1
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Rincon Pabon JP, Akbar Z, Politis A. MSe Collision Energy Optimization for the Analysis of Membrane Proteins Using HDX-cIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1383-1389. [PMID: 38842540 PMCID: PMC11228973 DOI: 10.1021/jasms.4c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has evolved as an essential technique in structural proteomics. The use of ion mobility separation (IMS) coupled to HDX-MS has increased the applicability of the technique to more complex systems and has been shown to improve data quality and robustness. The first step when running any HDX-MS workflow is to confirm the sequence and retention time of the peptides resulting from the proteolytic digestion of the nondeuterated protein. Here, we optimized the collision energy ramp of HDMSE experiments for membrane proteins using a Waters SELECT SERIES cIMS-QTOF system following an HDX workflow using Phosphorylase B, XylE transporter, and Smoothened receptor (SMO) as model systems. Although collision energy (CE) ramp 10-50 eV gave the highest amount of positive identified peptides when using Phosphorylase B, XylE, and SMO, results suggest optimal CE ramps are protein specific, and different ramps can produce a unique set of peptides. We recommend cIMS users use different CE ramps in their HDMSE experiments and pool the results to ensure maximum peptide identifications. The results show how selecting an appropriate CE ramp can change the sequence coverage of proteins ranging from 4 to 94%.
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Affiliation(s)
- Juan Pablo Rincon Pabon
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Zulaikha Akbar
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Argyris Politis
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
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2
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Vo ADP, Kim SK, Yang MY, Ondrus AE, Goddard WA. Fully activated structure of the sterol-bound Smoothened GPCR-Gi protein complex. Proc Natl Acad Sci U S A 2023; 120:e2300919120. [PMID: 38015850 PMCID: PMC10710022 DOI: 10.1073/pnas.2300919120] [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: 01/17/2023] [Accepted: 10/22/2023] [Indexed: 11/30/2023] Open
Abstract
Smoothened (SMO) is an oncoprotein and signal transducer in the Hedgehog signaling pathway that regulates cellular differentiation and embryogenesis. As a member of the Frizzled (Class F) family of G protein-coupled receptors (GPCRs), SMO biochemically and functionally interacts with Gi family proteins. However, key molecular features of fully activated, G protein-coupled SMO remain elusive. We present the atomistic structure of activated human SMO complexed with the heterotrimeric Gi protein and two sterol ligands, equilibrated at 310 K in a full lipid bilayer at physiological salt concentration and pH. In contrast to previous experimental structures, our equilibrated SMO complex exhibits complete breaking of the pi-cation interaction between R4516.32 and W5357.55, a hallmark of Class F receptor activation. The Gi protein couples to SMO at seven strong anchor points similar to those in Class A GPCRs: intracellular loop 1, intracellular loop 2, transmembrane helix 6, and helix 8. On the path to full activation, we find that the extracellular cysteine-rich domain (CRD) undergoes a dramatic tilt, following a trajectory suggested by positions of the CRD in active and inactive experimental SMO structures. Strikingly, a sterol ligand bound to a shallow transmembrane domain (TMD) site in the initial structure migrates to a deep TMD pocket found exclusively in activator-bound SMO complexes. Thus, our results indicate that SMO interacts with Gi prior to full activation to break the molecular lock, form anchors with Gi subunits, tilt the CRD, and facilitate migration of a sterol ligand in the TMD to an activated position.
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Affiliation(s)
- Amy-Doan P. Vo
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Moon Young Yang
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Alison E. Ondrus
- Department of Chemistry, University of Illinois Chicago, Chicago, IL60607
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, IL60607
| | - William A. Goddard
- Materials and Process Simulation Center, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA91125
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3
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Kumari S, Mitra A, Bulusu G. Putative Role of Cholesterol in Shaping the Structural and Functional Dynamics of Smoothened (SMO). J Phys Chem B 2023; 127:9476-9495. [PMID: 37878627 DOI: 10.1021/acs.jpcb.3c02255] [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: 10/27/2023]
Abstract
The smoothened (SMO) receptor belongs to the superfamily of class F G protein-coupled receptors (GPCRs) and is a potential drug target in several types of cancer. It has two ligand binding sites, respectively, in the cysteine-rich domain (CRD) and the transmembrane domain (TMD). It has been shown that cholesterol is important for its activation and function. However, the molecular-level understanding of SMO dynamics in the presence of cholesterol has not been explored in sufficient detail. In this work, we have carried out atomistic molecular dynamics simulations totaling 3.6 μs to analyze the effect of cholesterol binding to TMD and/or CRD on the structure and dynamics of the SMO receptor. Our results show that the presence of cholesterol in the CRD and TMD, respectively, alters the conformational dynamics of SMO differently. We reported that the reorganization of the D-R-E network at the extracellular end of the TMD is important for the high activity of SMO. In general, the transmembrane helices 5, 6, and 7 and helix 8 are most affected, which, in turn, leads to changes in the CRD and intracellular cytoplasmic domain (ICD) dynamics patterns depending on the presence or absence of cholesterol in the CRD and/or the TMD. We have also reported that the interaction of membrane lipids with SMO is different in different SMO states. These results agree with the experimental structural observations and data of cholesterol-bound and unbound structures of SMO and add to our molecular understanding of the SMO-cholesterol interaction.
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Affiliation(s)
- Shweta Kumari
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Gopalakrishnan Bulusu
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
- IHub-Data, International Institute of Information Technology, Hyderabad 500032, India
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad 500046, India
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4
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Li C, Wu Y, Wang W, Xu L, Zhou Y, Yue Y, Wu T, Yang M, Qiu Y, Huang M, Zhou F, Zhou Y, Hao P, Lin Z, Wang MW, Zhao S, Yang D, Xu F, Tao H. Structure-Based Ligand Discovery Targeting the Transmembrane Domain of Frizzled Receptor FZD7. J Med Chem 2023; 66:11855-11868. [PMID: 37669317 DOI: 10.1021/acs.jmedchem.2c01795] [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: 09/07/2023]
Abstract
Despite the essential roles of Frizzled receptors (FZDs) in mediating Wnt signaling in embryonic development and tissue homeostasis, ligands targeting FZDs are rare. A few antibodies and peptide modulators have been developed that mainly bind to the family-conserved extracellular cysteine-rich domain of FZDs, while the canonical binding sites in the transmembrane domain (TMD) are far from sufficiently addressed. Based on the recent structures of FZDs, we explored small-molecule ligand discovery by targeting TMD. From the ChemDiv library with ∼1.6 million compounds, we identified compound F7H as an antagonist of FZD7 with an IC50 at 1.25 ± 0.38 μM. Focusing on this hit, the structural dissection study, together with computing studies such as molecular docking, molecular dynamics simulation, and free energy perturbation calculations, defined the binding pocket with key residue recognition. Our results revealed the structural basis of ligand recognition and demonstrated the feasibility of structure-guided ligand discovery for FZD7-TMD.
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Affiliation(s)
- Cuixia Li
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenli Wang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Lu Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yan Zhou
- The National Center for Drug Screening, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Yang Yue
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Tingting Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Meifang Yang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yanli Qiu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Minhao Huang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Fangfang Zhou
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yiqing Zhou
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Ming-Wei Wang
- The National Center for Drug Screening, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Dehua Yang
- The National Center for Drug Screening, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Houchao Tao
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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5
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Bansal PD, Dutta S, Shukla D. Activation mechanism of the human Smoothened receptor. Biophys J 2023; 122:1400-1413. [PMID: 36883002 PMCID: PMC10111369 DOI: 10.1016/j.bpj.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/17/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Smoothened (SMO) is a membrane protein of the class F subfamily of G protein-coupled receptors (GPCRs) and maintains homeostasis of cellular differentiation. SMO undergoes conformational change during activation, transmitting the signal across the membrane, making it amenable to bind to its intracellular signaling partner. Receptor activation has been studied at length for class A receptors, but the mechanism of class F receptor activation remains unknown. Agonists and antagonists bound to SMO at sites in the transmembrane domain (TMD) and the cysteine-rich domain have been characterized, giving a static view of the various conformations SMO adopts. Although the structures of the inactive and active SMO outline the residue-level transitions, a kinetic view of the overall activation process remains unexplored for class F receptors. We describe SMO's activation process in atomistic detail by performing 300 μs of molecular dynamics simulations and combining it with Markov state model theory. A molecular switch, conserved across class F and analogous to the activation-mediating D-R-Y motif in class A receptors, is observed to break during activation. We also show that this transition occurs in a stage-wise movement of the transmembrane helices: TM6 first, followed by TM5. To see how modulators affect SMO activity, we simulated agonist and antagonist-bound SMO. We observed that agonist-bound SMO has an expanded hydrophobic tunnel in SMO's core TMD, whereas antagonist-bound SMO shrinks this tunnel, further supporting the hypothesis that cholesterol travels through a tunnel inside Smoothened to activate it. In summary, this study elucidates the distinct activation mechanism of class F GPCRs and shows that SMO's activation process rearranges the core TMD to open a hydrophobic conduit for cholesterol transport.
