID: PMC9509322 DOI: 10.1038/s41598-022-20065-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/08/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractRecently, academic and industrial scientific communities involved in kinetics-based drug development have become immensely interested in predicting the drug target residence time. Screening drug candidates in terms of their computationally predicted residence times, which is a measure of drug efficacy in vivo, and simultaneously assessing computational binding affinities are becoming inevitable. Non-equilibrium molecular simulation approaches are proven to be useful in this purpose. Here, we have implemented an optimized approach of combining the data derived from steered molecular dynamics simulations and the Bell-Evans model to predict the absolute residence times of the antagonist ZMA241385 and agonist NECA that target the A2A adenosine receptor of the G-protein-coupled receptor (GPCR) protein family. We have predicted the absolute ligand residence times on the timescale of seconds. However, our predictions were many folds shorter than those determined experimentally. Additionally, we calculated the thermodynamics of ligand binding in terms of ligand binding energies and the per-residue contribution of the receptor. Subsequently, binding pocket hotspot residues that would be important for further computational mutagenesis studies were identified. In the experiment, similar sets of residues were found to be in significant contact with both ligands under study. Our results build a strong foundation for further improvement of our approach by rationalizing the kinetics of ligand unbinding with the thermodynamics of ligand binding.
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47
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GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A 2A Adenosine Receptor. J Med Chem 2022; 65:11648-11657. [PMID: 35977382 PMCID: PMC9469204 DOI: 10.1021/acs.jmedchem.2c00462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Modulators of the G protein-coupled A2A adenosine
receptor
(A2AAR) have been considered promising agents to treat
Parkinson’s disease, inflammation, cancer, and central nervous
system disorders. Herein, we demonstrate that a thiophene modification
at the C8 position in the common adenine scaffold converted an A2AAR agonist into an antagonist. We synthesized and characterized
a novel A2AAR antagonist, 2 (LJ-4517), with Ki = 18.3 nM. X-ray crystallographic structures
of 2 in complex with two thermostabilized A2AAR constructs were solved at 2.05 and 2.80 Å resolutions. In
contrast to A2AAR agonists, which simultaneously interact
with both Ser2777.42 and His2787.43, 2 only transiently contacts His2787.43, which can be direct
or water-mediated. The n-hexynyl group of 2 extends into an A2AAR exosite. Structural analysis revealed
that the introduced thiophene modification restricted receptor conformational
rearrangements required for subsequent activation. This approach can
expand the repertoire of adenosine receptor antagonists that can be
designed based on available agonist scaffolds.
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48
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Abiko LA, Dias Teixeira R, Engilberge S, Grahl A, Mühlethaler T, Sharpe T, Grzesiek S. Filling of a water-free void explains the allosteric regulation of the β 1-adrenergic receptor by cholesterol. Nat Chem 2022; 14:1133-1141. [PMID: 35953642 DOI: 10.1038/s41557-022-01009-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
Recent high-pressure NMR results indicate that the preactive conformation of the β1-adrenergic receptor (β1AR) harbours completely empty cavities of ~100 Å3 volume, which disappear in the active conformation of the receptor. Here we have localized these cavities using X-ray crystallography of xenon-derivatized β1AR crystals. One of the cavities is in direct contact with the cholesterol-binding pocket. Solution NMR shows that addition of the cholesterol analogue cholesteryl hemisuccinate impedes the formation of the active conformation of detergent-solubilized β1AR by blocking conserved G protein-coupled receptor microswitches, concomitant with an affinity reduction of both isoprenaline and G protein-mimicking nanobody Nb80 for β1AR detected by isothermal titration calorimetry. This wedge-like action explains the function of cholesterol as a negative allosteric modulator of β1AR. A detailed understanding of G protein-coupled receptor regulation by cholesterol by filling of a dry void and the easy scouting for such voids by xenon may provide new routes for the development of allosteric drugs.
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Affiliation(s)
| | | | - Sylvain Engilberge
- Paul Scherrer Institut, Villigen, Switzerland.,European Synchrotron Radiation Facility, Grenoble, France
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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49
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Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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50
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Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions. Molecules 2022; 27:molecules27154676. [PMID: 35897852 PMCID: PMC9331671 DOI: 10.3390/molecules27154676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
The adenosine A2A receptor (A2AAR) is a class A G-protein-coupled receptor (GPCR). It is an immune checkpoint in the tumor micro-environment and has become an emerging target for cancer treatment. In this study, we aimed to explore the effects of cancer-patient-derived A2AAR mutations on ligand binding and receptor functions. The wild-type A2AAR and 15 mutants identified by Genomic Data Commons (GDC) in human cancers were expressed in HEK293T cells. Firstly, we found that the binding affinity for agonist NECA was decreased in six mutants but increased for the V275A mutant. Mutations A165V and A265V decreased the binding affinity for antagonist ZM241385. Secondly, we found that the potency of NECA (EC50) in an impedance-based cell-morphology assay was mostly correlated with the binding affinity for the different mutants. Moreover, S132L and H278N were found to shift the A2AAR towards the inactive state. Importantly, we found that ZM241385 could not inhibit the activation of V275A and P285L stimulated by NECA. Taken together, the cancer-associated mutations of A2AAR modulated ligand binding and receptor functions. This study provides fundamental insights into the structure–activity relationship of the A2AAR and provides insights for A2AAR-related personalized treatment in cancer.
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