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Li X, Zhang X, Wen X, Zhang D, Qu C, Miao X, Zhang W, Zhang R, Liu G, Xiao P, Sun JP, Gong W. Structural basis for ligand recognition and activation of the prostanoid receptors. Cell Rep 2024; 43:113893. [PMID: 38446662 DOI: 10.1016/j.celrep.2024.113893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/16/2024] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Prostaglandin F2α (PGF2α) and thromboxane A2 (TXA2) are endogenous arachidonic acid metabolites, modulating diverse physiological processes including inflammation and cardiovascular homeostasis through activating PGF2α receptor (FP) and TXA2 receptor (TP). Ligands targeting FP and TP have demonstrated efficacy in treating conditions like glaucoma and cardiovascular diseases in humans, as well as reproductive-related diseases in animals. Here, we present five cryoelectron microscopy structures illustrating FP and TP in complex with Gq and bound to PGF2α (endogenous ligand), latanoprost acid (a clinical drug), and two other synthetic agonists. Combined with mutational and functional studies, these structures reveal not only structural features for the specific recognition of endogenous ligands and attainment of receptor selectivity of FP and TP but also the common mechanisms of receptor activation and Gq protein coupling. The findings may enrich our knowledge of ligand recognition and signal transduction of the prostanoid receptor family and facilitate rational ligand design toward these two receptors.
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Affiliation(s)
- Xiu Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xuan Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Xin Wen
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Daolai Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Changxiu Qu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xinyi Miao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Wenkai Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Ru Zhang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Guibing Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing 100191, China; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| | - Weimin Gong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China.
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2
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VanSchouwen B, Melacini G. Probing ligand selectivity in pathogens. eLife 2023; 12:e94720. [PMID: 38126364 PMCID: PMC10735216 DOI: 10.7554/elife.94720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Why does protein kinase A respond to purine nucleosides in certain pathogens, but not to the cyclic nucleotides that activate this kinase in most other organisms?
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster UniversityHamiltonCanada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, and the Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamiltonCanada
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3
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Zhu S, Yuan Q, Li X, He X, Shen S, Wang D, Li J, Cheng X, Duan X, Xu HE, Duan J. Molecular recognition of niacin and lipid-lowering drugs by the human hydroxycarboxylic acid receptor 2. Cell Rep 2023; 42:113406. [PMID: 37952153 DOI: 10.1016/j.celrep.2023.113406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/26/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Niacin, an age-old lipid-lowering drug, acts through the hydroxycarboxylic acid receptor 2 (HCAR2), a G-protein-coupled receptor (GPCR). Yet, its use is hindered by side effects like skin flushing. To address this, specific HCAR2 agonists, like MK-6892 and GSK256073, with fewer adverse effects have been created. However, the activation mechanism of HCAR2 by niacin and these new agonists is not well understood. Here, we present three cryoelectron microscopy structures of Gi-coupled HCAR2 bound to niacin, MK-6892, and GSK256073. Our findings show that different ligands induce varying binding pockets in HCAR2, influenced by aromatic amino acid clusters (W91ECL1, H1614.59, W1885.38, H1895.39, and F1935.43) from receptors ECL1, TM4, and TM5. Additionally, conserved residues R1113.36 and Y2847.43, unique to the HCA receptor family, likely initiate activation signal propagation in HCAR2. This study provides insights into ligand recognition, receptor activation, and G protein coupling mediated by HCAR2, laying the groundwork for developing HCAR2-targeted drugs.
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Affiliation(s)
- Shengnan Zhu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau 999078, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Pharmacology, Guilin Medical University, Guilin 541004, China
| | - Qingning Yuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xinzhu Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shiyi Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dongxue Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Junrui Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, China
| | - Xiaoqun Duan
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau 999078, China; Department of Pharmacology, Guilin Medical University, Guilin 541004, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Jia Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China.
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4
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Son J, Choi W, Kim H, Kim M, Lee JH, Shin SC, Kim HW. Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4. IUCrJ 2023; 10:220-232. [PMID: 36862488 PMCID: PMC9980389 DOI: 10.1107/s2052252523001562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure-function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix-turn-helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.