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Affiliation(s)
- Prateek D Bansal
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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6
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Wang J, Cui B, Li X, Zhao X, Huang T, Ding X. The emerging roles of Hedgehog signaling in tumor immune microenvironment. Front Oncol 2023; 13:1171418. [PMID: 37213270 PMCID: PMC10196179 DOI: 10.3389/fonc.2023.1171418] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/26/2023] [Indexed: 05/23/2023] Open
Abstract
The Hedgehog (Hh) signaling pathway is pervasively involved in human malignancies, making it an effective target for cancer treatment for decades. In addition to its direct role in regulating cancer cell attributes, recent work indicates that it has an immunoregulatory effect on tumor microenvironments. An integrated understanding of these actions of Hh signaling pathway in tumor cells and tumor microenvironments will pave the way for novel tumor treatments and further advances in anti-tumor immunotherapy. In this review, we discuss the most recent research about Hh signaling pathway transduction, with a particular emphasis on its role in modulating tumor immune/stroma cell phenotype and function, such as macrophage polarity, T cell response, and fibroblast activation, as well as their mutual interactions between tumor cells and nonneoplastic cells. We also summarize the recent advances in the development of Hh pathway inhibitors and nanoparticle formulation for Hh pathway modulation. We suggest that targeting Hh signaling effects on both tumor cells and tumor immune microenvironments could be more synergistic for cancer treatment.
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Affiliation(s)
- Juan Wang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, China
| | - Baiping Cui
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, China
| | - Xiaojie Li
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, China
| | - Xinyue Zhao
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, China
| | - Taomin Huang
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, China
- *Correspondence: Taomin Huang, ; Xiaolei Ding,
| | - Xiaolei Ding
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai, China
- *Correspondence: Taomin Huang, ; Xiaolei Ding,
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7
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Luo W, Yang M, Zhao Y, Wang H, Yang X, Zhang W, Zhao F, Zhao S, Tao H. Transition-Linker Containing Detergents for Membrane Protein Studies. Chemistry 2022; 28:e202202242. [PMID: 36053145 DOI: 10.1002/chem.202202242] [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: 07/18/2022] [Indexed: 12/14/2022]
Abstract
It is a pressing need, but still challenging to explore the structure and function of membrane proteins (MPs). One of the main obstacles is the limited availability of matched detergents for the handling of specific MPs. We describe herein the design of new detergents by incorporation of a transition linker between the hydrophilic head and the hydrophobic tail. This design allows a gradual change of hydrophobicity between the outside and inside of micelles, in contrast to the abrupt switch in conventional detergents. Notably, many of these detergents assembled into micelles in while retaining low critical micelle concentrations. Meanwhile, thermal stabilizing evaluation identified superior detergents for representative MPs, including G protein-coupled receptors and a transporter protein. Among them, further improved the NMR study of MPs. We anticipate these that results will encourage future detergent expansion through new remodeling on the traditional detergent scaffold.
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Affiliation(s)
- Weiling Luo
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P. R. China.,iHuman Institute, ShanghaiTech University, 201210, Shanghai, P. R. China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Meifang Yang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P. R. China
| | - Yitian Zhao
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P. R. China
| | - Huixia Wang
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Xiaodi Yang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P. R. China
| | - Wei Zhang
- College of Chemistry and Materials Science, Hebei Normal University, 050024, Shijiazhuang, P. R. China
| | - Fei Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, P. R. China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Houchao Tao
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P. R. China
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8
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Nicheperovich A, Townsend-Nicholson A. Towards Precision Oncology: The Role of Smoothened and Its Variants in Cancer. J Pers Med 2022; 12:jpm12101648. [PMID: 36294790 PMCID: PMC9605185 DOI: 10.3390/jpm12101648] [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: 09/12/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
The G protein-coupled receptor Smoothened (Smo) is a central signal transducer of the Hedgehog (Hh) pathway which has been linked to diverse forms of tumours. Stimulated by advancements in structural and functional characterisation, the Smo receptor has been recognised as an important therapeutic target in Hh-driven cancers, and several Smo inhibitors have now been approved for cancer therapy. This receptor is also known to be an oncoprotein itself and its gain-of-function variants have been associated with skin, brain, and liver cancers. According to the COSMIC database, oncogenic mutations of Smo have been identified in various other tumours, although their oncogenic effect remains unknown in these tissues. Drug resistance is a common challenge in cancer therapies targeting Smo, and data analysis shows that healthy individuals also harbour resistance mutations. Based on the importance of Smo in cancer progression and the high incidence of resistance towards Smo inhibitors, this review suggests that detection of Smo variants through tumour profiling could lead to increased precision and improved outcomes of anti-cancer treatments.
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9
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Yeagle PL. Unraveling a mystery: Why human cells require cholesterol. SCIENCE ADVANCES 2022; 8:eade5927. [PMID: 36103540 PMCID: PMC9473577 DOI: 10.1126/sciadv.ade5927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 05/21/2023]
Abstract
Understanding how cholesterol binds to mammalian cells offers critical insights into the waxy substance's role in protein modulation and cell function.
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Affiliation(s)
- Philip L Yeagle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
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10
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Zhao F, Zhu Z, Xie L, Luo F, Wang H, Qiu Y, Luo W, Zhou F, Xue D, Zhang Z, Hua T, Wu D, Liu Z, Le Z, Tao H. Two‐Dimensional Detergent Expansion Strategy for Membrane Protein Studies. Chemistry 2022; 28:e202201388. [DOI: 10.1002/chem.202201388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Fei Zhao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihao Zhu
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Linshan Xie
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Feng Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Huixia Wang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Yanli Qiu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Weiling Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Fang Zhou
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Dongxiang Xue
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihui Zhang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Tian Hua
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Dong Wu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhi‐Jie Liu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Zhiping Le
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Houchao Tao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- Shanghai Frontiers Science Center of TCM Chemical Biology Innovation Research Institute of Traditional Chinese Medicine Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
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11
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Zhang K, Wu H, Hoppe N, Manglik A, Cheng Y. Fusion protein strategies for cryo-EM study of G protein-coupled receptors. Nat Commun 2022; 13:4366. [PMID: 35902590 PMCID: PMC9334595 DOI: 10.1038/s41467-022-32125-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/19/2022] [Indexed: 11/15/2022] Open
Abstract
Single particle cryogenic-electron microscopy (cryo-EM) is used extensively to determine structures of activated G protein-coupled receptors (GPCRs) in complex with G proteins or arrestins. However, applying it to GPCRs without signaling proteins remains challenging because most receptors lack structural features in their soluble domains to facilitate image alignment. In GPCR crystallography, inserting a fusion protein between transmembrane helices 5 and 6 is a highly successful strategy for crystallization. Although a similar strategy has the potential to broadly facilitate cryo-EM structure determination of GPCRs alone without signaling protein, the critical determinants that make this approach successful are not yet clear. Here, we address this shortcoming by exploring different fusion protein designs, which lead to structures of antagonist bound A2A adenosine receptor at 3.4 Å resolution and unliganded Smoothened at 3.7 Å resolution. The fusion strategies explored here are likely applicable to cryo-EM interrogation of other GPCRs and small integral membrane proteins.
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Affiliation(s)
- Kaihua Zhang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA.
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, CA, 94158, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, 94158, USA.
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12
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Kinnebrew M, Woolley RE, Ansell TB, Byrne EFX, Frigui S, Luchetti G, Sircar R, Nachtergaele S, Mydock-McGrane L, Krishnan K, Newstead S, Sansom MSP, Covey DF, Siebold C, Rohatgi R. Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain. SCIENCE ADVANCES 2022; 8:eabm5563. [PMID: 35658032 PMCID: PMC9166294 DOI: 10.1126/sciadv.abm5563] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/15/2022] [Indexed: 05/06/2023]
Abstract
Smoothened (SMO) transduces the Hedgehog (Hh) signal across the plasma membrane in response to accessible cholesterol. Cholesterol binds SMO at two sites: one in the extracellular cysteine-rich domain (CRD) and a second in the transmembrane domain (TMD). How these two sterol-binding sites mediate SMO activation in response to the ligand Sonic Hedgehog (SHH) remains unknown. We find that mutations in the CRD (but not the TMD) reduce the fold increase in SMO activity triggered by SHH. SHH also promotes the photocrosslinking of a sterol analog to the CRD in intact cells. In contrast, sterol binding to the TMD site boosts SMO activity regardless of SHH exposure. Mutational and computational analyses show that these sites are in allosteric communication despite being 45 angstroms apart. Hence, sterols function as both SHH-regulated orthosteric ligands at the CRD and allosteric ligands at the TMD to regulate SMO activity and Hh signaling.
