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Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol 2024; 20:751-760. [PMID: 38480980 PMCID: PMC11142920 DOI: 10.1038/s41589-024-01562-z] [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: 02/14/2023] [Accepted: 01/25/2024] [Indexed: 05/30/2024]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.
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Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Li He
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Huong T Kratochvil
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Sarah E Nick
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Weiya Bai
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Anne Edwards
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, New Haven, CT, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
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2
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Abraham BG, Haikarainen T, Vuorio J, Girych M, Virtanen AT, Kurttila A, Karathanasis C, Heilemann M, Sharma V, Vattulainen I, Silvennoinen O. Molecular basis of JAK2 activation in erythropoietin receptor and pathogenic JAK2 signaling. SCIENCE ADVANCES 2024; 10:eadl2097. [PMID: 38457493 PMCID: PMC10923518 DOI: 10.1126/sciadv.adl2097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
Janus kinase 2 (JAK2) mediates type I/II cytokine receptor signaling, but JAK2 is also activated by somatic mutations that cause hematological malignancies by mechanisms that are still incompletely understood. Quantitative superresolution microscopy (qSMLM) showed that erythropoietin receptor (EpoR) exists as monomers and dimerizes upon Epo stimulation or through the predominant JAK2 pseudokinase domain mutations (V617F, K539L, and R683S). Crystallographic analysis complemented by kinase activity analysis and atomic-level simulations revealed distinct pseudokinase dimer interfaces and activation mechanisms for the mutants: JAK V617F activity is driven by dimerization, K539L involves both increased receptor dimerization and kinase activity, and R683S prevents autoinhibition and increases catalytic activity and drives JAK2 equilibrium toward activation state through a wild-type dimer interface. Artificial intelligence-guided modeling and simulations revealed that the pseudokinase mutations cause differences in the pathogenic full-length JAK2 dimers, particularly in the FERM-SH2 domains. A detailed molecular understanding of mutation-driven JAK2 hyperactivation may enable novel therapeutic approaches to selectively target pathogenic JAK2 signaling.
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Affiliation(s)
| | - Teemu Haikarainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Anniina T. Virtanen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Antti Kurttila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Olli Silvennoinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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3
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Bernstein ZJ, Shenoy A, Chen A, Heller NM, Spangler JB. Engineering the IL-4/IL-13 axis for targeted immune modulation. Immunol Rev 2023; 320:29-57. [PMID: 37283511 DOI: 10.1111/imr.13230] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/19/2023] [Indexed: 06/08/2023]
Abstract
The structurally and functionally related interleukin-4 (IL-4) and IL-13 cytokines play pivotal roles in shaping immune activity. The IL-4/IL-13 axis is best known for its critical role in T helper 2 (Th2) cell-mediated Type 2 inflammation, which protects the host from large multicellular pathogens, such as parasitic helminth worms, and regulates immune responses to allergens. In addition, IL-4 and IL-13 stimulate a wide range of innate and adaptive immune cells, as well as non-hematopoietic cells, to coordinate various functions, including immune regulation, antibody production, and fibrosis. Due to its importance for a broad spectrum of physiological activities, the IL-4/IL-13 network has been targeted through a variety of molecular engineering and synthetic biology approaches to modulate immune behavior and develop novel therapeutics. Here, we review ongoing efforts to manipulate the IL-4/IL-13 axis, including cytokine engineering strategies, formulation of fusion proteins, antagonist development, cell engineering approaches, and biosensor design. We discuss how these strategies have been employed to dissect IL-4 and IL-13 pathways, as well as to discover new immunotherapies targeting allergy, autoimmune diseases, and cancer. Looking ahead, emerging bioengineering tools promise to continue advancing fundamental understanding of IL-4/IL-13 biology and enabling researchers to exploit these insights to develop effective interventions.
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Affiliation(s)
- Zachary J Bernstein
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anjali Shenoy
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amy Chen
- Department of Molecular and Cellular Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicola M Heller
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Division of Allergy and Clinical Immunology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jamie B Spangler
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Sidney Kimmel Cancer Center, The Johns Hopkins University, Baltimore, Maryland, USA
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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4
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Zhang P, Jiang Y, Xu C, Zhou L, Zheng H, Xie D, Guo M, Huang X, Lu G, Jiang H, Qiu H, Liu B, Li S, Chen Q, Xia Y, Sun B, Yang X, Zhang S, Du S, Sun M, Chen M, Zhong A, Wang X, Zhao Z, Zhou H, Li G, Ren Y, Luo Q, Yang A, Luo P, Tang S, Xu C, Wang Q, Wang X, Yan T, He W, Qin S, Zhang W, Lv L, Wang C, Liu H, Li J, Wu Q, Pan C, Li C, He L, Chen J. Pegmolesatide for the treatment of anemia in patients undergoing dialysis: a randomized clinical trial. EClinicalMedicine 2023; 65:102273. [PMID: 37954906 PMCID: PMC10632410 DOI: 10.1016/j.eclinm.2023.102273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 11/14/2023] Open
Abstract
Background Pegmolesatide, a synthetic peptide-based erythropoietin (EPO) receptor agonist, is being evaluated as an alternative to epoetin alfa for treating anemia of chronic kidney disease (CKD) in Chinese dialysis patients. There is a critical need for a long-acting, cost-effective erythropoiesis-stimulating agent that does not produce EPO antibodies. Methods A randomized, open-label, active-comparator, non-inferiority phase three trial was conducted at 43 dialysis centers in China between May 17th, 2019, and March 28th, 2022. Eligible patients aged 18-70 years were randomly assigned (2:1) to receive pegmolesatide once every four weeks or epoetin alfa one to three times per week, with doses adjusted to maintain a hemoglobin level between 10.0 and 12.0 g/dL. The primary efficacy endpoint was the mean change in hemoglobin level from baseline to the efficacy evaluation period in the per-protocol set (PPS) population. Non-inferiority of pegmolesatide to epoetin alfa was established if the lower limit of the two-sided 95% confidence interval for the between-group difference was ≥ -1.0 g/dL. Safety assessment included adverse events and potential anaphylaxis reactions. This trial is registered at ClinicalTrials.gov, NCT03902691. Findings Three hundreds and seventy-two patients were randomly assigned to the pegmolesatide group (248 patients) or the epoetin alfa group (124 patients). A total of 347 patients (233 in the pegmolesatide group and 114 in the epoetin alfa group) were included in the PPS population. In the PPS, the mean change (standard deviation, SD) in hemoglobin level from baseline to the efficacy evaluation period was 0.07 (0.92) g/dL in the pegmolesatide group and -0.22 (0.97) g/dL in the epoetin alfa group. The between-group difference was 0.29 g/dL (95% confidence interval: 0.11-0.47), verifying non-inferiority of pegmolesatide to epoetin alfa. Adverse events occurred in 231 (94%) participants in the pegmolesatide group and in 110 (89%) in the epoetin alfa group. Hypertension was the most common treatment-related adverse event. No fatal cases of anaphylaxis or hypotension were reported. Interpretation Monthly subcutaneously injection of pegmolesatide was as effective and safe as conventional epoetin alfa administrated one to three times a week in treating anemia in Chinese dialysis patients. Funding The study was supported by Hansoh Medical Development Group.