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Affiliation(s)
- Jonghyeon Son
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- New Drug Development Center, Daegu–Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Woong Choi
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hyun Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Minseo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
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5
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Wang Y, Zhuang Y, DiBerto JF, Zhou XE, Schmitz GP, Yuan Q, Jain MK, Liu W, Melcher K, Jiang Y, Roth BL, Xu HE. Structures of the entire human opioid receptor family. Cell 2023; 186:413-427.e17. [PMID: 36638794 DOI: 10.1016/j.cell.2022.12.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/11/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023]
Abstract
Opioids are effective analgesics, but their use is beset by serious side effects, including addiction and respiratory depression, which contribute to the ongoing opioid crisis. The human opioid system contains four opioid receptors (μOR, δOR, κOR, and NOPR) and a set of related endogenous opioid peptides (EOPs), which show distinct selectivity toward their respective opioid receptors (ORs). Despite being key to the development of safer analgesics, the mechanisms of molecular recognition and selectivity of EOPs to ORs remain unclear. Here, we systematically characterize the binding of EOPs to ORs and present five structures of EOP-OR-Gi complexes, including β-endorphin- and endomorphin-bound μOR, deltorphin-bound δOR, dynorphin-bound κOR, and nociceptin-bound NOPR. These structures, supported by biochemical results, uncover the specific recognition and selectivity of opioid peptides and the conserved mechanism of opioid receptor activation. These results provide a structural framework to facilitate rational design of safer opioid drugs for pain relief.
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Affiliation(s)
- Yue Wang
- The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youwen Zhuang
- The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jeffrey F DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - X Edward Zhou
- Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gavin P Schmitz
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Qingning Yuan
- The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Manish K Jain
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Weiyi Liu
- The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karsten Melcher
- Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Lingang Laboratory, Shanghai 200031, China
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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6
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Shim T, Pacalon J, Kim WC, Cong X, Topin J, Golebiowski J, Moon C. The Third Extracellular Loop of Mammalian Odorant Receptors Is Involved in Ligand Binding. Int J Mol Sci 2022; 23. [PMID: 36293357 DOI: 10.3390/ijms232012501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/22/2022] [Accepted: 10/06/2022] [Indexed: 12/30/2022] Open
Abstract
Mammals recognize chemicals in the air via G protein-coupled odorant receptors (ORs). In addition to their orthosteric binding site, other segments of these receptors modulate ligand recognition. Focusing on human hOR1A1, which is considered prototypical of class II ORs, we used a combination of molecular modeling, site-directed mutagenesis, and in vitro functional assays. We showed that the third extracellular loop of ORs (ECL3) contributes to ligand recognition and receptor activation. Indeed, site-directed mutations in ECL3 showed differential effects on the potency and efficacy of both carvones, citronellol, and 2-nonanone.
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Wu G, Sharina I, Martin E. Soluble guanylyl cyclase: Molecular basis for ligand selectivity and action in vitro and in vivo. Front Mol Biosci 2022; 9:1007768. [PMID: 36304925 PMCID: PMC9592903 DOI: 10.3389/fmolb.2022.1007768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/27/2022] [Indexed: 01/14/2023] Open
Abstract
Nitric oxide (NO), carbon monoxide (CO), oxygen (O2), hydrogen sulfide (H2S) are gaseous molecules that play important roles in the physiology and pathophysiology of eukaryotes. Tissue concentrations of these physiologically relevant gases vary remarkable from nM range for NO to high μM range of O2. Various hemoproteins play a significant role in sensing and transducing cellular signals encoded by gaseous molecules or in transporting them. Soluble guanylyl cyclase (sGC) is a hemoprotein that plays vital roles in a wide range of physiological functions and combines the functions of gaseous sensor and signal transducer. sGC uniquely evolved to sense low non-toxic levels of NO and respond to elevated NO levels by increasing its catalytic ability to generate the secondary signaling messenger cyclic guanosine monophosphate (cGMP). This review discusses sGC's gaseous ligand selectivity and the molecular basis for sGC function as high-affinity and selectivity NO receptor. The effects of other gaseous molecules and small molecules of cellular origin on sGC's function are also discussed.
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Affiliation(s)
- Gang Wu
- Hematology-Oncology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States,*Correspondence: Gang Wu, ; Emil Martin,
| | - Iraida Sharina
- Cardiology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States
| | - Emil Martin
- Cardiology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States,*Correspondence: Gang Wu, ; Emil Martin,
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8
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Singh KD, Karnik SS. Structural perspectives on the mechanism of signal activation, ligand selectivity and allosteric modulation in angiotensin receptors: IUPHAR Review 34. Br J Pharmacol 2022; 179:4461-4472. [PMID: 35318654 PMCID: PMC9398925 DOI: 10.1111/bph.15840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Functional advances have guided our knowledge of physiological and fatal pathological mechanisms of the hormone angiotensin II (AngII) and its antagonists. Such studies revealed that tissue response to a given dose of the hormone or its antagonist depends on receptors that engage the ligand. Thus, we need to know much more about the structures of receptor-ligand complexes at high resolution. Recently, X-ray structures of both AngII receptors (AT1 and AT2 receptors) bound to peptide and non-peptide ligands have been elucidated, providing new opportunities to examine the dynamic fluxes in the 3D architecture of the receptors, as the basis of ligand selectivity, efficacy, and regulation of the molecular functions of the receptors. Constituent structural motifs cooperatively transform ligand selectivity into specific functions, thus conceptualizing the primacy of the 3D structure over individual motifs of receptors. This review covers the new data elucidating the structural dynamics of AngII receptors and how structural knowledge can be transformative in understanding the mechanisms underlying the physiology of AngII.