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Affiliation(s)
- Maia Kinnebrew
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel E. Woolley
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Eamon F. X. Byrne
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Frigui
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanni Luchetti
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ria Sircar
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sigrid Nachtergaele
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Laurel Mydock-McGrane
- Department of Developmental Biology, Washington School of Medicine, St. Louis, MO, USA
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington School of Medicine, St. Louis, MO, USA
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | | | - Douglas F. Covey
- Department of Developmental Biology, Washington School of Medicine, St. Louis, MO, USA
- Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
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13
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Pan D, Oyama R, Sato T, Nakane T, Mizunuma R, Matsuoka K, Joti Y, Tono K, Nango E, Iwata S, Nakatsu T, Kato H. Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX. IUCRJ 2022; 9:134-145. [PMID: 35059217 PMCID: PMC8733880 DOI: 10.1107/s2052252521011611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open-close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono-acyl-glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy-droxy-propyl methyl-cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.
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Affiliation(s)
- Dongqing Pan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryo Oyama
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomomi Sato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Mizunuma
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keita Matsuoka
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroaki Kato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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14
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Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
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Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
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15
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Kricker JA, Page CP, Gardarsson FR, Baldursson O, Gudjonsson T, Parnham MJ. Nonantimicrobial Actions of Macrolides: Overview and Perspectives for Future Development. Pharmacol Rev 2021; 73:233-262. [PMID: 34716226 DOI: 10.1124/pharmrev.121.000300] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Macrolides are among the most widely prescribed broad spectrum antibacterials, particularly for respiratory infections. It is now recognized that these drugs, in particular azithromycin, also exert time-dependent immunomodulatory actions that contribute to their therapeutic benefit in both infectious and other chronic inflammatory diseases. Their increased chronic use in airway inflammation and, more recently, of azithromycin in COVID-19, however, has led to a rise in bacterial resistance. An additional crucial aspect of chronic airway inflammation, such as chronic obstructive pulmonary disease, as well as other inflammatory disorders, is the loss of epithelial barrier protection against pathogens and pollutants. In recent years, azithromycin has been shown with time to enhance the barrier properties of airway epithelial cells, an action that makes an important contribution to its therapeutic efficacy. In this article, we review the background and evidence for various immunomodulatory and time-dependent actions of macrolides on inflammatory processes and on the epithelium and highlight novel nonantibacterial macrolides that are being studied for immunomodulatory and barrier-strengthening properties to circumvent the risk of bacterial resistance that occurs with macrolide antibacterials. We also briefly review the clinical effects of macrolides in respiratory and other inflammatory diseases associated with epithelial injury and propose that the beneficial epithelial effects of nonantibacterial azithromycin derivatives in chronic inflammation, even given prophylactically, are likely to gain increasing attention in the future. SIGNIFICANCE STATEMENT: Based on its immunomodulatory properties and ability to enhance the protective role of the lung epithelium against pathogens, azithromycin has proven superior to other macrolides in treating chronic respiratory inflammation. A nonantibiotic azithromycin derivative is likely to offer prophylactic benefits against inflammation and epithelial damage of differing causes while preserving the use of macrolides as antibiotics.
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Affiliation(s)
- Jennifer A Kricker
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Clive P Page
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Fridrik Runar Gardarsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Olafur Baldursson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Thorarinn Gudjonsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Michael J Parnham
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
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16
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Liu Y, Zhou F, Ding K, Xue D, Zhu Z, Li C, Li F, Xu Y, Xu F, Le Z, Zhao S, Tao H. Structure-Activity Relationship Studies of Hydantoin-Cored Ligands for Smoothened Receptor. ChemistryOpen 2021; 10:1028-1032. [PMID: 34648230 PMCID: PMC8515922 DOI: 10.1002/open.202100216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
An underside binding site was recently identified in the transmembrane domain of smoothened receptor (SMO). Herein, we report efforts in the exploration of new insights into the interactions between the ligand and SMO. The hydantoin core in the middle of the parent compound was found to be highly conservative in chirality, ring size, and substituents. On each benzene at two ends, a plethora of variations, particularly halogen substitutions, were introduced and investigated. Analysis of the structure-activity relationship revealed miscellaneous halogen effects. The ligands with double halogen substituents exhibit remarkably enhanced potency, providing promising candidates that potentially overcome the common drug resistance and useful heavy-atom labeled chemical tools for co-crystallization studies of SMO.
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Affiliation(s)
- Yang Liu
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Fang Zhou
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Kang Ding
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Dongxiang Xue
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Zhihao Zhu
- Department of ChemistryNanchang University999 Xuefu AvenueNanchang330031China
| | - Cuixia Li
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
- School of Life Science and TechnologyShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Fei Li
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Yueming Xu
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Fei Xu
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
- School of Life Science and TechnologyShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Zhiping Le
- Department of ChemistryNanchang University999 Xuefu AvenueNanchang330031China
| | - Suwen Zhao
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
- School of Life Science and TechnologyShanghaiTech University393 Middle Huaxia RoadShanghai201210China
| | - Houchao Tao
- iHuman InstituteShanghaiTech University393 Middle Huaxia RoadShanghai201210China
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17
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Zhao F, Wu Y, Zhou F, Xue D, Zhao S, Lu W, Liu X, Hu T, Qiu Y, Li R, Gu T, Xu Y, Xu F, Zhong G, Jiang Z, Zhao S, Tao H. Elucidation of Distinct Modular Assemblies of Smoothened Receptor by Bitopic Ligand Measurement. J Med Chem 2021; 64:13830-13840. [PMID: 34492176 DOI: 10.1021/acs.jmedchem.1c01220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Class F G protein-coupled receptors are characterized by a large extracellular domain (ECD) in addition to the common transmembrane domain (TMD) with seven α-helixes. For smoothened receptor (SMO), structural studies revealed dissected ECD and TMD, and their integrated assemblies. However, distinct assemblies were reported under different circumstances. Using an unbiased approach based on four series of cross-conjugated bitopic ligands, we explore the relationship between the active status and receptor assembly. Different activity dependency on the linker length for these bitopic ligands corroborates the various occurrences of SMO assembly. These results reveal a rigid "near" assembly for active SMO, which is in contrast to previous results. Conversely, inactive SMO adopts a free ECD, which would be remotely captured at "far" assembly by cholesterol. Altogether, we propose a mechanism of cholesterol flow-caused SMO activation involving an erection of ECD from far to near assembly.
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Affiliation(s)
- Fei Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Fang Zhou
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Dongxiang Xue
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Simeng Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Wanglong Lu
- School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Xiaoyan Liu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Tao Hu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanli Qiu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Rongyan Li
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tangjie Gu
- School of Physics Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yueming Xu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guisheng Zhong
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhongxing Jiang
- School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
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18
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Reinmuth L, Hsiao CC, Hamann J, Rosenkilde M, Mackrill J. Multiple Targets for Oxysterols in Their Regulation of the Immune System. Cells 2021; 10:cells10082078. [PMID: 34440846 PMCID: PMC8391951 DOI: 10.3390/cells10082078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Oxysterols, or cholesterol oxidation products, are naturally occurring lipids which regulate the physiology of cells, including those of the immune system. In contrast to effects that are mediated through nuclear receptors or by epigenetic mechanism, which take tens of minutes to occur, changes in the activities of cell-surface receptors caused by oxysterols can be extremely rapid, often taking place within subsecond timescales. Such cell-surface receptor effects of oxysterols allow for the regulation of fast cellular processes, such as motility, secretion and endocytosis. These cellular processes play critical roles in both the innate and adaptive immune systems. This review will survey the two broad classes of cell-surface receptors for oxysterols (G-protein coupled receptors (GPCRs) and ion channels), the mechanisms by which cholesterol oxidation products act on them, and their presence and functions in the different cell types of the immune system. Overall, this review will highlight the potential of oxysterols, synthetic derivatives and their receptors for physiological and therapeutic modulation of the immune system.
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Affiliation(s)
- Lisa Reinmuth
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark;
| | - Cheng-Chih Hsiao
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands; (C.-C.H.); (J.H.)
- Neuroimmunology Research Group, The Netherlands Institute for Neuroscience, 1105BA Amsterdam, The Netherlands
| | - Jörg Hamann
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands; (C.-C.H.); (J.H.)