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Affiliation(s)
- Ping Zhang
- Kidney Disease Center, The First Affiliated Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Yan Jiang
- Kidney Disease Center, The First Affiliated Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Chunping Xu
- Kidney Disease Center, The First Affiliated Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Linghui Zhou
- The Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Hongguang Zheng
- The Department of Nephrology, General Hospital of Northern Theater Command, Shengyang, China
| | - Deqiong Xie
- The Department of Nephrology, The Second People's Hospital of Yibin, Yibin, China
| | - Minghao Guo
- The Department of Nephrology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiangyang Huang
- The Department of Nephrology, Liuzhou Worker's Hospital, Liuzhou, China
| | - Guoyuan Lu
- The Department of Nephrology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hongli Jiang
- The Department of Blood Purification, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Hongyu Qiu
- The Department of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Bicheng Liu
- The Institute of Nephrology, Zhongda Hospital Southeast University, Nanjing, China
| | - Shaomei Li
- The Department of Nephrology, The Second Hospital of HeBei Medical University, Shijiazhuang, China
| | - Qinkai Chen
- The Department of Nephrology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yu'ou Xia
- The Department of Nephrology, Siping Central People's Hospital, Siping, China
| | - Bengui Sun
- The Department of Nephrology, The Second People's Hospital of Hefei, Hefei, China
| | - Xiao Yang
- The Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Shiying Zhang
- The Department of Nephrology, Jilin Province People's Hospital, Changchun, China
| | - Shutong Du
- The Department of Nephrology, Cangzhou People's Hospital, Cangzhou, China
| | - Mindan Sun
- The Department of Nephrology, The First Bethune Hospital of Jilin University, Changchun, China
| | - Menghua Chen
- The Department of Nephrology, General Hospital of Ningxia Medical University, Yinchuang, China
| | - Aimin Zhong
- The Department of Nephrology, People's Hospital of Jiangxi Province, Nanchang, China
| | - Xiaoling Wang
- The Department of Nephrology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhanzheng Zhao
- The Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hua Zhou
- The Department of Nephrology, Shengjing Hospital of China Medicine University, Shengyang, China
| | - Guisen Li
- The Department of Nephrology, Sichuan Academy of Medical Sciences – Sichuan Provincial People's Hospital (SAMSPH), Chengdu, China
| | - Yueqin Ren
- The Department of Nephrology, LinYi People's Hospital, Linyi, China
| | - Qun Luo
- The Department of Nephrology, Hwamei Hospital, University of Chinese Academy of Sciences, China
| | - Aicheng Yang
- The Department of Nephrology, Wuyi Hospital of T.C.M, Jiangmen City (Affiliated Jiangmen TCM Hospital of Jinan University), China
| | - Ping Luo
- The Department of Nephrology, The Second Norman Bethune Hospital of Jilin University, Changchun, China
| | - Shuifu Tang
- The Department of Nephrology, The First Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chengyun Xu
- The Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qin Wang
- The Department of Nephrology, Shanghai Fengxian Center Hospital, Shanghai, China
| | - Xiaoxia Wang
- The Department of Nephrology, Tong Ren Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiekun Yan
- The Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Wei He
- The Department of Nephrology, Traditional Chinese Medical Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Shuguang Qin
- The Department of Nephrology, Guangzhou First People's Hospital, Guangzhou, China
| | - Weili Zhang
- The Department of Nephrology, The First Hospital of Qiqihar, Qiqihar, China
| | - Lu Lv
- The Department of Nephrology, The First Affiliated Hospital/The First Clinical Medicine School of Guangdong Pharmaceutical University, Guangzhou, China
| | - Cheng Wang
- The Department of Nephrology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Hong Liu
- The Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jing Li
- The Department of Nephrology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Qiong Wu
- Hansoh Pharmaceutical Group Co, Ltd, Shanghai, China
| | - Chao Pan
- Hansoh Pharmaceutical Group Co, Ltd, Shanghai, China
| | - Chuan Li
- Hansoh Pharmaceutical Group Co, Ltd, Shanghai, China
| | - Liangliang He
- Hansoh Pharmaceutical Group Co, Ltd, Shanghai, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, Medical School of Zhejiang University, Hangzhou, China
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5
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Tsutsumi N, Masoumi Z, James SC, Tucker JA, Winkelmann H, Grey W, Picton LK, Moss L, Wilson SC, Caveney NA, Jude KM, Gati C, Piehler J, Hitchcock IS, Garcia KC. Structure of the thrombopoietin-MPL receptor complex is a blueprint for biasing hematopoiesis. Cell 2023; 186:4189-4203.e22. [PMID: 37633268 PMCID: PMC10528194 DOI: 10.1016/j.cell.2023.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Thrombopoietin (THPO or TPO) is an essential cytokine for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Here, we report the 3.4 Å resolution cryoelectron microscopy structure of the extracellular TPO-TPO receptor (TpoR or MPL) signaling complex, revealing the basis for homodimeric MPL activation and providing a structural rationalization for genetic loss-of-function thrombocytopenia mutations. The structure guided the engineering of TPO variants (TPOmod) with a spectrum of signaling activities, from neutral antagonists to partial- and super-agonists. Partial agonist TPOmod decoupled JAK/STAT from ERK/AKT/CREB activation, driving a bias for megakaryopoiesis and platelet production without causing significant HSC expansion in mice and showing superior maintenance of human HSCs in vitro. These data demonstrate the functional uncoupling of the two primary roles of TPO, highlighting the potential utility of TPOmod in hematology research and clinical HSC transplantation.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.
| | - Zahra Masoumi
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Sophie C James
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Julie A Tucker
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - William Grey
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Lora K Picton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucie Moss
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Ian S Hitchcock
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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6
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McFarlane A, Pohler E, Moraga I. Molecular and cellular factors determining the functional pleiotropy of cytokines. FEBS J 2023; 290:2525-2552. [PMID: 35246947 PMCID: PMC10952290 DOI: 10.1111/febs.16420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022]
Abstract
Cytokines are soluble factors vital for mammalian physiology. Cytokines elicit highly pleiotropic activities, characterized by their ability to induce a wide spectrum of functional responses in a diverse range of cell subsets, which makes their study very challenging. Cytokines activate signalling via receptor dimerization/oligomerization, triggering activation of the JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling pathway. Given the strong crosstalk and shared usage of key components of cytokine signalling pathways, a long-standing question in the field pertains to how functional diversity is achieved by cytokines. Here, we discuss how biophysical - for example, ligand-receptor binding affinity and topology - and cellular - for example, receptor, JAK and STAT protein levels, endosomal compartment - parameters contribute to the modulation and diversification of cytokine responses. We review how these parameters ultimately converge into a common mechanism to fine-tune cytokine signalling that involves the control of the number of Tyr residues phosphorylated in the receptor intracellular domain upon cytokine stimulation. This results in different kinetics of STAT activation, and induction of specific gene expression programs, ensuring the generation of functional diversity by cytokines using a limited set of signalling intermediaries. We describe how these first principles of cytokine signalling have been exploited using protein engineering to design cytokine variants with more specific and less toxic responses for immunotherapy.
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Affiliation(s)
- Alison McFarlane
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
| | - Elizabeth Pohler
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
| | - Ignacio Moraga
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
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7
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Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
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8
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Wesseler F, Riege D, Puthanveedu M, Halver J, Müller E, Bertrand J, Antonchick AP, Sievers S, Waldmann H, Schade D. Probing Embryonic Development Enables the Discovery of Unique Small-Molecule Bone Morphogenetic Protein Potentiators. J Med Chem 2022; 65:3978-3990. [PMID: 35108017 DOI: 10.1021/acs.jmedchem.1c01800] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report on the feasibility to harness embryonic development in vitro for the identification of small-molecule cytokine mimetics and signaling activators. Here, a phenotypic, target-agnostic, high-throughput assay is presented that probes bone morphogenetic protein (BMP) signaling during mesodermal patterning of embryonic stem cells. The temporal discrimination of BMP- and transforming growth factor-β (TGFβ)-driven stages of cardiomyogenesis underpins a selective, authentic orchestration of BMP cues that can be recapitulated for the discovery of BMP activator chemotypes. Proof of concept is shown from a chemical screen of 7000 compounds, provides a robust hit validation workflow, and afforded 2,3-disubstituted 4H-chromen-4-ones as potent BMP potentiators with osteogenic efficacy. Mechanistic studies suggest that Chromenone 1 enhances canonical BMP outputs at the expense of TGFβ-Smads in an unprecedented manner. Pharmacophoric features were defined, providing a set of novel chemical probes for various applications in (stem) cell biology, regenerative medicine, and basic research on the BMP pathway.