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Affiliation(s)
- Khuraijam Dhanachandra Singh
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Sadashiva S. Karnik
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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Huang S, Xu P, Shen DD, Simon IA, Mao C, Tan Y, Zhang H, Harpsøe K, Li H, Zhang Y, You C, Yu X, Jiang Y, Zhang Y, Gloriam DE, Xu HE. GPCRs steer G i and G s selectivity via TM5-TM6 switches as revealed by structures of serotonin receptors. Mol Cell 2022; 82:2681-2695.e6. [PMID: 35714614 DOI: 10.1016/j.molcel.2022.05.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 04/27/2022] [Accepted: 05/26/2022] [Indexed: 01/23/2023]
Abstract
Serotonin (or 5-hydroxytryptamine, 5-HT) is an important neurotransmitter that activates 12 different G protein-coupled receptors (GPCRs) through selective coupling of Gs, Gi, or Gq proteins. The structural basis for G protein subtype selectivity by these GPCRs remains elusive. Here, we report the structures of the serotonin receptors 5-HT4, 5-HT6, and 5-HT7 with Gs, and 5-HT4 with Gi1. The structures reveal that transmembrane helices TM5 and TM6 alternate lengths as a macro-switch to determine receptor's selectivity for Gs and Gi, respectively. We find that the macro-switch by the TM5-TM6 length is shared by class A GPCR-G protein structures. Furthermore, we discover specific residues within TM5 and TM6 that function as micro-switches to form specific interactions with Gs or Gi. Together, these results present a common mechanism of Gs versus Gi protein coupling selectivity or promiscuity by class A GPCRs and extend the basis of ligand recognition at serotonin receptors.
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Affiliation(s)
- Sijie Huang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Peiyu Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan-Dan Shen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Icaro A Simon
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; SARomics Biostructures AB, Scheelevägen 2, 223 63 Lund, Sweden; Present address: Vrije Universiteit Amsterdam, Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, De Boelelaan 1108, 1081 HZ Amsterdam, Netherlands
| | - Chunyou Mao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yangxia Tan
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huibing Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Huadong Li
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yumu Zhang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chongzhao You
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuekui Yu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Key Laboratory of Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou 310058, China.
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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10
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Nagiri C, Kobayashi K, Tomita A, Kato M, Kobayashi K, Yamashita K, Nishizawa T, Inoue A, Shihoya W, Nureki O. Cryo-EM structure of the β3-adrenergic receptor reveals the molecular basis of subtype selectivity. Mol Cell 2021; 81:3205-3215.e5. [PMID: 34314699 DOI: 10.1016/j.molcel.2021.06.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/17/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
The β3-adrenergic receptor (β3AR) is predominantly expressed in adipose tissue and urinary bladder and has emerged as an attractive drug target for the treatment of type 2 diabetes, obesity, and overactive bladder (OAB). Here, we report the cryogenic electron microscopy structure of the β3AR-Gs signaling complex with the selective agonist mirabegron, a first-in-class drug for OAB. Comparison of this structure with the previously reported β1AR and β2AR structures reveals a receptor activation mechanism upon mirabegron binding to the orthosteric site. Notably, the narrower exosite in β3AR creates a perpendicular pocket for mirabegron. Mutational analyses suggest that a combination of both the exosite shape and the amino-acid-residue substitutions defines the drug selectivity of the βAR agonists. Our findings provide a molecular basis for βAR subtype selectivity, allowing the design of more-selective agents with fewer adverse effects.