- Neuroimmunology Research Group, The Netherlands Institute for Neuroscience, 1105BA Amsterdam, The Netherlands
| | - Mette Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark;
- Correspondence: (M.R.); (J.M.); Tel.: +353-(0)21-490-1400 (J.M.)
| | - John Mackrill
- Department of Physiology, School of Medicine, BioSciences Institute, University College Cork, College Road, Cork T12 YT20, Ireland
- Correspondence: (M.R.); (J.M.); Tel.: +353-(0)21-490-1400 (J.M.)
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19
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Yang J, Wang J, Liu Y, Zhang Y, Huang W, Zou Y, Qiu Y, Cai W, Gao J, Zhou H, Wu Y, Liu W, Ding Q, Zhang Y, Yin PH, Tan W. PGE2-JNK signaling axis non-canonically promotes Gli activation by protecting Gli2 from ubiquitin-proteasomal degradation. Cell Death Dis 2021; 12:707. [PMID: 34267186 PMCID: PMC8282835 DOI: 10.1038/s41419-021-03995-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022]
Abstract
Both bench and bedside investigations have challenged the supportive role of Hedgehog (Hh) activity in the progression of colorectal cancers, thus raising a critical need to further deeply determine the contribution of Hh to the growth of colorectal cancer. Combining multiple complementary means, including in vitro and in vivo inflammatory colorectal cancer models, and pathological analysis of clinical colorectal cancer patients samples. We report that colorectal cancer cells hijack prostaglandin E2 (PGE2) to non-canonically promote Hh transcriptional factor Gli activity and Gli-dependent proliferation of colorectal cancer cells in a Smo-independent manner. Mechanistically, PGE2 activates c-Jun N-terminal kinase (JNK), which in turn enables Gli2 to evade ubiquitin-proteasomal degradation by phosphorylating Gli2 at Thr1546. This study not only presents evidence for understanding the contribution of Hh to colorectal cancers, but also provides a novel molecular portrait underlying how PGE2-activated JNK fine-tunes the evasion of Gli2 from ubiquitin-proteasomal degradation. Therefore, it proposes a rationale for the future evaluation of chemopreventive and selective therapeutic strategies for colorectal cancers by targeting PGE2-JNK-Gli signaling route.
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Affiliation(s)
- Jun Yang
- Department of Pharmacology, School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Juan Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Yuan Liu
- Department of Pharmacology, School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Yu Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Wenjing Huang
- Department of Pharmacology, School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Yu Zou
- Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 200062, Shanghai, China.,Department of General Surgery, Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, 230601, Hefei, Anhui, China
| | - Yanyan Qiu
- Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 200062, Shanghai, China.,Department of General Surgery, Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, 230601, Hefei, Anhui, China
| | - Weiyang Cai
- Department of Oncology, Shanghai 9th pepople's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, 201999, Shanghai, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weijun Liu
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, 63108, USA
| | - Qingqing Ding
- Department of pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yanjie Zhang
- Department of Oncology, Shanghai 9th pepople's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, 201999, Shanghai, China
| | - Pei-Hao Yin
- Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 200062, Shanghai, China. .,Department of General Surgery, Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, 230601, Hefei, Anhui, China.
| | - Wenfu Tan
- Department of Pharmacology, School of Pharmacy, Fudan University, 201203, Shanghai, China.
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20
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The structural biology of canonical Wnt signalling. Biochem Soc Trans 2021; 48:1765-1780. [PMID: 32725184 PMCID: PMC7458405 DOI: 10.1042/bst20200243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022]
Abstract
The Wnt signalling pathways are of great importance in embryonic development and oncogenesis. Canonical and non-canonical Wnt signalling pathways are known, with the canonical (or β-catenin dependent) pathway being perhaps the best studied of these. While structural knowledge of proteins and interactions involved in canonical Wnt signalling has accumulated over the past 20 years, the pace of discovery has increased in recent years, with the structures of several key proteins and assemblies in the pathway being released. In this review, we provide a brief overview of canonical Wnt signalling, followed by a comprehensive overview of currently available X-ray, NMR and cryoEM data elaborating the structures of proteins and interactions involved in canonical Wnt signalling. While the volume of structures available is considerable, numerous gaps in knowledge remain, particularly a comprehensive understanding of the assembly of large multiprotein complexes mediating key aspects of pathway, as well as understanding the structure and activation of membrane receptors in the pathway. Nonetheless, the presently available data affords considerable opportunities for structure-based drug design efforts targeting canonical Wnt signalling.
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21
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Yang D, Zhou Q, Labroska V, Qin S, Darbalaei S, Wu Y, Yuliantie E, Xie L, Tao H, Cheng J, Liu Q, Zhao S, Shui W, Jiang Y, Wang MW. G protein-coupled receptors: structure- and function-based drug discovery. Signal Transduct Target Ther 2021; 6:7. [PMID: 33414387 PMCID: PMC7790836 DOI: 10.1038/s41392-020-00435-w] [Citation(s) in RCA: 208] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023] Open
Abstract
As one of the most successful therapeutic target families, G protein-coupled receptors (GPCRs) have experienced a transformation from random ligand screening to knowledge-driven drug design. We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace. This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.
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Affiliation(s)
- Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Sanaz Darbalaei
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Elita Yuliantie
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linshan Xie
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Qing Liu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,School of Pharmacy, Fudan University, 201203, Shanghai, China.
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22
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Radhakrishnan A, Rohatgi R, Siebold C. Cholesterol access in cellular membranes controls Hedgehog signaling. Nat Chem Biol 2020; 16:1303-1313. [PMID: 33199907 PMCID: PMC7872078 DOI: 10.1038/s41589-020-00678-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022]
Abstract
The Hedgehog (Hh) signaling pathway coordinates cell-cell communication in development and regeneration. Defects in this pathway underlie diseases ranging from birth defects to cancer. Hh signals are transmitted across the plasma membrane by two proteins, Patched 1 (PTCH1) and Smoothened (SMO). PTCH1, a transporter-like tumor-suppressor protein, binds to Hh ligands, but SMO, a G-protein-coupled-receptor family oncoprotein, transmits the Hh signal across the membrane. Recent structural, biochemical and cell-biological studies have converged at the surprising model that a specific pool of plasma membrane cholesterol, termed accessible cholesterol, functions as a second messenger that conveys the signal between PTCH1 and SMO. Beyond solving a central puzzle in Hh signaling, these studies are revealing new principles in membrane biology: how proteins respond to and remodel cholesterol accessibility in membranes and how the cholesterol composition of organelle membranes is used to regulate protein function.
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Affiliation(s)
- Arun Radhakrishnan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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23
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Yang S, Bahl K, Chou HT, Woodsmith J, Stelzl U, Walz T, Nachury MV. Near-atomic structures of the BBSome reveal the basis for BBSome activation and binding to GPCR cargoes. eLife 2020; 9:55954. [PMID: 32510327 PMCID: PMC7311171 DOI: 10.7554/elife.55954] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Dynamic trafficking of G protein-coupled receptors (GPCRs) out of cilia is mediated by the BBSome. In concert with its membrane recruitment factor, the small GTPase ARL6/BBS3, the BBSome ferries GPCRs across the transition zone, a diffusion barrier at the base of cilia. Here, we present the near-atomic structures of the BBSome by itself and in complex with ARL6GTP, and we describe the changes in BBSome conformation induced by ARL6GTP binding. Modeling the interactions of the BBSome with membranes and the GPCR Smoothened (SMO) reveals that SMO, and likely also other GPCR cargoes, must release their amphipathic helix 8 from the membrane to be recognized by the BBSome.
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Affiliation(s)
- Shuang Yang
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Kriti Bahl
- Department of Ophthalmology, University of California San Francisco, San Francisco, United States
| | - Hui-Ting Chou
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Jonathan Woodsmith
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria
| | - Ulrich Stelzl
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Maxence V Nachury
- Department of Ophthalmology, University of California San Francisco, San Francisco, United States
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24
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Kozielewicz P, Turku A, Bowin CF, Petersen J, Valnohova J, Cañizal MCA, Ono Y, Inoue A, Hoffmann C, Schulte G. Structural insight into small molecule action on Frizzleds. Nat Commun 2020; 11:414. [PMID: 31964872 PMCID: PMC6972889 DOI: 10.1038/s41467-019-14149-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/09/2019] [Indexed: 01/05/2023] Open
Abstract
WNT-Frizzled (FZD) signaling plays a critical role in embryonic development, stem cell regulation and tissue homeostasis. FZDs are linked to severe human pathology and are seen as a promising target for therapy. Despite intense efforts, no small molecule drugs with distinct efficacy have emerged. Here, we identify the Smoothened agonist SAG1.3 as a partial agonist of FZD6 with limited subtype selectivity. Employing extensive in silico analysis, resonance energy transfer- and luciferase-based assays we describe the mode of action of SAG1.3. We define the ability of SAG1.3 to bind to FZD6 and to induce conformational changes in the receptor, recruitment and activation of G proteins and dynamics in FZD–Dishevelled interaction. Our results provide the proof-of-principle that FZDs are targetable by small molecules acting on their seven transmembrane spanning core. Thus, we provide a starting point for a structure-guided and mechanism-based drug discovery process to exploit the potential of FZDs as therapeutic targets. WNT-Frizzled (FZD) signaling plays a critical role in embryonic development, tissue homeostasis and human disease but no small molecule drugs targeting FZD with distinct efficacy have emerged so far. Here, authors identify the Smoothened agonist SAG1.3 as a partial agonist for FZD6 with limited subtype selectivity.