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Affiliation(s)
- Fabian Wesseler
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.,Compound Management and Screening Center, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Daniel Riege
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Mahesh Puthanveedu
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Jonas Halver
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Eva Müller
- Department of Orthopedic Surgery, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Jessica Bertrand
- Department of Orthopedic Surgery, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Andrey P Antonchick
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Department of Chemistry and Forensics, College of Science and Technology, Nottingham Trent University, Clifton Lane, NG11 8NS Nottingham, United Kingdom
| | - Sonja Sievers
- Compound Management and Screening Center, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Dennis Schade
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Partner Site Kiel, DZHK, German Center for Cardiovascular Research, 24105 Kiel, Germany
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9
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Hashemi ZS, Zarei M, Fath MK, Ganji M, Farahani MS, Afsharnouri F, Pourzardosht N, Khalesi B, Jahangiri A, Rahbar MR, Khalili S. In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions. Front Mol Biosci 2021; 8:669431. [PMID: 33996914 PMCID: PMC8113820 DOI: 10.3389/fmolb.2021.669431] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Large contact surfaces of protein-protein interactions (PPIs) remain to be an ongoing issue in the discovery and design of small molecule modulators. Peptides are intrinsically capable of exploring larger surfaces, stable, and bioavailable, and therefore bear a high therapeutic value in the treatment of various diseases, including cancer, infectious diseases, and neurodegenerative diseases. Given these promising properties, a long way has been covered in the field of targeting PPIs via peptide design strategies. In silico tools have recently become an inevitable approach for the design and optimization of these interfering peptides. Various algorithms have been developed to scrutinize the PPI interfaces. Moreover, different databases and software tools have been created to predict the peptide structures and their interactions with target protein complexes. High-throughput screening of large peptide libraries against PPIs; "hotspot" identification; structure-based and off-structure approaches of peptide design; 3D peptide modeling; peptide optimization strategies like cyclization; and peptide binding energy evaluation are among the capabilities of in silico tools. In the present study, the most recent advances in the field of in silico approaches for the design of interfering peptides against PPIs will be reviewed. The future perspective of the field and its advantages and limitations will also be pinpointed.
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Affiliation(s)
- Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research, Tehran, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahboube Shahrabi Farahani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Afsharnouri
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Department of Biochemistry, Guilan University of Medical Sciences, Rasht, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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10
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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11
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Saha I, Dang EK, Svatunek D, Houk KN, Harran PG. Computational generation of an annotated gigalibrary of synthesizable, composite peptidic macrocycles. Proc Natl Acad Sci U S A 2020; 117:24679-24690. [PMID: 32948694 PMCID: PMC7547232 DOI: 10.1073/pnas.2007304117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptidomimetic macrocycles have the potential to regulate challenging therapeutic targets. Structures of this type having precise shapes and drug-like character are particularly coveted, but are relatively difficult to synthesize. Our laboratory has developed robust methods that integrate small-peptide units into designed scaffolds. These methods create macrocycles and embed condensed heterocycles to diversify outcomes and improve pharmacological properties. The hypothetical scope of the methodology is vast and far outpaces the capacity of our experimental format. We now describe a computational rendering of our methodology that creates an in silico three-dimensional library of composite peptidic macrocycles. Our open-source platform, CPMG (Composite Peptide Macrocycle Generator), has algorithmically generated a library of 2,020,794,198 macrocycles that can result from the multistep reaction sequences we have developed. Structures are generated based on predicted site reactivity and filtered on the basis of physical and three-dimensional properties to identify maximally diverse compounds for prioritization. For conformational analyses, we also introduce ConfBuster++, an RDKit port of the open-source software ConfBuster, which allows facile integration with CPMG and ready parallelization for better scalability. Our approach deeply probes ligand space accessible via our synthetic methodology and provides a resource for large-scale virtual screening.
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Affiliation(s)
- Ishika Saha
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Eric K Dang
- Department of Computer Science, University of California, Los Angeles, CA 90095
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
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12
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Affiliation(s)
- Gerhard M. Gahl
- Department of Nephrology and Medical Intensive Care, Virchow Klinikum, Humboldt University, Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Virchow Klinikum, Humboldt University, Berlin, Germany
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13
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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14
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Mohan K, Ueda G, Kim AR, Jude KM, Fallas JA, Guo Y, Hafer M, Miao Y, Saxton RA, Piehler J, Sankaran VG, Baker D, Garcia KC. Topological control of cytokine receptor signaling induces differential effects in hematopoiesis. Science 2019; 364:eaav7532. [PMID: 31123111 PMCID: PMC7274355 DOI: 10.1126/science.aav7532] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Although tunable signaling by G protein-coupled receptors can be exploited through medicinal chemistry, a comparable pharmacological approach has been lacking for the modulation of signaling through dimeric receptors, such as those for cytokines. We present a strategy to modulate cytokine receptor signaling output by use of a series of designed C2-symmetric cytokine mimetics, based on the designed ankyrin repeat protein (DARPin) scaffold, that can systematically control erythropoietin receptor (EpoR) dimerization orientation and distance between monomers. We sampled a range of EpoR geometries by varying intermonomer angle and distance, corroborated by several ligand-EpoR complex crystal structures. Across the range, we observed full, partial, and biased agonism as well as stage-selective effects on hematopoiesis. This surrogate ligand strategy opens access to pharmacological modulation of therapeutically important cytokine and growth factor receptor systems.
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Affiliation(s)
- Kritika Mohan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ah Ram Kim
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Maximillian Hafer
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
- Center for Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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15
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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16
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Scheide-Noeth JP, Rosen M, Baumstark D, Dietz H, Mueller TD. Structural Basis of Interleukin-5 Inhibition by the Small Cyclic Peptide AF17121. J Mol Biol 2018; 431:714-731. [PMID: 30529748 DOI: 10.1016/j.jmb.2018.11.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
Interleukin-5 (IL-5) is a T-helper cell of subtype 2 cytokine involved in many aspects of eosinophil life. Eosinophilic granulocytes play a pathogenic role in the progression of atopic diseases, such as allergy, asthma and atopic dermatitis and hypereosinophilic syndromes. Here, eosinophils upon activation degranulate leading to the release of proinflammatory proteins and mediators stored in intracellular vesicles termed granula thereby causing local inflammation, which when persisting leads to tissue damage and organ failure. As a key regulator of eosinophil function, IL-5 therefore presents a major pharmaceutical target and approaches to interfere with IL-5 receptor activation are of great interest. Here we present the structure of the IL-5 inhibiting peptide AF17121 bound to the extracellular domain of the IL-5 receptor IL-5Rα. The small 18mer cyclic peptide snugly fits into the wrench-like cleft of the IL-5 receptor, thereby blocking access of key residues for IL-5 binding. While AF17121 and IL-5 seemingly bind to a similar epitope at IL-5Rα, functional studies show that recognition and binding of both ligands differ. Using the structure data, peptide variants with improved IL-5 inhibition have been generated, which might present valuable starting points for superior peptide-based IL-5 antagonists.
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Affiliation(s)
- Jan-Philipp Scheide-Noeth
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - Maximilian Rosen
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - David Baumstark
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - Harald Dietz
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany
| | - Thomas D Mueller
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute of the University Wuerzburg, Julius-von-Sachs-Platz 2, D-97082, Wuerzburg, Germany.