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Affiliation(s)
- Chisae Nagiri
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiko Kato
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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11
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Borah R, Ninakanti R, Nuyts G, Peeters H, Pedrazo-Tardajos A, Nuti S, Vande Velde C, De Wael K, Lenaerts S, Bals S, Verbruggen SW. Selectivity in the Ligand Functionalization of Photocatalytic Metal Oxide Nanoparticles for Phase Transfer and Self-Assembly Applications. Chemistry 2021; 27:9011-9021. [PMID: 33880788 DOI: 10.1002/chem.202100029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Indexed: 01/04/2023]
Abstract
The functionalization of photocatalytic metal oxide nanoparticles of TiO2 , ZnO, WO3 and CuO with amine-terminated (oleylamine) and thiol-terminated (dodecane-1-thiol) alkyl-chain ligands was studied under ambient conditions. A high selectivity was observed in the binding specificity of a ligand towards nanoparticles of these different oxides. It was observed that oleylamine binds stably to only TiO2 and WO3 , whereas dodecane-1-thiol binds stably only to ZnO and CuO. Similarly, polar-to-nonpolar solvent phase transfer of TiO2 and WO3 nanoparticles could be achieved by using oleylamine, but not dodecane-1-thiol, whereas the opposite holds for ZnO and CuO. The surface chemistry of ligand-functionalized nanoparticles was probed by attenuated total reflectance (ATR)-FTIR spectroscopy, which enabled the occupation of the ligands at the active sites to be elucidated. The photostability of the ligands on the nanoparticle surface was determined by the photocatalytic self-cleaning properties of the material. Although TiO2 and WO3 degrade the ligands within 24 h under both UV and visible light, ligands on ZnO and CuO remain unaffected. The gathered insights are also highly relevant from an application point of view. As an example, because the ligand-functionalized nanoparticles are hydrophobic in nature, they can be self-assembled at the air-water interface to give nanoparticle films with demonstrated photocatalytic as well as anti-fogging properties.
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Affiliation(s)
- Rituraj Borah
- Sustainable Energy, Air & Water Technology (DuEL), Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Rajeshreddy Ninakanti
- Sustainable Energy, Air & Water Technology (DuEL), Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Electron Microscopy for Material Science (EMAT), Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Gert Nuyts
- NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Antwerp X-ray Analysis, Electrochemistry and Speciation (AXES), Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Hannelore Peeters
- Sustainable Energy, Air & Water Technology (DuEL), Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Adrián Pedrazo-Tardajos
- Electron Microscopy for Material Science (EMAT), Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Silvia Nuti
- Sustainable Energy, Air & Water Technology (DuEL), Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Electron Microscopy for Material Science (EMAT), Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Christophe Vande Velde
- Intelligence in Processes, Advanced Catalysts and Solvents (iPRACS), University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Karolien De Wael
- NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Antwerp X-ray Analysis, Electrochemistry and Speciation (AXES), Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Silvia Lenaerts
- Sustainable Energy, Air & Water Technology (DuEL), Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Sara Bals
- Electron Microscopy for Material Science (EMAT), Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Sammy W Verbruggen
- Sustainable Energy, Air & Water Technology (DuEL), Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
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12
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Liao C, Remington JM, May V, Li J. Molecular Basis of Class B GPCR Selectivity for the Neuropeptides PACAP and VIP. Front Mol Biosci 2021; 8:644644. [PMID: 33842547 PMCID: PMC8027070 DOI: 10.3389/fmolb.2021.644644] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
The related neuropeptides PACAP and VIP, and their shared PAC1, VPAC1 and VPAC2 receptors, regulate a large array of physiological activities in the central and peripheral nervous systems. However, the lack of comparative and molecular mechanistic investigations hinder further understanding of their preferred binding selectivity and function. PACAP and VIP have comparable affinity at the VPAC1 and VPAC2 receptor, but PACAP is 400-1,000 fold more potent than VIP at the PAC1 receptor. A molecular understanding of the differing neuropeptide-receptor interactions and the details underlying the receptor transitions leading to receptor activation are much needed for the rational design of selective ligands. To these ends, we have combined structural information and advanced simulation techniques to study PACAP/VIP binding selectivity, full-length receptor conformation ensembles and transitions of the PACAP/VIP receptor variants and subtypes, and a few key interactions in the orthosteric-binding pocket. Our results reveal differential peptide-receptor interactions (at the atomistic detail) important for PAC1, VPAC1 and VPAC2 receptor ligand selectivity. Using microsecond-long molecular dynamics simulations and the Markov State Models, we have also identified diverse receptor conformational ensembles and microstate transition paths for each receptor, the potential mechanisms underlying receptor open and closed states, and the interactions and dynamics at the transmembrane orthosteric pocket for receptor activation. These analyses reveal important features in class B GPCR structure-dynamics-function relationships, which provide novel insights for structure-based drug discovery.