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Affiliation(s)
- Paweł Kozielewicz
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, S-17165, Stockholm, Sweden
| | - Ainoleena Turku
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, S-17165, Stockholm, Sweden
| | - Carl-Fredrik Bowin
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, S-17165, Stockholm, Sweden
| | - Julian Petersen
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, S-17165, Stockholm, Sweden
| | - Jana Valnohova
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, S-17165, Stockholm, Sweden
| | - Maria Consuelo Alonso Cañizal
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany.,Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich-Schiller University Jena, Hans-Knöll-Strasse 2, 07745, Jena, Germany
| | - Yuki Ono
- Department of Pharmacological Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Asuka Inoue
- Department of Pharmacological Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Carsten Hoffmann
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany.,Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich-Schiller University Jena, Hans-Knöll-Strasse 2, 07745, Jena, Germany
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, S-17165, Stockholm, Sweden.
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25
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Xue D, Ye L, Zheng J, Wu Y, Zhang X, Xu Y, Li T, Stevens RC, Xu F, Zhuang M, Zhao S, Zhao F, Tao H. The structure-based traceless specific fluorescence labeling of the smoothened receptor. Org Biomol Chem 2019; 17:6136-6142. [PMID: 31180094 DOI: 10.1039/c9ob00654k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The smoothened receptor (SMO) mediates the hedgehog (Hh) signaling pathway and plays a vital role in embryonic development and tumorigenesis. The visualization of SMO has the potential to provide new insights into its enigmatic mechanisms and associated disease pathogenesis. Based on recent progress in structural studies of SMO, we have designed and characterized a group of affinity probes to facilitate the turn-on fluorescence labeling of SMO at the ε-amine of K395. These chemical probes were derived from a potent SMO antagonist skeleton by the conjugation of a small non-fluorescent unit, O-nitrobenzoxadiazole (O-NBD). In this context, optimal probes were developed to be capable of efficiently and selectively lighting up SMO regardless of whether it is in micelles or in native membranes. More importantly, the resulting labeled SMO only bears a very small fluorophore and allows for the recovery of the unoccupied pocket by dissociation of the residual ligand module. These advantages should allow the probe to serve as a potential tool for monitoring SMO trafficking, understanding Hh activation mechanisms, and even the diagnosis of tumorigenesis in the future.
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Affiliation(s)
- Dongxiang Xue
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Rd, Pudong New District, Shanghai 201210, China.
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26
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Zhou F, Ding K, Zhou Y, Liu Y, Liu X, Zhao F, Wu Y, Zhang X, Tan Q, Xu F, Tan W, Xiao Y, Zhao S, Tao H. Colocalization Strategy Unveils an Underside Binding Site in the Transmembrane Domain of Smoothened Receptor. J Med Chem 2019; 62:9983-9989. [PMID: 31408335 DOI: 10.1021/acs.jmedchem.9b00283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We unveiled an underside binding site on smoothened receptor (SMO) by a colocalization strategy using two structurally complementary photoaffinity probes derived from a known ligand Allo-1. Docking study and structural dissection identified key interactions within the site, including hydrogen bonding, π-π interactions, and hydrophobic interactions between Allo-1 and its contacting residues. Taken together, our results reveal the molecular base of Allo-1 binding and provide a basis for the design of new-generation ligands to overcome drug resistance.
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Affiliation(s)
- Fang Zhou
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China.,Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road, Building 3, Room 426 , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Kang Ding
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031 , China.,University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China.,School of Biotechnology and Food Engineering , Changshu Institute of Technology , Suzhou , Jiangsu 215500 , China
| | - Yang Liu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China
| | - Xiaoyan Liu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China
| | - Fei Zhao
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China
| | - Yiran Wu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China
| | - Xianjun Zhang
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China.,University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China.,Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031 , China
| | - Qiwen Tan
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China
| | - Fei Xu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Wenfu Tan
- Department of Pharmacology, School of Pharmacy , Fudan University , Shanghai 201203 , China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China.,University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
| | - Suwen Zhao
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Houchao Tao
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Pudong New District, Shanghai 201210 , China
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27
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Kozielewicz P, Turku A, Schulte G. Molecular Pharmacology of Class F Receptor Activation. Mol Pharmacol 2019; 97:62-71. [PMID: 31591260 DOI: 10.1124/mol.119.117986] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022] Open
Abstract
The class Frizzled (FZD) or class F of G protein-coupled receptors consists of 10 FZD paralogues and Smoothened (SMO). FZDs coordinate wingless/Int-1 signaling and SMO mediates Hedgehog signaling. Class F receptor signaling is intrinsically important for embryonic development and its dysregulation leads to diseases, including diverse forms of tumors. With regard to the importance of class F signaling in human disease, these receptors provide an attractive target for therapeutics, exemplified by the use of SMO antagonists for the treatment of basal cell carcinoma. Here, we review recent structural insights in combination with a more detailed functional understanding of class F receptor activation, G protein coupling, conformation-based functional selectivity, and mechanistic details of activating cancer mutations, which will lay the basis for further development of class F-targeting small molecules for human therapy. SIGNIFICANCE STATEMENT: Stimulated by recent insights into the activation mechanisms of class F receptors from structural and functional analysis of Frizzled and Smoothened, we aim to summarize what we know about the molecular details of ligand binding, agonist-driven conformational changes, and class F receptor activation. A better understanding of receptor activation mechanisms will allow us to engage in structure- and mechanism-driven drug discovery with the potential to develop more isoform-selective and potentially pathway-selective drugs for human therapy.
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Affiliation(s)
- Pawel Kozielewicz
- Section of Receptor Biology and Signaling, Department Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ainoleena Turku
- Section of Receptor Biology and Signaling, Department Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Schulte
- Section of Receptor Biology and Signaling, Department Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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28
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Lao Z, Chen Y, Tang Y, Wei G. Molecular Dynamics Simulations Reveal the Inhibitory Mechanism of Dopamine against Human Islet Amyloid Polypeptide (hIAPP) Aggregation and Its Destabilization Effect on hIAPP Protofibrils. ACS Chem Neurosci 2019; 10:4151-4159. [PMID: 31436406 DOI: 10.1021/acschemneuro.9b00393] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The aberrant self-assembly of human islet amyloid polypeptide (hIAPP) into toxic oligomers, protofibrils, and mature fibrils is associated with the pathogenesis of type 2 diabetes (T2D). Inhibition of hIAPP aggregation and destabilization of preformed hIAPP fibrils are considered as two major therapeutic strategies for treating T2D. Previous experimental studies reported that dopamine prevented the formation of hIAPP oligomers and fibrils. However, the underlying inhibitory mechanism at the atomic level remains elusive. Herein we investigated the conformational ensembles of hIAPP dimer with and without dopamine using replica-exchange molecular dynamics simulations. The simulations demonstrated that dopamine preferentially bound to R11, L12, F15, H18, F23, I26, L27, and Y37 residues, inhibited the formation of β-sheets in the amyloidogenic regions spanning residues 11RLANFLVH18, 22NFGAIL27, and 30TNVGSNT36, and resulted in more disordered hIAPP dimers, thus hindering the amyloid formation of hIAPP. Protonated and deprotonated dopamine molecules displayed distinct binding capabilities but bound to similar residue sites on hIAPP. Additional microsecond molecular dynamics simulations showed that dopamine mainly bound to the β1 and turn regions of hIAPP protofibril and destabilized the protofibril structure. This study not only revealed the molecular mechanism of dopamine toward the inhibition of hIAPP aggregation but also demonstrated the protofibril-destabilizing effects of dopamine, which may be helpful for the design of drug candidates to treat T2D.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
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29
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Xue D, Xu T, Wang H, Wu M, Yuan Y, Wang W, Tan Q, Zhao F, Zhou F, Hu T, Jiang Z, Liu Z, Zhao S, Liu D, Wüthrich K, Tao H. Disulfide‐Containing Detergents (DCDs) for the Structural Biology of Membrane Proteins. Chemistry 2019; 25:11635-11640. [DOI: 10.1002/chem.201903190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Dongxiang Xue
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- Shanghai Institute of Materia Medica Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Tiandan Xu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Huixia Wang
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Meng Wu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Ya Yuan
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Wei Wang
- Hubei Province Engineering and Technology Research Center, for Fluorinated Pharmaceuticals School of Pharmaceutical Sciences Wuhan University Wuhan 430071 China
| | - Qiwen Tan
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Fei Zhao
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Fang Zhou
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- Shanghai Institute of Materia Medica Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Tao Hu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- University of Chinese Academy of Sciences No. 19A, Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai 200031 China
| | - Zhongxing Jiang
- Hubei Province Engineering and Technology Research Center, for Fluorinated Pharmaceuticals School of Pharmaceutical Sciences Wuhan University Wuhan 430071 China
| | - Zhi‐Jie Liu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Suwen Zhao
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Dongsheng Liu
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
| | - Kurt Wüthrich
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Houchao Tao
- iHuman Institute ShanghaiTech University Ren Building 393 Middle Huaxia Road Pudong New District Shanghai 201210 China
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30
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Kowatsch C, Woolley RE, Kinnebrew M, Rohatgi R, Siebold C. Structures of vertebrate Patched and Smoothened reveal intimate links between cholesterol and Hedgehog signalling. Curr Opin Struct Biol 2019; 57:204-214. [PMID: 31247512 PMCID: PMC6744280 DOI: 10.1016/j.sbi.2019.05.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 12/21/2022]
Abstract
The Hedgehog (HH) signalling pathway is a cell-cell communication system that controls the patterning of multiple tissues during embryogenesis in metazoans. In adults, HH signals regulate tissue stem cells and regenerative responses. Abnormal signalling can cause birth defects and cancer. The HH signal is received on target cells by Patched (PTCH1), the receptor for HH ligands, and then transmitted across the plasma membrane by Smoothened (SMO). Recent structural and biochemical studies have pointed to a sterol lipid, likely cholesterol itself, as the elusive second messenger that communicates the HH signal between PTCH1 and SMO, thus linking ligand reception to transmembrane signalling.