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17
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Cellular signaling and gene expression profiles evoked by a bivalent macrocyclic peptide that serves as an artificial MET receptor agonist. Sci Rep 2018; 8:16492. [PMID: 30405161 PMCID: PMC6220203 DOI: 10.1038/s41598-018-34835-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/26/2018] [Indexed: 11/11/2022] Open
Abstract
Non-native ligands for growth factor receptors that are generated by chemical synthesis are applicable to therapeutics. However, non-native ligands often regulate cellular signaling and biological responses in a different manner than native ligands. Generation of surrogate ligands comparable to native ligands is a challenging need. Here we investigated changes in signal transduction and gene expression evoked by a bivalent macrocyclic peptide (aMD5-PEG11) capable of high-affinity binding to the MET/hepatocyte growth factor (HGF) receptor. Binding of aMD5-PEG11 to the MET extracellular region was abolished by deletion of the IPT3−IPT4 domain, indicating the involvement of IPT3−IPT4 in the binding of aMD5-PEG11 to the MET receptor. aMD5-PEG11 induced dimerization and activation of the MET receptor and promoted cell migration that was comparable to induction of these activities by HGF. Signal activation profiles indicated that aMD5-PEG11 induced phosphorylation of intracellular signaling molecules, with a similar intensity and time dependency as HGF. In 3-D culture, aMD5-PEG11 as well as HGF induced epithelial tubulogenesis and up-regulated the same sets of functionally classified genes involved in multicellular organism development. Thus, a non-native surrogate ligand that consisted of a bivalent macrocyclic peptide can serve as an artificial MET receptor agonist that functionally substitutes for the native ligand, HGF.
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18
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Feng S, Chang S, Yan L, Dong H, Xu X, Wang C, Liang Y, Liu K. Design, synthesis, and activity evaluation of novel erythropoietin mimetic peptides. Bioorg Med Chem Lett 2018; 28:3038-3041. [PMID: 30097369 DOI: 10.1016/j.bmcl.2018.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 11/19/2022]
Abstract
The approval of the erythropoietin (EPO) mimetic peptide drug peginesatide in 2012 was a breakthrough for the treatment of secondary anemia. However, due to severe allergic reactions, peginesatide was recalled a year later. In this study, 12 novel peptides were designed and synthesized by substituting specific amino acids of the monomeric peptide in peginesatide, with the aim of obtaining new EPO mimetic peptides with higher activities and lower side effects than the parent compound. Their cell proliferation activities were evaluated, and the structure-activity relationships were analyzed. Five compounds had equal cell proliferation activity to the control peptide. Among them, one compound showed a higher in vivo activity than the control peptide, with no obvious side effects.
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Affiliation(s)
- Siliang Feng
- Beijing Institute of Pharmacology and Toxicology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing 100850, China
| | - Shaohua Chang
- Beijing Prowincan Pharmaceutical Technology Co. Ltd., Beijing 102600, China
| | - Lingdi Yan
- Beijing Institute of Pharmacology and Toxicology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing 100850, China
| | - Huajin Dong
- Beijing Institute of Pharmacology and Toxicology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing 100850, China
| | - Xiaoyu Xu
- Beijing Prowincan Pharmaceutical Technology Co. Ltd., Beijing 102600, China
| | - Chenhong Wang
- Beijing Institute of Pharmacology and Toxicology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing 100850, China
| | - Yuanjun Liang
- Beijing Prowincan Pharmaceutical Technology Co. Ltd., Beijing 102600, China.
| | - Keliang Liu
- Beijing Institute of Pharmacology and Toxicology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing 100850, China.
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19
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Ferrao RD, Wallweber HJ, Lupardus PJ. Receptor-mediated dimerization of JAK2 FERM domains is required for JAK2 activation. eLife 2018; 7:38089. [PMID: 30044226 PMCID: PMC6078494 DOI: 10.7554/elife.38089] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
Cytokines and interferons initiate intracellular signaling via receptor dimerization and activation of Janus kinases (JAKs). How JAKs structurally respond to changes in receptor conformation induced by ligand binding is not known. Here, we present two crystal structures of the human JAK2 FERM and SH2 domains bound to Leptin receptor (LEPR) and Erythropoietin receptor (EPOR), which identify a novel dimeric conformation for JAK2. This 2:2 JAK2/receptor dimer, observed in both structures, identifies a previously uncharacterized receptor interaction essential to dimer formation that is mediated by a membrane-proximal peptide motif called the ‘switch’ region. Mutation of the receptor switch region disrupts STAT phosphorylation but does not affect JAK2 binding, indicating that receptor-mediated formation of the JAK2 FERM dimer is required for kinase activation. These data uncover the structural and molecular basis for how a cytokine-bound active receptor dimer brings together two JAK2 molecules to stimulate JAK2 kinase activity.
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Affiliation(s)
- Ryan D Ferrao
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
| | - Heidi Ja Wallweber
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
| | - Patrick J Lupardus
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
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20
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Erythropoietin mimetic peptides and erythropoietin fusion proteins for treating anemia of chronic kidney disease. Curr Opin Nephrol Hypertens 2018; 27:345-350. [PMID: 29746307 DOI: 10.1097/mnh.0000000000000430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW First generation erythropoiesis stimulating agents (ESAs) have short duration of action which requires administration once weekly or greater. Second generation ESAs were developed which have longer duration of action and can be administered one to two times monthly. Erythropoietin (EPO) mimetic peptides (EMPs) activate the EPO receptor but have no structural analogy to EPO, offering the potential for lower cost as they are not biologic drugs. The first approved EMP, peginesatide, was withdrawn from the market within a year of its approval because of fatal anaphylactic reactions. In this review, we summarize recent progress regarding the development of newer, possibly less toxic, EMPs. We also summarize the development of EPO fusion proteins which fuse EPO with a portion of an immunoglobulin molecule or another EPO molecule, achieving a longer duration of action and less frequent dosing. RECENT FINDINGS AGEM400(hydroxyethyl starch) and pegolsihematide are EMPs in phase II clinical trials. Three EPO fusion proteins are under development, two in phase I and one in phase II. SUMMARY The future success of EMPs is limited by the prior experience with peginesatide and EPO fusion proteins do not offer cost savings or longer duration of action than currently available ESAs.
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21
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David M, Lécorché P, Masse M, Faucon A, Abouzid K, Gaudin N, Varini K, Gassiot F, Ferracci G, Jacquot G, Vlieghe P, Khrestchatisky M. Identification and characterization of highly versatile peptide-vectors that bind non-competitively to the low-density lipoprotein receptor for in vivo targeting and delivery of small molecules and protein cargos. PLoS One 2018; 13:e0191052. [PMID: 29485998 PMCID: PMC5828360 DOI: 10.1371/journal.pone.0191052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/27/2017] [Indexed: 01/09/2023] Open
Abstract
Insufficient membrane penetration of drugs, in particular biotherapeutics and/or low target specificity remain a major drawback in their efficacy. We propose here the rational characterization and optimization of peptides to be developed as vectors that target cells expressing specific receptors involved in endocytosis or transcytosis. Among receptors involved in receptor-mediated transport is the LDL receptor. Screening complex phage-displayed peptide libraries on the human LDLR (hLDLR) stably expressed in cell lines led to the characterization of a family of cyclic and linear peptides that specifically bind the hLDLR. The VH411 lead cyclic peptide allowed endocytosis of payloads such as the S-Tag peptide or antibodies into cells expressing the hLDLR. Size reduction and chemical optimization of this lead peptide-vector led to improved receptor affinity. The optimized peptide-vectors were successfully conjugated to cargos of different nature and size including small organic molecules, siRNAs, peptides or a protein moiety such as an Fc fragment. We show that in all cases, the peptide-vectors retain their binding affinity to the hLDLR and potential for endocytosis. Following i.v. administration in wild type or ldlr-/- mice, an Fc fragment chemically conjugated or fused in C-terminal to peptide-vectors showed significant biodistribution in LDLR-enriched organs. We have thus developed highly versatile peptide-vectors endowed with good affinity for the LDLR as a target receptor. These peptide-vectors have the potential to be further developed for efficient transport of therapeutic or imaging agents into cells -including pathological cells-or organs that express the LDLR.