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Affiliation(s)
- Chenyi Liao
- Department of Chemistry, University of Vermont, Burlington, VT, United States.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, China
| | - Jacob M Remington
- Department of Chemistry, University of Vermont, Burlington, VT, United States
| | - Victor May
- Department of Neuroscience, University of Vermont, Burlington, VT, United States
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT, United States
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13
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Zhuang Y, Xu P, Mao C, Wang L, Krumm B, Zhou XE, Huang S, Liu H, Cheng X, Huang XP, Shen DD, Xu T, Liu YF, Wang Y, Guo J, Jiang Y, Jiang H, Melcher K, Roth BL, Zhang Y, Zhang C, Xu HE. Structural insights into the human D1 and D2 dopamine receptor signaling complexes. Cell 2021; 184:931-942.e18. [PMID: 33571431 PMCID: PMC8215686 DOI: 10.1016/j.cell.2021.01.027] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/02/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022]
Abstract
The D1- and D2-dopamine receptors (D1R and D2R), which signal through Gs and Gi, respectively, represent the principal stimulatory and inhibitory dopamine receptors in the central nervous system. D1R and D2R also represent the main therapeutic targets for Parkinson's disease, schizophrenia, and many other neuropsychiatric disorders, and insight into their signaling is essential for understanding both therapeutic and side effects of dopaminergic drugs. Here, we report four cryoelectron microscopy (cryo-EM) structures of D1R-Gs and D2R-Gi signaling complexes with selective and non-selective dopamine agonists, including two currently used anti-Parkinson's disease drugs, apomorphine and bromocriptine. These structures, together with mutagenesis studies, reveal the conserved binding mode of dopamine agonists, the unique pocket topology underlying ligand selectivity, the conformational changes in receptor activation, and potential structural determinants for G protein-coupling selectivity. These results provide both a molecular understanding of dopamine signaling and multiple structural templates for drug design targeting the dopaminergic system.
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MESH Headings
- 2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine/analogs & derivatives
- 2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine/pharmacology
- Amino Acid Sequence
- Conserved Sequence
- Cryoelectron Microscopy
- Cyclic AMP/metabolism
- GTP-Binding Proteins/metabolism
- HEK293 Cells
- Humans
- Ligands
- Models, Molecular
- Mutant Proteins/chemistry
- Mutant Proteins/metabolism
- Receptors, Adrenergic, beta-2/metabolism
- Receptors, Dopamine D1/chemistry
- Receptors, Dopamine D1/metabolism
- Receptors, Dopamine D1/ultrastructure
- Receptors, Dopamine D2/chemistry
- Receptors, Dopamine D2/metabolism
- Receptors, Dopamine D2/ultrastructure
- Signal Transduction
- Structural Homology, Protein
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Affiliation(s)
- Youwen Zhuang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyu Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chunyou Mao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems and Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lei Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Brian Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Sijie Huang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Heng Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xi Cheng
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - Dan-Dan Shen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems and Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tinghai Xu
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Yong-Feng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - Yue Wang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Guo
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
| | - Yan Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems and Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Immunity and Inflammatory Diseases, Hangzhou 310058, China.
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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14
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Xu P, Huang S, Mao C, Krumm BE, Zhou XE, Tan Y, Huang XP, Liu Y, Shen DD, Jiang Y, Yu X, Jiang H, Melcher K, Roth BL, Cheng X, Zhang Y, Xu HE. Structures of the human dopamine D3 receptor-G i complexes. Mol Cell 2021; 81:1147-1159.e4. [PMID: 33548201 DOI: 10.1016/j.molcel.2021.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/21/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
The dopamine system, including five dopamine receptors (D1R-D5R), plays essential roles in the central nervous system (CNS), and ligands that activate dopamine receptors have been used to treat many neuropsychiatric disorders. Here, we report two cryo-EM structures of human D3R in complex with an inhibitory G protein and bound to the D3R-selective agonists PD128907 and pramipexole, the latter of which is used to treat patients with Parkinson's disease. The structures reveal agonist binding modes distinct from the antagonist-bound D3R structure and conformational signatures for ligand-induced receptor activation. Mutagenesis and homology modeling illuminate determinants of ligand specificity across dopamine receptors and the mechanisms for Gi protein coupling. Collectively our work reveals the basis of agonist binding and ligand-induced receptor activation and provides structural templates for designing specific ligands to treat CNS diseases targeting the dopaminergic system.
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Affiliation(s)
- Peiyu Xu
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijie Huang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Chunyou Mao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Yangxia Tan
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
| | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
| | - Dan-Dan Shen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xuekui Yu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA.
| | - Xi Cheng
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Yan Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precison Medicine, Zhejiang University Medical Center, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; Key Laboratory of Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou 310058, Zhejiang, China.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China.
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15
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Safe S, Jin UH, Park H, Chapkin RS, Jayaraman A. Aryl Hydrocarbon Receptor (AHR) Ligands as Selective AHR Modulators (SAhRMs). Int J Mol Sci 2020; 21:E6654. [PMID: 32932962 DOI: 10.3390/ijms21186654] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/01/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023] Open
Abstract
The aryl hydrocarbon receptor (AhR) was first identified as the intracellular protein that bound and mediated the toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin) and dioxin-like compounds (DLCs). Subsequent studies show that the AhR plays an important role in maintaining cellular homeostasis and in pathophysiology, and there is increasing evidence that the AhR is an important drug target. The AhR binds structurally diverse compounds, including pharmaceuticals, phytochemicals and endogenous biochemicals, some of which may serve as endogenous ligands. Classification of DLCs and non-DLCs based on their persistence (metabolism), toxicities, binding to wild-type/mutant AhR and structural similarities have been reported. This review provides data suggesting that ligands for the AhR are selective AhR modulators (SAhRMs) that exhibit tissue/cell-specific AhR agonist and antagonist activities, and that their functional diversity is similar to selective receptor modulators that target steroid hormone and other nuclear receptors.