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Affiliation(s)
- Christiane Kowatsch
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rachel E Woolley
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maia Kinnebrew
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, United States.
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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31
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Zhang Q, Cherezov V. Chemical tools for membrane protein structural biology. Curr Opin Struct Biol 2019; 58:278-285. [PMID: 31285102 DOI: 10.1016/j.sbi.2019.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/24/2023]
Abstract
Solving high-resolution structures of membrane proteins has been an important challenge for decades, still lagging far behind that of soluble proteins even with the recent remarkable technological advances in X-ray crystallography and electron microscopy. Central to this challenge is the necessity to isolate and solubilize membrane proteins in a stable, natively folded and functional state, a process influenced by not only the proteins but also their surrounding chemical environment. This review highlights recent community efforts in the development and characterization of novel membrane agents and ligand tools to stabilize individual proteins and protein complexes, which together have accelerated progress in membrane protein structural biology.
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Affiliation(s)
- Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
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32
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Deshpande I, Liang J, Hedeen D, Roberts KJ, Zhang Y, Ha B, Latorraca NR, Faust B, Dror RO, Beachy PA, Myers BR, Manglik A. Smoothened stimulation by membrane sterols drives Hedgehog pathway activity. Nature 2019; 571:284-288. [PMID: 31263273 PMCID: PMC6709672 DOI: 10.1038/s41586-019-1355-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/04/2019] [Indexed: 12/21/2022]
Abstract
Hedgehog signalling is fundamental to embryonic development and postnatal tissue regeneration1. Aberrant postnatal Hedgehog signalling leads to several malignancies, including basal cell carcinoma and paediatric medulloblastoma2. Hedgehog proteins bind to and inhibit the transmembrane cholesterol transporter Patched-1 (PTCH1), which permits activation of the seven-transmembrane transducer Smoothened (SMO) via a mechanism that is poorly understood. Here we report the crystal structure of active mouse SMO bound to both the agonist SAG21k and to an intracellular binding nanobody that stabilizes a physiologically relevant active state. Analogous to other G protein-coupled receptors, the activation of SMO is associated with subtle motions in the extracellular domain, and larger intracellular changes. In contrast to recent models3-5, a cholesterol molecule that is critical for SMO activation is bound deep within the seven-transmembrane pocket. We propose that the inactivation of PTCH1 by Hedgehog allows a transmembrane sterol to access this seven-transmembrane site (potentially through a hydrophobic tunnel), which drives the activation of SMO. These results-combined with signalling studies and molecular dynamics simulations-delineate the structural basis for PTCH1-SMO regulation, and suggest a strategy for overcoming clinical resistance to SMO inhibitors.
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Affiliation(s)
- Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jiahao Liang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Danielle Hedeen
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kelsey J Roberts
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yunxiao Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Betty Ha
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Naomi R Latorraca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Philip A Beachy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
- Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin R Myers
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA.
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33
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An X, Bai Q, Bai F, Shi D, Liu H, Yao X. Deciphering the Allosteric Effect of Antagonist Vismodegib on Smoothened Receptor Deactivation Using Metadynamics Simulation. Front Chem 2019; 7:406. [PMID: 31214579 PMCID: PMC6558189 DOI: 10.3389/fchem.2019.00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/20/2019] [Indexed: 01/12/2023] Open
Abstract
The smoothened receptor (Smo) plays a key role in Hedgehog (Hh) signaling pathway and it has been regarded as an efficacious therapeutic target for basal cell carcinoma (BCC) and medulloblastoma (MB). Nevertheless, the resistance mutation and active mutants of Smo have put forward the requirement of finding more effective inhibitors. Herein, we performed metadynamics simulations on Smo bound with vismodegib (Smo-Vismod) and with cholesterol (Smo-CLR), respectively, to explore the inhibition mechanism of vismodegib. The simulation results indicated that vismodegib-induced shifts of TM5, TM6, and TM7, which permitted the extracellular extension of TM6 and extracellular loop3 (ECL3) to enter the extracellular cysteine-rich domain (CRD) groove. Therefore, an open CRD groove that has not been noticed previously was observed in Smo-Vismod complex. As a consequence, the occupied CRD groove prevents the binding of cholesterol. In addition, the HD and ECLs play crucial roles in the interaction of CRD and TMD. These results reveal that TM5, TM6, and TM7 play important roles in allosteric inhibition the activation of Smo and disrupting cholesterol binding by vismodegib binding. Our results are expected to contribute to understanding the allosteric inhibition mechanism of Smo by vismodegib. Moreover, the detailed conformational changes contribute to the development of novel Smo inhibitors against resistance mutation and active mutants of Smo.
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Affiliation(s)
- Xiaoli An
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Qifeng Bai
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Fang Bai
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
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34
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Zhang H, Nielsen AL, Strømgaard K. Recent achievements in developing selective Gqinhibitors. Med Res Rev 2019; 40:135-157. [DOI: 10.1002/med.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Hang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co‐innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical SciencesZhengzhou UniversityZhengzhou Henan China
| | - Alexander L. Nielsen
- Department of Drug Design and Pharmacology, Center for BiopharmaceuticalsUniversity of CopenhagenCopenhagen Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for BiopharmaceuticalsUniversity of CopenhagenCopenhagen Denmark
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35
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Tajhya R, Delling M. New insights into ion channel-dependent signalling during left-right patterning. J Physiol 2019; 598:1741-1752. [PMID: 31106399 DOI: 10.1113/jp277835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/23/2019] [Indexed: 01/20/2023] Open
Abstract
The left-right organizer (LRO) in the mouse consists of pit cells within the depression, located at the end of the developing notochord, also known as the embryonic node and crown cells lining the outer periphery of the node. Cilia on pit cells are posteriorly tilted, rotate clockwise and generate leftward fluid flow. Primary cilia on crown cells are required to interpret the directionality of fluid movement and initiate flow-dependent gene transcription. Crown cells express PC1-L1 and PC2, which may form a heteromeric polycystin channel complex on primary cilia. It is still only poorly understood how fluid flow activates the ciliary polycystin complex. Besides polycystin channels voltage gated channels like HCN4 and KCNQ1 have been implicated in establishing asymmetry. How this electrical network of ion channels initiates left-sided signalling cascades and differential gene expression is currently only poorly defined.
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Affiliation(s)
- Rajeev Tajhya
- Department of Physiology, University of California, 1550 4th Street, San Francisco, CA, 94518, USA
| | - Markus Delling
- Department of Physiology, University of California, 1550 4th Street, San Francisco, CA, 94518, USA
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36
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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37
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Abstract
Signaling pathways that mediate cell-cell communication are essential for collective cell behaviors in multicellular systems. The hedgehog (HH) pathway, first discovered and elucidated in Drosophila, is one of these iconic signaling systems that plays many roles during embryogenesis and in adults; abnormal HH signaling can lead to birth defects and cancer. We review recent structural and biochemical studies that have advanced our understanding of the vertebrate HH pathway, focusing on the mechanisms by which the HH signal is received by patched on target cells, transduced across the cell membrane by smoothened, and transmitted to the nucleus by GLI proteins to influence gene-expression programs.