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Affiliation(s)
| | | | | | | | | | | | - Karine Varini
- VECT-HORUS SAS, Marseille, France
- Aix Marseille Univ, CNRS, NICN, Marseille, France
| | | | - Géraldine Ferracci
- Aix Marseille Univ, CNRS, CRN2M, Marseille, France
- Aix Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | | | | | - Michel Khrestchatisky
- Aix Marseille Univ, CNRS, NICN, Marseille, France
- Aix Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
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22
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23
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Deyle K, Kong XD, Heinis C. Phage Selection of Cyclic Peptides for Application in Research and Drug Development. Acc Chem Res 2017; 50:1866-1874. [PMID: 28719188 DOI: 10.1021/acs.accounts.7b00184] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclic peptides can bind to protein targets with high affinities and selectivities, which makes them an attractive modality for the development of research reagents and therapeutics. Additional properties, including low inherent toxicity, efficient chemical synthesis, and facile modification with labels or immobilization reagents, increase their attractiveness. Cyclic peptide ligands against a wide range of protein targets have been isolated from natural sources such as bacteria, fungi, plants, and animals. Many of them are currently used as research tools, and several have found application as therapeutics, such as the peptide hormones oxytocin and vasopressin and the antibiotics vancomycin and daptomycin, proving the utility of cyclic peptides in research and medicine. With the advent of phage display and other in vitro evolution techniques, it has become possible to generate cyclic peptide binders to diverse protein targets for which no natural peptides have been discovered. A highly robust and widely applied approach is based on the cyclization of peptides displayed on phage via a disulfide bridge. Disulfide-cyclized peptide ligands to more than a hundred different proteins have been reported in the literature. Technology advances achieved over the last three decades, including methods for generating larger phage display libraries, improved phage panning protocols, new cyclic peptide formats, and high-throughput sequencing, have enabled the generation of cyclic peptides with ever better binding affinities to more challenging targets. A relatively new cyclic peptide format developed using phage display involves bicyclic peptides. These molecules consist of two macrocyclic peptide rings cyclized through a chemical linker. Compared to monocyclic peptides of comparable molecular mass, bicyclic peptides are more constrained in their conformation. As a result, they can bind to their targets with a higher affinity and are more resistant to proteolytic degradation. Phage-encoded bicyclic peptides are generated by chemically cyclizing random peptide libraries on phage. Binders are identified by conventional phage panning and DNA sequencing. Next-generation sequencing and new sequence alignment tools have enabled the rapid identification of bicyclic peptides. Bicyclic peptide ligands were developed against a range of diverse target classes including enzymes, receptors, and cytokines. Most ligands bind with nanomolar affinities, with some reaching the picomolar range. To date, several bicyclic peptides have been positively evaluated in preclinical studies, and the first clinical tests are in sight. While bicyclic peptide phage display was developed with therapeutic applications in mind, these peptides are increasingly used as research tools for target evaluation or as basic research probes as well. Given the efficient development method, the ease of synthesis and handling, and the favorable binding and biophysical properties, bicyclic peptides are being developed against more and more targets, ever increasing their potential applications in research and medicine.
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Affiliation(s)
- Kaycie Deyle
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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24
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Corbett MSP, Mark AE, Poger D. Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study. Biophys J 2017; 112:595-604. [PMID: 28256220 PMCID: PMC5340159 DOI: 10.1016/j.bpj.2016.12.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/20/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022] Open
Abstract
Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion.
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Affiliation(s)
- Michael S P Corbett
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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25
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Zorzi A, Deyle K, Heinis C. Cyclic peptide therapeutics: past, present and future. Curr Opin Chem Biol 2017; 38:24-29. [PMID: 28249193 DOI: 10.1016/j.cbpa.2017.02.006] [Citation(s) in RCA: 462] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/27/2017] [Accepted: 02/06/2017] [Indexed: 01/07/2023]
Abstract
Cyclic peptides combine several favorable properties such as good binding affinity, target selectivity and low toxicity that make them an attractive modality for the development of therapeutics. Over 40 cyclic peptide drugs are currently in clinical use and around one new cyclic peptide drug enters the market every year on average. The vast majority of clinically approved cyclic peptides are derived from natural products, such as antimicrobials or human peptide hormones. New powerful techniques based on rational design and in vitro evolution have enabled the de novo development of cyclic peptide ligands to targets for which nature does not offer solutions. A look at the cyclic peptides currently under clinical evaluation shows that several have been developed using such techniques. This new source for cyclic peptide ligands introduces a freshness to the field, and it is likely that de novo developed cyclic peptides will be in clinical use in the near future.
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Affiliation(s)
- Alessandro Zorzi
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kaycie Deyle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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26
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Analysis of the Asymmetry of Activated EPO Receptor Enables Designing Small Molecule Agonists. VITAMINS AND HORMONES 2017. [DOI: 10.1016/bs.vh.2017.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Ohnishi T, Sakamoto K, Asami-Odaka A, Nakamura K, Shimizu A, Ito T, Asami T, Ohtaki T, Inooka H. Generation of a novel artificial TrkB agonist, BM17d99, using T7 phage-displayed random peptide libraries. Biochem Biophys Res Commun 2017; 483:101-106. [DOI: 10.1016/j.bbrc.2016.12.186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 12/29/2016] [Indexed: 11/30/2022]
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28
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Discovery of an artificial peptide agonist to the fibroblast growth factor receptor 1c/βKlotho complex from random peptide T7 phage display. Biochem Biophys Res Commun 2016; 480:55-60. [DOI: 10.1016/j.bbrc.2016.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 02/06/2023]
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29
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Marcuzzi F, Zucchelli S, Bertuzzi M, Santoro C, Tell G, Carninci P, Gustincich S. Isoforms of the Erythropoietin receptor in dopaminergic neurons of the Substantia Nigra. J Neurochem 2016; 139:596-609. [PMID: 27488413 DOI: 10.1111/jnc.13757] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 11/29/2022]
Abstract
Erythropoietin receptor (EpoR) regulates erythrocytes differentiation in blood. In the brain, EpoR has been shown to protect several neuronal cell types from cell death, including the A9 dopaminergic neurons (DA) of the Substantia Nigra (SN). These cells form the nigrostriatal pathway and are devoted to the control of postural reflexes and voluntary movements. Selective degeneration of A9 DA neurons leads to Parkinson's disease. By the use of nanoCAGE, a technology that allows the identification of Transcription Start Sites (TSSs) at a genome-wide level, we have described the promoter-level expression atlas of mouse A9 DA neurons purified with Laser Capture Microdissection (LCM). Here, we identify mRNA variants of the Erythropoietin Receptor (DA-EpoR) transcribed from alternative TSSs. Experimental validation and full-length cDNA cloning is integrated with gene expression analysis in the FANTOM5 database. In DA neurons, the EpoR gene encodes for a N-terminal truncated receptor. Based on STAT5 phosphorylation assays, we show that the new variant of N-terminally truncated EpoR acts as decoy when co-expressed with the full-length form. A similar isoform is also found in human. This work highlights new complexities in the regulation of Erythropoietin (EPO) signaling in the brain.