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16
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Krah A, Huber RG, McMillan DGG, Bond PJ. The Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit. Chembiochem 2020; 21:3249-3254. [PMID: 32608105 DOI: 10.1002/cbic.202000291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Indexed: 12/21/2022]
Abstract
The ϵ subunit of ATP synthases has been proposed to regulate ATP hydrolysis in bacteria. Prevailing evidence supports the notion that when the ATP concentration falls below a certain threshold, the ϵ subunit changes its conformation from a non-inhibitory down-state to an extended up-state that then inhibits enzymatic ATP hydrolysis by binding to the catalytic domain. It has been demonstrated that the ϵ subunit from Bacillus PS3 is selective for ATP over other nucleotides, including GTP. In this study, the purine triphosphate selectivity is rationalized by using results from MD simulations and free energy calculations for the R103A/R115A mutant of the ϵ subunit from Bacillus PS3, which binds ATP more strongly than the wild-type protein. Our results are in good agreement with experimental data, and the elucidated molecular basis for selectivity could help to guide the design of novel GTP sensors.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,Korea Institute for Advanced Study, School of Computational Sciences, 85 Hoegiro, Dongdaemun-gu, Seoul, 02455, Republic of Korea
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore
| | - Duncan G G McMillan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str. #07-01 Matrix, Singapore, 138671, Singapore.,National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore, 117543, Singapore
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17
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Wu G, Tillo D, Ray S, Chang TC, Schneekloth JS Jr, Vinson C, Yang D. Custom G4 Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity. Molecules 2020; 25:E3465. [PMID: 32751510 DOI: 10.3390/molecules25153465] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplexes (G4) are considered new drug targets for human diseases such as cancer. More than 10,000 G4s have been discovered in human chromatin, posing challenges for assessing the selectivity of a G4-interactive ligand. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent small molecule for G4 detection in vivo. Our previous structural study shows that BMVC binds to the MYC promoter G4 (MycG4) with high specificity. Here, we utilize high-throughput, large-scale custom DNA G4 microarrays to analyze the G4-binding selectivity of BMVC. BMVC preferentially binds to the parallel MycG4 and selectively recognizes flanking sequences of parallel G4s, especially the 3′-flanking thymine. Importantly, the microarray results are confirmed by orthogonal NMR and fluorescence binding analyses. Our study demonstrates the potential of custom G4 microarrays as a platform to broadly and unbiasedly assess the binding selectivity of G4-interactive ligands, and to help understand the properties that govern molecular recognition.
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18
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Miyazaki Y, Ono N, Huang M, Altaf‐Ul‐Amin M, Kanaya S. Comprehensive Exploration of Target-specific Ligands Using a Graph Convolution Neural Network. Mol Inform 2020; 39:e1900095. [PMID: 31815371 PMCID: PMC7050504 DOI: 10.1002/minf.201900095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/08/2019] [Indexed: 11/10/2022]
Abstract
Machine learning approaches are widely used to evaluate ligand activities of chemical compounds toward potential target proteins. Especially, exploration of highly selective ligands is important for the development of new drugs with higher safety. One difficulty in constructing well-performing model predicting such a ligand activity is the absence of data on true negative ligand-protein interactions. In other words, in many cases we can access to plenty of information on ligands that bind to specific protein, but less or almost no information showing that compounds don't bind to proteins of interest. In this paper, we suggested an approach to comprehensively explore candidates for ligands specifically targeting toward proteins without using information on the true negative interaction. The approach consists of 4 steps: 1) constructing a model that distinguishes ligands for the target proteins of interest from those targeting proteins that cause off-target effects, by using graph convolution neural network (GCNN); 2) extracting feature vectors after convolution/pooling processes and mapping their principal components in two dimensions; 3) specifying regions with higher density for two ligand groups through kernel density estimation; and 4) investigating the distribution of compounds for exploration on the density map using the same classifier and decomposer. If compounds for exploration are located in higher-density regions of ligand compounds, these compounds can be regarded as having relatively high binding affinity to the major target or off-target proteins compared with other compounds. We applied the approach to the exploration of ligands for β-site amyloid precursor protein [APP]-cleaving enzyme 1 (BACE1), a major target for Alzheimer Disease (AD), with less off-target effect toward cathepsin D. We demonstrated that the density region of BACE1 and cathepsin D ligands are well-divided, and a group of natural compounds as a target for exploration of new drug candidates also has significantly different distribution on the density map.