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Affiliation(s)
- Jennifer H Kong
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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38
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Schulte G, Kozielewicz P. Structural insight into Class F receptors - What have we learnt regarding agonist-induced activation? Basic Clin Pharmacol Toxicol 2019; 126 Suppl 6:17-24. [PMID: 30925000 DOI: 10.1111/bcpt.13235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022]
Abstract
Class F receptors, including the ten Frizzleds (FZD1-10 ) and SMO, mediate the effects of WNTs and hedgehog proteins and belong to the superfamily of G protein-coupled receptors (GPCRs). While the recent, high-resolution insight into mechanisms of GPCR activation provides a better understanding of receptor activation in Class A, B and C GPCRs, it remains unclear how Class F receptors bind their ligands, how ligand binding is translated to receptor activation and how signal initiation and specification are achieved. Here, we summarize recent efforts in elucidating Class F receptor structure and activation mechanisms and critically discuss the progress made in this area. A better understanding of the activation mechanisms of Class F receptors is required to engage in mechanism-based and structure-guided drug discovery to exploit the large therapeutic potential of targeting these receptors pharmacologically.
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Affiliation(s)
- Gunnar Schulte
- Section of Receptor Biology & Signaling, Department Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Paweł Kozielewicz
- Section of Receptor Biology & Signaling, Department Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
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39
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Xue D, Wang J, Song X, Wang W, Hu T, Ye L, Liu Y, Zhou Q, Zhou F, Jiang ZX, Liu ZJ, Tao H. A Chemical Strategy for Amphiphile Replacement in Membrane Protein Research. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4319-4327. [PMID: 30781953 DOI: 10.1021/acs.langmuir.8b04072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Membrane mimics are indispensable tools in the structural and functional understanding of membrane proteins (MPs). Given stringent requirements of integral MP manipulations, amphiphile replacement is often required in sample preparation for various biophysical purposes. Current protocols generally rely on physical methodologies and rarely reach complete replacement. In comparison, we report herein a chemical alternative that facilitates the exhaustive exchange of membrane-mimicking systems for MP reconstitution. This method, named sacrifice-replacement strategy, was enabled by a class of chemically cleavable detergents (CCDs), derived from the disulfide incorporation in the traditional detergent n-dodecyl-β-d-maltopyranoside. The representative CCD behaved well in both solubilizing the diverse α-helical human G protein-coupled receptors and refolding of the β-barrel bacterial outer membrane protein X, and more importantly, it could also be readily degraded under mild conditions. By this means, the A2A adenosine receptor was successfully reconstituted into a series of commercial detergents for stabilization screening and nanodiscs for electron microscopy analysis. Featured by the simplicity and compatibility, this CCD-mediated strategy would later find more applications when being integrated in other biophysics studies.
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Affiliation(s)
- Dongxiang Xue
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Jingjing Wang
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai 200031 , China
| | - Xiyong Song
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Wei Wang
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China
| | - Tao Hu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Lintao Ye
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Yang Liu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Qingtong Zhou
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Fang Zhou
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Zhong-Xing Jiang
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China
| | - Zhi-Jie Liu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Houchao Tao
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
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40
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Hedger G, Koldsø H, Chavent M, Siebold C, Rohatgi R, Sansom MSP. Cholesterol Interaction Sites on the Transmembrane Domain of the Hedgehog Signal Transducer and Class F G Protein-Coupled Receptor Smoothened. Structure 2019; 27:549-559.e2. [PMID: 30595453 PMCID: PMC6408332 DOI: 10.1016/j.str.2018.11.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/28/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022]
Abstract
Transduction of Hedgehog signals across the plasma membrane is facilitated by the class F G-protein-coupled-receptor (GPCR) Smoothened (SMO). Recent studies suggest that SMO is modulated via interactions of its transmembrane (TM) domain with cholesterol. We apply molecular dynamics simulations of SMO embedded in cholesterol containing lipid bilayers, revealing a direct interaction of cholesterol with the TM domain at regions distinct from those observed in class A GPCRs. In particular the extracellular tips of helices TM2 and TM3 form a well-defined cholesterol interaction site. Potential of mean force calculations yield a free energy landscape for cholesterol binding. Alongside analysis of equilibrium cholesterol occupancy, this reveals the existence of a dynamic "greasy patch" interaction with the TM domain of SMO, which may be compared with previously identified lipid interaction sites on other membrane proteins. These predictions provide molecular-level insights into cholesterol interactions with a class F GPCR, suggesting potential druggable sites.
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Affiliation(s)
- George Hedger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthieu Chavent
- Institut de Pharmacologie et de Biologie Structurale IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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41
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Zhu M, Wang H, Wang C, Fang Y, Zhu T, Zhao W, Dong X, Zhang X. L-4, a Well-Tolerated and Orally Active Inhibitor of Hedgehog Pathway, Exhibited Potent Anti-tumor Effects Against Medulloblastoma in vitro and in vivo. Front Pharmacol 2019; 10:89. [PMID: 30846937 PMCID: PMC6393386 DOI: 10.3389/fphar.2019.00089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/23/2019] [Indexed: 02/02/2023] Open
Abstract
Inhibition of aberrant Hedgehog (Hh) pathway had been proved to be a promising therapeutic intervention in cancers like basal cell carcinoma (BCC), medulloblastoma (MB), and so on. Two drugs (Vismodegib, Sonidegib) were approved to treat BCC and more inhibitors are in clinical investigation. However, the adverse effects and drug resistance restricted the use of Hh inhibitors. In the present study, 61 synthesized compounds containing central backbone of phthalazine or dimethylpyridazine were screened as candidates of new Hh signaling inhibitors by performing dual luciferase reporter assay. Among the compounds, L-4 exhibited an IC50 value of 2.33 nM in the Shh-Light II assay. L-4 strongly inhibited the Hh pathway in vitro and blocked the Hh pathway by antagonizing the smoothened receptor (Smo). Remarkably, L-4 could significantly suppress the Hh pathway activity provoked by Smo mutant (D473H) which showed strong resistant properties to existing drugs such as Vismodegib. Orally administered L-4 exhibited prominent dose-dependent anti-tumor efficacy in vivo in Ptch+/-; p53-/- MB allograft model. Furthermore, L-4 showed good tolerance in acute toxicity test using ICR mice. These evidences indicated that L-4 was a potent, well-tolerated, orally active inhibitor of Hedgehog pathway, and might be a promising candidate in development of Hh-targeted anti-cancer drugs.
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Affiliation(s)
- Mingfei Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Hong Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Chenglin Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Yanfen Fang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Weili Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Xiaochun Dong
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Xiongwen Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
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42
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Wright SC, Kozielewicz P, Kowalski-Jahn M, Petersen J, Bowin CF, Slodkowicz G, Marti-Solano M, Rodríguez D, Hot B, Okashah N, Strakova K, Valnohova J, Babu MM, Lambert NA, Carlsson J, Schulte G. A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection. Nat Commun 2019; 10:667. [PMID: 30737406 PMCID: PMC6368630 DOI: 10.1038/s41467-019-08630-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Class F receptors are considered valuable therapeutic targets due to their role in human disease, but structural changes accompanying receptor activation remain unexplored. Employing population and cancer genomics data, structural analyses, molecular dynamics simulations, resonance energy transfer-based approaches and mutagenesis, we identify a conserved basic amino acid in TM6 in Class F receptors that acts as a molecular switch to mediate receptor activation. Across all tested Class F receptors (FZD4,5,6,7, SMO), mutation of the molecular switch confers an increased potency of agonists by stabilizing an active conformation as assessed by engineered mini G proteins as conformational sensors. Disruption of the switch abrogates the functional interaction between FZDs and the phosphoprotein Dishevelled, supporting conformational selection as a prerequisite for functional selectivity. Our studies reveal the molecular basis of a common activation mechanism conserved in all Class F receptors, which facilitates assay development and future discovery of Class F receptor-targeting drugs. Class F receptors are therapeutic targets in human disease and understanding their structural changes during receptor activation may provide important pharmacological insight. Here, the authors combine computational and experimental methods to identify a molecular switch in TM6/7 of Class F receptors that mediates receptor activation.
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Affiliation(s)
- Shane C Wright
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Paweł Kozielewicz
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Maria Kowalski-Jahn
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Julian Petersen
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Carl-Fredrik Bowin
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Greg Slodkowicz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Maria Marti-Solano
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - David Rodríguez
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24, Uppsala, Sweden
| | - Belma Hot
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Najeah Okashah
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, 30912, USA
| | - Katerina Strakova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - Jana Valnohova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, 30912, USA
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24, Uppsala, Sweden
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17165, Stockholm, Sweden.