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Affiliation(s)
| | - Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy.,Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | | | - Claudio Santoro
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Gianluca Tell
- Department of Medical and Biological Sciences (DSMB), University of Udine, Udine, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
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30
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Esposito A, Capalbo D, De Martino L, Rezzuto M, Di Mase R, Pignata C, Salerno M. Long-term effects of growth hormone (GH) replacement therapy on hematopoiesis in a large cohort of children with GH deficiency. Endocrine 2016; 53:192-8. [PMID: 26511947 DOI: 10.1007/s12020-015-0781-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
The aim of our prospective case-control study was to evaluate long-term effects of GH replacement therapy on erythrocytes parameters, leukocytes, and platelets numbers in a large cohort of children with isolated GH deficiency (GHD). Hemoglobin (Hb) concentration, hematocrit (Hct), mean corpuscular volume, mean corpuscular hemoglobin, red cell distribution width, number of erythrocytes, leukocytes, neutrophils, lymphocytes, monocytes and platelets, ferritin, and C-reactive protein were evaluated in 85 children with isolated GHD (10.20 ± 3.50 years) before and annually during the first 5 years of GH replacement therapy and in 85 healthy children age and sex comparable to patients during 5 years of follow-up. Compared with controls, GHD children at study entry showed lower Hb (-1.18 ± 0.87 vs. -0.40 ± 0.90 SDS, p < 0.0001), red cells number (-0.24 ± 0.81 vs. 0.25 ± 1.14 SDS, p < 0.0001), and Hct (-1.18 ± 0.86 vs. -0.68 ± 0.99 SDS, p < 0.0001). Twelve GHD patients (14 %) showed a normocytic anemia. GH therapy was associated with a significant increase in Hb, Hct, and red cells number which became all comparable to controls within the first 2 years of treatment. Moreover, hemoglobin levels normalized in all anemic GHD patients after 5 years of therapy. No difference between patients and controls was found in leukocytes and platelets numbers neither at baseline nor during the study. GHD in childhood is associated with an impairment of erythropoiesis which causes a normocytic anemia in a considerable percentage of patients. GH replacement therapy exerts a beneficial effect leading to a significant increase of erythrocytes parameters and recovery from anemia. Neither GHD nor GH replacement treatment exerts effects on leukocytes or platelets numbers.
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Affiliation(s)
- Andrea Esposito
- Pediatric Endocrinology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy
| | - Donatella Capalbo
- Pediatric Endocrinology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy
| | - Lucia De Martino
- Pediatric Endocrinology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy
| | - Martina Rezzuto
- Pediatric Endocrinology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy
| | - Raffaella Di Mase
- Pediatric Endocrinology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy
| | - Claudio Pignata
- Pediatric Immunology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy
| | - Mariacarolina Salerno
- Pediatric Endocrinology Unit, Department of Translational Medical Sciences, University of Naples "Federico II", via Sergio Pansini 5, 80131, Naples, Italy.
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31
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Jelkmann W. Watch out for a revival of peginesatide in sports. Drug Test Anal 2016; 9:157-160. [DOI: 10.1002/dta.1979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Wolfgang Jelkmann
- Institute of Physiology; University of Lübeck; D-23562 Lübeck Germany
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32
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Bonomini M, Del Vecchio L, Sirolli V, Locatelli F. New Treatment Approaches for the Anemia of CKD. Am J Kidney Dis 2016; 67:133-42. [DOI: 10.1053/j.ajkd.2015.06.030] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/29/2015] [Indexed: 12/20/2022]
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33
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Wu Y, Wang N, Lei Y, Hu T, You Q, Zhang X. Small-molecule inhibitors of HIF-PHD2: a valid strategy to renal anemia treatment in clinical therapy. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00240d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Patients with chronic kidney diseases (CKD) always suffer from anemia with severe impacts on their quality of life.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Natural Medicines
- and Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Nan Wang
- State Key Laboratory of Natural Medicines
- and Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Yonghua Lei
- State Key Laboratory of Natural Medicines
- and Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Tianhan Hu
- State Key Laboratory of Natural Medicines
- and Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Qidong You
- State Key Laboratory of Natural Medicines
- and Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines
- and Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 210009
- China
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34
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Abstract
Erythropoietin (EPO) is a protein made by the kidneys in response to low red blood cell count that is secreted into the bloodstream and binds to a receptor on hematopoietic stem cells in the bone marrow inducing them to become new red blood cells. EPO made with recombinant DNA technology was brought to market in the 1980s to treat anemia caused by kidney disease and cancer chemotherapy. Because EPO infusion was able to replace blood transfusions in many cases, it rapidly became a multibillion dollar per year drug and as the first biologic created with recombinant technology it launched the biotech industry. For many years intense research was focused on creating a small molecule orally available EPO mimetic. The Robert Wood Johnson (RWJ) group seemed to definitively establish that only large peptides with a minimum of 60 residues could replace EPO, as anything less was not a full agonist. An intense study of the published work led me to hypothesize that the size of the mimetic is not the real issue, but the symmetry making and breaking of the EPO receptor induced by the ligand is the key to activating the stem cells. This analysis meant that residues in the binding site of the receptor deemed absolutely essential for ligand binding and activation from mutagenesis experiments, were probably not really that important. My fundamental hypotheses were: (a) the symmetric state of the homodimeric receptor is the most stable state and thus must be the off-state, (b) a highly localized binding site exists at a pivot point where the two halves of the receptor meet, (c) small molecules can be created that have high potency for this site that will be competitive with EPO and thus can displace the protein-protein interaction, (d) small symmetric molecules will stabilize the symmetric off-state of the receptor, and (e) a key asymmetry in the small molecule will stabilize a mirror image asymmetry in the receptor resulting in the stabilization of the on-state and proliferation of the stem cells into red blood cells. Researchers at Amgen published a co-crystal structure of EPO bound to the EPO receptor, which has a beautiful twofold symmetry-it was argued that this is the active state of the receptor. Activating the EPO receptor with EPO induces an almost instantaneous shutdown mechanism to sharply curtail any proliferative signal transduction, and thus, my hypotheses lead to the conclusion that the Amgen co-crystal is actually the state after receptor downregulation and thus an off-state. To put these hypotheses to the test, my computational method of Simulated Annealing of Chemical Potential was run using the co-crystal created at RWJ, which is the receptor trapped in a partial agonist state. The simulations predicted a previously unknown high affinity binding site at the pivot point where the two halves of the dimeric receptor meet, and detailed analysis of the fragment patterns led to the prediction of a molecule less than 300 MW that is basically twofold symmetric with a chiral center on one side and not the other. Thus, to the degree that computer simulations can be taken seriously, these results support my hypotheses on small molecule receptor activation. When this small molecule was synthesized and tested it indeed induced human hematopoietic stems cells to become red blood cells. When the predicted chiral center of this molecule was removed eliminating its one asymmetric feature, the resulting molecule was an antagonist-it could potently displace hot EPO but could no longer induce stem cell proliferation and differentiation. These results provided strong support for my theories on how to create potent small molecule EPO agonists and were used to launch the new company Locus Pharmaceuticals. These molecules, however, required significant chemical changes in order to make them stable in other in vitro assays and to be in vivo active, but these alterations had to be done in a way that maintained the symmetry-asymmetry considerations that led to the creation of an in vitro active molecule. The combination of changing functional groups to enable good pharmacokinetics, while not changing the key intrinsic symmetry properties were never seriously pursued at Locus and the program died. Investigations into how red blood cells are created have occupied many prominent researchers for the entire twentieth century. In the second half of the century EPO was discovered and by the end of the century it became a blockbuster commercial product that launched the biotech revolution.