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Affiliation(s)
- Yu Miyazaki
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Naoaki Ono
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
- Data Science Center, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Ming Huang
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Md. Altaf‐Ul‐Amin
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
| | - Shigehiko Kanaya
- Division of Information Science, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
- Data Science Center, Graduate School of Science and TechnologyNara Institute of Science and Technology8916-5 Takayama, IkomaNara630-0192Japan
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19
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Leypold T, Bonus M, Spiegelhalter F, Schwede F, Schwabe T, Gohlke H, Kusch J. N 6-modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels. J Biol Chem 2019; 294:17978-17987. [PMID: 31615893 DOI: 10.1074/jbc.ra119.010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/15/2019] [Indexed: 11/06/2022] Open
Abstract
cAMP acts as a second messenger in many cellular processes. Three protein types mainly mediate cAMP-induced effects: PKA, exchange protein directly activated by cAMP (Epac), and cyclic nucleotide-modulated channels (cyclic nucleotide-gated or hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels). Discrimination among these cAMP signaling pathways requires specific targeting of only one protein. Previously, cAMP modifications at position N 6 of the adenine ring (PKA) and position 2'-OH of the ribose (Epac) have been used to produce target-selective compounds. However, cyclic nucleotide-modulated ion channels were usually outside of the scope of these previous studies. These channels are widely distributed, so possible channel cross-activation by PKA- or Epac-selective agonists warrants serious consideration. Here we demonstrate the agonistic effects of three PKA-selective cAMP derivatives, N 6-phenyladenosine-3',5'-cyclic monophosphate (N 6-Phe-cAMP), N 6-benzyladenosine-3',5'-cyclic monophosphate (N 6-Bn-cAMP), and N 6-benzoyl-adenosine-3',5'-cyclic monophosphate (N 6-Bnz-cAMP), on murine HCN2 pacemaker channels. Electrophysiological characterization in Xenopus oocytes revealed that these derivatives differ in apparent affinities depending on the modification type but that their efficacy and effects on HCN2 activation kinetics are similar to those of cAMP. Docking experiments suggested a pivotal role of Arg-635 at the entrance of the binding pocket in HCN2, either causing stabilizing cation-π interactions with the aromatic ring in N 6-Phe-cAMP or N 6-Bn-cAMP or a steric clash with the aromatic ring in N 6-Bnz-cAMP. A reduced apparent affinity of N 6-Phe-cAMP toward the variants R635A and R635E strengthened that notion. We conclude that some PKA activators also effectively activate HCN2 channels. Hence, when studying PKA-mediated cAMP signaling with cAMP derivatives in a native environment, activation of HCN channels should be considered.
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Affiliation(s)
- Tim Leypold
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
| | - Michele Bonus
- Institute for Pharmaceutical and Medical Chemistry, Heinrich Heine University, Universitätsstraβe 1, 40225 Düsseldorf, Germany
| | - Felix Spiegelhalter
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
| | | | - Tina Schwabe
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medical Chemistry, Heinrich Heine University, Universitätsstraβe 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing, Jülich Supercomputing Centre and Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Jana Kusch
- Friedrich Schiller University, University Hospital Jena, Institute of Physiology II, Kollegiengasse 9, 07743 Jena, Germany
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20
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Dong F, Rues RB, Kazemi S, Dötsch V, Bernhard F. Molecular Determinants for Ligand Selectivity of the Cell-Free Synthesized Human Endothelin B Receptor. J Mol Biol 2018; 430:5105-5119. [PMID: 30342934 DOI: 10.1016/j.jmb.2018.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/02/2018] [Accepted: 10/12/2018] [Indexed: 01/14/2023]
Abstract
Extracellular domains of G-protein-coupled receptors act as initial molecular selectivity filters for subtype specific ligands and drugs. Chimeras of the human endothelin-B receptor containing structural units from the extracellular domains of the endothelin-A receptor were analyzed after their co-translational insertion into preformed nanodiscs. A short β-strand and a linker region in the second extracellular loop as well as parts of the extracellular N-terminal domain were identified as molecular discrimination sites for the endothelin-B receptor-selective agonists IRL1620, sarafotoxin 6c, 4Ala-ET-1 and ET-3, but not for the non-selective agonist ET-1 recognized by both endothelin receptors. A proposed second disulfide bridge in the endothelin-B receptor tethering the N-terminal domain with the third extracellular loop was not essential for ET-1 recognition and binding, but increased the receptor thermostability. We further demonstrate an experimental approach with cell-free synthesized engineered agonists to analyze the differential discrimination of peptide ligand topologies by the two endothelin receptors. The study is based on the engineering and cell-free insertion of G-protein-coupled receptors into defined membranes and may become interesting also for other targets as an alternative platform to reveal molecular details of ligand selectivity and ligand binding mechanisms.