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43
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Wu Y, Tong J, Ding K, Zhou Q, Zhao S. GPCR Allosteric Modulator Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:225-251. [PMID: 31707706 DOI: 10.1007/978-981-13-8719-7_10] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology; about one-third of all marketed drugs target members of this family. GPCR allosteric ligands hold the promise of improved subtype selectivity, spatiotemporal sensitivity, and possible biased property over typical orthosteric ligands. However, only a small number of GPCR allosteric ligands have been approved as drugs or in clinical trials since the discovery process is very challenging. The rapid development of GPCR structural biology leads to the discovery of several allosteric sites and sheds light on understanding the mechanism of GPCR allosteric ligands, which is critical for discovering novel therapeutics. This book chapter summarized different GPCR allosteric modulating mechanisms and discussed validated mechanisms based on allosteric modulator-GPCR complex structures.
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Affiliation(s)
- Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Jiahui Tong
- iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kang Ding
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Qingtong Zhou
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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44
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Pietrobono S, Stecca B. Targeting the Oncoprotein Smoothened by Small Molecules: Focus on Novel Acylguanidine Derivatives as Potent Smoothened Inhibitors. Cells 2018; 7:cells7120272. [PMID: 30558232 PMCID: PMC6316656 DOI: 10.3390/cells7120272] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 12/13/2022] Open
Abstract
Hedgehog-GLI (HH) signaling was originally identified as a critical morphogenetic pathway in embryonic development. Since its discovery, a multitude of studies have reported that HH signaling also plays key roles in a variety of cancer types and in maintaining tumor-initiating cells. Smoothened (SMO) is the main transducer of HH signaling, and in the last few years, it has emerged as a promising therapeutic target for anticancer therapy. Although vismodegib and sonidegib have demonstrated effectiveness for the treatment of basal cell carcinoma (BCC), their clinical use has been hampered by severe side effects, low selectivity against cancer stem cells, and the onset of mutation-driven drug resistance. Moreover, SMO antagonists are not effective in cancers where HH activation is due to mutations of pathway components downstream of SMO, or in the case of noncanonical, SMO-independent activation of the GLI transcription factors, the final mediators of HH signaling. Here, we review the current and rapidly expanding field of SMO small-molecule inhibitors in experimental and clinical settings, focusing on a class of acylguanidine derivatives. We also discuss various aspects of SMO, including mechanisms of resistance to SMO antagonists.
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Affiliation(s)
- Silvia Pietrobono
- Tumor Cell Biology Unit⁻Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy.
| | - Barbara Stecca
- Tumor Cell Biology Unit⁻Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy.
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45
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Wright SC, Cañizal MCA, Benkel T, Simon K, Le Gouill C, Matricon P, Namkung Y, Lukasheva V, König GM, Laporte SA, Carlsson J, Kostenis E, Bouvier M, Schulte G, Hoffmann C. FZD 5 is a Gα q-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs. Sci Signal 2018; 11:11/559/eaar5536. [PMID: 30514810 DOI: 10.1126/scisignal.aar5536] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Frizzleds (FZDs) are a group of seven transmembrane-spanning (7TM) receptors that belong to class F of the G protein-coupled receptor (GPCR) superfamily. FZDs bind WNT proteins to stimulate diverse signaling cascades involved in embryonic development, stem cell regulation, and adult tissue homeostasis. Frizzled 5 (FZD5) is one of the most studied class F GPCRs that promote the functional inactivation of the β-catenin destruction complex in response to WNTs. However, whether FZDs function as prototypical GPCRs has been heavily debated and, in particular, FZD5 has not been shown to activate heterotrimeric G proteins. Here, we show that FZD5 exhibited a conformational change after the addition of WNT-5A, which is reminiscent of class A and class B GPCR activation. In addition, we performed several live-cell imaging and spectrometric-based approaches, such as dual-color fluorescence recovery after photobleaching (dcFRAP) and resonance energy transfer (RET)-based assays that demonstrated that FZD5 activated Gαq and its downstream effectors upon stimulation with WNT-5A. Together, these findings suggest that FZD5 is a 7TM receptor with a bona fide GPCR activation profile and suggest novel targets for drug discovery in WNT-FZD signaling.
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Affiliation(s)
- Shane C Wright
- Section of Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, S17165 Stockholm, Sweden.,Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3C 3J7, Canada
| | - Maria Consuelo Alonso Cañizal
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany.,Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich-Schiller University Jena, Hans-Knöll-Strasse 2, 07745 Jena, Germany
| | - Tobias Benkel
- Institute for Pharmaceutical Biology, University of Bonn, 53115 Bonn, Germany
| | - Katharina Simon
- Institute for Pharmaceutical Biology, University of Bonn, 53115 Bonn, Germany
| | - Christian Le Gouill
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3C 3J7, Canada
| | - Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden
| | - Yoon Namkung
- Department of Medicine, Research Institute of the McGill University Health Center, McGill University, Montréal, QC H4A 3J1, Canada
| | - Viktoria Lukasheva
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3C 3J7, Canada
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, 53115 Bonn, Germany
| | - Stéphane A Laporte
- Department of Medicine, Research Institute of the McGill University Health Center, McGill University, Montréal, QC H4A 3J1, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden
| | - Evi Kostenis
- Institute for Pharmaceutical Biology, University of Bonn, 53115 Bonn, Germany
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3C 3J7, Canada
| | - Gunnar Schulte
- Section of Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, S17165 Stockholm, Sweden.
| | - Carsten Hoffmann
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany. .,Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich-Schiller University Jena, Hans-Knöll-Strasse 2, 07745 Jena, Germany
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46
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Overcoming the emerging drug resistance of smoothened: an overview of small-molecule SMO antagonists with antiresistance activity. Future Med Chem 2018; 10:2855-2875. [PMID: 30557039 DOI: 10.4155/fmc-2018-0200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hedgehog (HH) signaling pathway plays vital roles in controlling embryonic cell fate and homeostatic, and becomes dormant in mature individuals, aberrant activation of HH signaling pathway is involved in a number of human cancers. Smoothened (SMO), a vital transducer of HH signaling pathway, attracts significant attentions in HH signaling pathway-related cancer therapy. The approval of SMO antagonists vismodegib proves that SMO is a promising therapeutic target, and a number of SMO antagonists are reported since then. However, high incidence of tumor recurrence with the clinical application of vismodegib urges exploring of novel drugs with antiresistance profiles. This review provides an overview of SMO mutations reported in the literature, crystal structures of SMO, as well as reported antagonists with antiresistance profiles.
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47
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Valnohova J, Kowalski-Jahn M, Sunahara RK, Schulte G. Functional dissection of the N-terminal extracellular domains of Frizzled 6 reveals their roles for receptor localization and Dishevelled recruitment. J Biol Chem 2018; 293:17875-17887. [PMID: 30237173 PMCID: PMC6240854 DOI: 10.1074/jbc.ra118.004763] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/18/2018] [Indexed: 11/06/2022] Open
Abstract
The Frizzled (FZD) proteins belong to class F of G protein-coupled receptors (GPCRs) and are essential for various pathways involving the secreted lipoglycoproteins of the wingless/int-1 (WNT) family. A WNT-binding cysteine-rich domain (CRD) in FZDs is N-terminally located and connected to the seven transmembrane domain-spanning receptor core by a linker domain that has a variable length in different FZD homologs. However, the function and importance of this linker domain are poorly understood. Here we used systematic mutagenesis of FZD6 to define the minimal N-terminal domain sufficient for receptor surface expression and recruitment of the intracellular scaffold protein Dishevelled (DVL). Further, we identified a triad of evolutionarily conserved cysteines in the FZD linker domain that is crucial for receptor membrane expression and recruitment of DVL. Our results are in agreement with the concept that the conserved cysteines in the linker domain of FZDs assist with the formation of a common secondary structure in this region. We propose that this structure could be involved in agonist binding and receptor activation mechanisms that are similar to the binding and activation mechanisms known for other GPCRs.
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Affiliation(s)
- Jana Valnohova
- From the Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maria Kowalski-Jahn
- From the Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, California 92093
| | - Gunnar Schulte
- From the Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, 171 65 Stockholm, Sweden.
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48
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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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49
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Abstract
New roles are discovered for cholesterol transport in a key developmental signaling pathway
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Affiliation(s)
- Anselm Sommer
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
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50
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Crystal structure of the Frizzled 4 receptor in a ligand-free state. Nature 2018; 560:666-670. [DOI: 10.1038/s41586-018-0447-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/10/2018] [Indexed: 01/07/2023]
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