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Affiliation(s)
- Frank Guarnieri
- Department of Physiology & Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA,
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35
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Vogel M, Thomas A, Schänzer W, Thevis M. EPOR-Based Purification and Analysis of Erythropoietin Mimetic Peptides from Human Urine by Cys-Specific Cleavage and LC/MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1617-1625. [PMID: 26122516 DOI: 10.1007/s13361-015-1189-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/04/2015] [Accepted: 05/08/2015] [Indexed: 06/04/2023]
Abstract
The development of a new class of erythropoietin mimetic agents (EMA) for treating anemic conditions has been initiated with the discovery of oligopeptides capable of dimerizing the erythropoietin (EPO) receptor and thus stimulating erythropoiesis. The most promising amino acid sequences have been mounted on various different polymeric structures or carrier molecules to obtain highly active EPO-like drugs exhibiting beneficial and desirable pharmacokinetic profiles. Concomitant with creating new therapeutic options, erythropoietin mimetic peptide (EMP)-based drug candidates represent means to artificially enhance endurance performance and necessitate coverage by sports drug testing methods. Therefore, the aim of the present study was to develop a strategy for the comprehensive detection of EMPs in doping controls, which can be used complementary to existing protocols. Three model EMPs were used to provide proof-of-concept data. Following EPO receptor-facilitated purification of target analytes from human urine, the common presence of the cysteine-flanked core structure of EMPs was exploited to generate diagnostic peptides with the aid of a nonenzymatic cleavage procedure. Sensitive detection was accomplished by targeted-SIM/data-dependent MS(2) analysis. Method characterization was conducted for the EMP-based drug peginesatide concerning specificity, linearity, precision, recovery, stability, ion suppression/enhancement, and limit of detection (LOD, 0.25 ng/mL). Additionally, first data for the identification of the erythropoietin mimetic peptides EMP1 and BB68 were generated, demonstrating the multi-analyte testing capability of the presented approach.
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Affiliation(s)
- Matthias Vogel
- Center for Preventive Doping Research/Institute of Biochemistry, German Sport University, Cologne, Germany
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36
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Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan R. Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Aminothiol Unnatural Amino Acids. ACS Chem Biol 2015; 10:1805-16. [PMID: 25933125 DOI: 10.1021/acschembio.5b00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A versatile method for orchestrating the formation of side chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Upon ribosomal incorporation into intein-containing precursor proteins, designer unnatural amino acids bearing side chain 1,3- or 1,2-aminothiol functionalities are able to promote the cyclization of a downstream target peptide sequence via a C-terminal ligation/ring contraction mechanism. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro or directly in living bacterial cells. This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. This strategy was applied to identify and isolate a low-micromolar streptavidin binder (KD = 1.1 μM) from a library of cyclic peptides produced in Escherichia coli, thereby illustrating its potential toward aiding the discovery of functional peptide macrocycles.
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Affiliation(s)
- John R. Frost
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Nicholas T. Jacob
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Louis J. Papa
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Andrew E. Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
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37
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Tsai Y, Holton T, Yeates TO. Diffusion accessibility as a method for visualizing macromolecular surface geometry. Protein Sci 2015; 24:1702-5. [PMID: 26189444 DOI: 10.1002/pro.2752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022]
Abstract
Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/.
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Affiliation(s)
- Yingssu Tsai
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Thomas Holton
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles.,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA
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38
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Miller JL, Church TJ, Leonoudakis D, Lariosa-Willingham K, Frigon NL, Tettenborn CS, Spencer JR, Punnonen J. Discovery and Characterization of Nonpeptidyl Agonists of the Tissue-Protective Erythropoietin Receptor. Mol Pharmacol 2015; 88:357-67. [PMID: 26018904 DOI: 10.1124/mol.115.098400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/27/2015] [Indexed: 11/22/2022] Open
Abstract
Erythropoietin (EPO) and its receptor are expressed in a wide variety of tissues, including the central nervous system. Local expression of both EPO and its receptor is upregulated upon injury or stress and plays a role in tissue homeostasis and cytoprotection. High-dose systemic administration or local injection of recombinant human EPO has demonstrated encouraging results in several models of tissue protection and organ injury, while poor tissue availability of the protein limits its efficacy. Here, we describe the discovery and characterization of the nonpeptidyl compound STS-E412 (2-[2-(4-chlorophenoxy)ethoxy]-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidine), which selectively activates the tissue-protective EPO receptor, comprising an EPO receptor subunit (EPOR) and the common β-chain (CD131). STS-E412 triggered EPO receptor phosphorylation in human neuronal cells. STS-E412 also increased phosphorylation of EPOR, CD131, and the EPO-associated signaling molecules JAK2 and AKT in HEK293 transfectants expressing EPOR and CD131. At low nanomolar concentrations, STS-E412 provided EPO-like cytoprotective effects in primary neuronal cells and renal proximal tubular epithelial cells. The receptor selectivity of STS-E412 was confirmed by a lack of phosphorylation of the EPOR/EPOR homodimer, lack of activity in off-target selectivity screening, and lack of functional effects in erythroleukemia cell line TF-1 and CD34(+) progenitor cells. Permeability through artificial membranes and Caco-2 cell monolayers in vitro and penetrance across the blood-brain barrier in vivo suggest potential for central nervous system availability of the compound. To our knowledge, STS-E412 is the first nonpeptidyl, selective activator of the tissue-protective EPOR/CD131 receptor. Further evaluation of the potential of STS-E412 in central nervous system diseases and organ protection is warranted.
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Gharanlar J, Hosseinkhani S, Sajedi RH, Yaghmaei P. The Effect of Surface Charge Saturation on Heat-induced Aggregation of Firefly Luciferase. Photochem Photobiol 2015; 91:1156-64. [PMID: 25989897 DOI: 10.1111/php.12467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
We present here the effect of firefly luciferase surface charge saturation and the presence of some additives on its thermal-induced aggregation. Three mutants of firefly luciferase prepared by introduction of surface Arg residues named as 2R, 3R and 5R have two, three and five additional arginine residues substituted at their surface compared to native luciferase; respectively. Turbidimetric study of heat-induced aggregation indicates that all three mutants were reproducibly aggregated at higher rates relative to wild type in spite of their higher thermostability. Among them, 2R had most evaluated propensity to heat-induced aggregation. Therefore, the hydrophilization followed by appearing of more substituted arginine residues with positive charge on the firefly luciferase surface was not reduced its thermal aggregation. Nevertheless, at the same condition in the presence of charged amino acids, e.g. Arg, Lys and Glu, as well as a hydrophobic amino acid, e.g. Val, the heat-induced aggregation of wild type and mutants of firefly luciferases was markedly decelerated than those in the absence of additives. On the basis of obtained results it seems, relinquishment of variety in charge of amino acid side chains, they via local interactions with proteins cause to decrease rate and extent of their thermal aggregation.