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Affiliation(s)
- Fang Dong
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ralf B Rues
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Sina Kazemi
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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21
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Saleh N, Kleinau G, Heyder N, Clark T, Hildebrand PW, Scheerer P. Binding, Thermodynamics, and Selectivity of a Non-peptide Antagonist to the Melanocortin-4 Receptor. Front Pharmacol 2018; 9:560. [PMID: 29910730 PMCID: PMC5992272 DOI: 10.3389/fphar.2018.00560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/10/2018] [Indexed: 11/22/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) is a potential drug target for treatment of obesity, anxiety, depression, and sexual dysfunction. Crystal structures for MC4R are not yet available, which has hindered successful structure-based drug design. Using microsecond-scale molecular-dynamics simulations, we have investigated selective binding of the non-peptide antagonist MCL0129 to a homology model of human MC4R (hMC4R). This approach revealed that, at the end of a multi-step binding process, MCL0129 spontaneously adopts a binding mode in which it blocks the agonistic-binding site. This binding mode was confirmed in subsequent metadynamics simulations, which gave an affinity for human hMC4R that matches the experimentally determined value. Extending our simulations of MCL0129 binding to hMC1R and hMC3R, we find that receptor subtype selectivity for hMC4R depends on few amino acids located in various structural elements of the receptor. These insights may support rational drug design targeting the melanocortin systems.
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Affiliation(s)
- Noureldin Saleh
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Berlin, Germany.,Computational Modelling and Dynamics of Molecular Complexes, Berlin, Germany
| | - Gunnar Kleinau
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Nicolas Heyder
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Timothy Clark
- Computer-Chemie-Centrum, Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter W Hildebrand
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Berlin, Germany.,Computational Modelling and Dynamics of Molecular Complexes, Berlin, Germany.,Institute of Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
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22
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Tian F, Zhou P, Kang W, Luo L, Fan X, Yan J, Liang H. The small-molecule inhibitor selectivity between IKKα and IKKβ kinases in NF-κB signaling pathway. J Recept Signal Transduct Res 2014; 35:307-18. [PMID: 25386663 DOI: 10.3109/10799893.2014.980950] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The enzyme complex IκB kinase (IKK) is an essential activator of NF-κB signaling pathway involved in propagating the cellular response to inflammation. The complex contains two functional subunits IKKα and IKKβ, which are structurally conserved kinases and selective inhibition of them would result in distinct biological effects. However, most existing IKK inhibitors show moderate or high promiscuity for the two homologous kinases. Understanding of the molecular mechanism and biological implication underlying the specific interactions in IKK-ligand recognition is thus fundamentally important for the rational design of selective IKK inhibitors. In the current work, we integrated molecular docking, quantum mechanics/molecular mechanics calculation and Poisson-Boltzmann/surface area analysis to investigate the structural basis and energetic property of the selective binding of small-molecule ligands to IKKα and IKKβ. It was found that the selectivity is primarily determined by the size and topology difference in ATP-binding pocket of IKKα and IKKβ kinase domains; bulky inhibitor molecules commonly have, respectively, low and appropriate affinities towards IKKα and IKKβ, and thus exhibit relatively high selectivity for IKKβ over IKKα, whereas small ligands can only bind weakly to both the two kinases with low selectivity. In addition, the conformation, arrangement and distribution of residues in IKK pockets are also responsible for constituting the exquisite specificity of ligand binding to KKα and IKKβ. Next, a novel quantitative structure-selectivity relationship model was developed to characterize the relative contribution of each kinase residue to inhibitor selectivity and to predict the selectivity and specificity for a number of known IKK inhibitors. Results showed that the active-site residues contribute significantly to the selectivity by directly interacting with inhibitor ligands, while those protein portions far away from the kinase active sites may also play an important role in determining the selectivity through long-range non-bonded forces and indirect allosteric effect.
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Affiliation(s)
- Feifei Tian
- a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China .,b School of Life Science and Engineering , Southwest Jiaotong University , Chengdu , China , and
| | - Peng Zhou
- c Center of Bioinformatics (COBI), School of Life Science and Technology , University of Electronic Science and Technology of China (UESTC) , Chengdu , China
| | - Wenyuan Kang
- b School of Life Science and Engineering , Southwest Jiaotong University , Chengdu , China , and
| | - Li Luo
- a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China
| | - Xia Fan
- a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China
| | - Jun Yan
- a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China
| | - Huaping Liang
- a State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital , Third Military Medical University , Chongqing , China
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