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Affiliation(s)
- Jamileh Gharanlar
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parichehr Yaghmaei
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
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Moraga I, Wernig G, Wilmes S, Gryshkova V, Richter CP, Hong WJ, Sinha R, Guo F, Fabionar H, Wehrman TS, Krutzik P, Demharter S, Plo I, Weissman IL, Minary P, Majeti R, Constantinescu SN, Piehler J, Garcia KC. Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands. Cell 2015; 160:1196-208. [PMID: 25728669 PMCID: PMC4766813 DOI: 10.1016/j.cell.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/22/2015] [Accepted: 02/03/2015] [Indexed: 01/07/2023]
Abstract
Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Erythropoietin (EPO) and its receptor (EpoR), to dimerize EpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism, and structures of these DA/EpoR complexes differed in EpoR dimer orientation and proximity. Diabodies also elicited biased or differential activation of signaling pathways and gene expression profiles compared to EPO. Non-signaling diabodies inhibited proliferation of erythroid precursors from patients with a myeloproliferative neoplasm due to a constitutively active JAK2V617F mutation. Thus, intracellular oncogenic mutations causing ligand-independent receptor activation can be counteracted by extracellular ligands that re-orient receptors into inactive dimer topologies. This approach has broad applications for tuning signaling output for many dimeric receptor systems.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Gerlinde Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Pathology, Division of Hematopathology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stephan Wilmes
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - Vitalina Gryshkova
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | | | - Wan-Jen Hong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Feng Guo
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Hyna Fabionar
- DiscoveRx, 42501 Albrae St, Fremont, California, 94538, USA
| | - Tom S. Wehrman
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Peter Krutzik
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Samuel Demharter
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Isabelle Plo
- Institut Gustave Roussy, INSERM U1009, 94805, Villejuif, France
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Peter Minary
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stefan N. Constantinescu
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Correspondence to:
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41
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Waters M, Brooks A. JAK2 activation by growth hormone and other cytokines. Biochem J 2015; 466:1-11. [PMID: 25656053 PMCID: PMC4325515 DOI: 10.1042/bj20141293] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/17/2014] [Accepted: 11/24/2014] [Indexed: 12/30/2022]
Abstract
Growth hormone (GH) and structurally related cytokines regulate a great number of physiological and pathological processes. They do this by coupling their single transmembrane domain (TMD) receptors to cytoplasmic tyrosine kinases, either as homodimers or heterodimers. Recent studies have revealed that many of these receptors exist as constitutive dimers rather than being dimerized as a consequence of ligand binding, which has necessitated a new paradigm for describing their activation process. In the present study, we describe a model for activation of the tyrosine kinase Janus kinase 2 (JAK2) by the GH receptor homodimer based on biochemical data and molecular dynamics simulations. Binding of the bivalent ligand reorientates and rotates the receptor subunits, resulting in a transition from a form with parallel TMDs to one where the TMDs separate at the point of entry into the cytoplasm. This movement slides the pseudokinase inhibitory domain of one JAK kinase away from the kinase domain of the other JAK within the receptor dimer-JAK complex, allowing the two kinase domains to interact and trans-activate. This results in phosphorylation and activation of STATs and other signalling pathways linked to this receptor which then regulate postnatal growth, metabolism and stem cell activation. We believe that this model will apply to most if not all members of the class I cytokine receptor family, and will be useful in the design of small antagonists and agonists of therapeutic value.
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Key Words
- class i cytokine receptors
- cytokine receptor signalling
- growth hormone
- growth hormone receptor
- janus kinase 2 (jak2)
- srk family kinases
- cntf, ciliary neurotropic factor
- crh, cytokine receptor homology
- ct-1, cardiotropin-1
- ecd, extracellular domain
- epo, erythropoietin
- fniii, fibronectin iii-like
- gh, growth hormone
- gm-csf, granulocyte-macrophage colony-stimulating factor
- jak, janus kinase
- jm, juxtamembrane
- mab, monoclonal antibody
- osm, oncostatin-m
- pk, pseudokinase
- tmd, transmembrane domain
- tpo, thrombopoietin
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Affiliation(s)
- Michael J. Waters
- *Institute for Molecular Bioscience, The University of Queensland Institute, QLD 4072, Australia
| | - Andrew J. Brooks
- *Institute for Molecular Bioscience, The University of Queensland Institute, QLD 4072, Australia
- †The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, QLD 4072, Australia
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Aumentado-Armstrong TT, Istrate B, Murgita RA. Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol 2015; 10:7. [PMID: 25713596 PMCID: PMC4338852 DOI: 10.1186/s13015-015-0033-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 01/07/2015] [Indexed: 12/19/2022] Open
Abstract
Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction of these sites have been produced at a rapid rate, and the field has seen significant advancement over the past decade. However, the most current methods have not yet been reviewed in a systematic and comprehensive fashion. Herein, we describe the intricacies of the biological theory, datasets, and features required for modern protein-protein interaction site (PPIS) prediction, and present an integrative analysis of the state-of-the-art algorithms and their performance. First, the major sources of data used by predictors are reviewed, including training sets, evaluation sets, and methods for their procurement. Then, the features employed and their importance in the biological characterization of PPISs are explored. This is followed by a discussion of the methodologies adopted in contemporary prediction programs, as well as their relative performance on the datasets most recently used for evaluation. In addition, the potential utility that PPIS identification holds for rational drug design, hotspot prediction, and computational molecular docking is described. Finally, an analysis of the most promising areas for future development of the field is presented.
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43
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Hsu PL, Horng LY, Peng KY, Wu CL, Sung HC, Wu RT. Activation of mitochondrial function and Hb expression in non-haematopoietic cells by an EPO inducer ameliorates ischaemic diseases in mice. Br J Pharmacol 2014; 169:1461-76. [PMID: 23530756 DOI: 10.1111/bph.12197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND PURPOSE Many organs suffer from ischaemic injuries that reduce their ability to generate sufficient energy, which is required for functional maintenance and repair. Erythropoietin (EPO) ameliorates ischaemic injuries by pleiotropic effects. The aim of this study was to investigate the effect and mechanism of a small molecule EH-201, and found it as a potent EPO inducer and its effect in non-haematopoietic cells for therapeutic potential in ischemic disorders. EXPERIMENTAL APPROACH Mice kidney slices, primary hepatocytes, primary cardiomyocytes and C2C12 myoblasts were treated with EH-201. The effects of this treatment on EPO, Hb expression and mitochondrial biogenesis were analysed. In vivo, doxorubicin-induced cardiomyopathic mice were treated with EH-201. The mice were subjected to an endurance test, electrocardiography and echocardiography, and a histological examination of the isolated hearts was performed. EH-201 was also administered to cisplatin-induced nephropathic mice. KEY RESULTS In non-haematopoietic cells, EH-201 was potent at inducing EPO. EH-201 also stimulated mitochondrial biogenesis and enhanced the expression of Hb by a mechanism dependent on EPO-mediated signalling. In mechanistic studies, using EPO and EPO receptor-neutralizing antibodies, we confirmed that EH-201 enhances EPO-EPOR autocrine activity. EH-201 robustly increased the endurance performance activity of healthy and cardiomyopathic mice during hypoxic stress, enhanced myocardial mitochondrial biogenesis and Hb expression, and also improved cardiac function. EH-201 ameliorated anaemia and renal dysfunction in nephropathic mice. CONCLUSIONS AND IMPLICATIONS The enhancement and recovery of cellular functions through the stimulation of mitochondrial activity and Hb production in non-haematopoietic cells by an inducer of endogenous EPO has potential as a therapeutic strategy for ischaemic diseases.
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Affiliation(s)
- Pei-Lun Hsu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
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44
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Lee J, Miyazaki M, Romeo GR, Shoelson SE. Insulin receptor activation with transmembrane domain ligands. J Biol Chem 2014; 289:19769-77. [PMID: 24867955 DOI: 10.1074/jbc.m114.578641] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Complementary surfaces are buried when peptide hormones, growth factors, or cytokines bind and activate cellular receptors. Although these extended surfaces provide high affinity and specificity to the interactions, they also present great challenges to the design of small molecules that might either mimic or antagonize the process. We show that the insulin receptor (IR) and downstream signals can be activated by targeting a site outside of its ligand-binding domain. A 24-residue peptide having the IR transmembrane (TM) domain sequence activates IR, but not related growth factor receptors, through specific interactions with the receptor TM domain. Like insulin-dependent activation, IR-TM requires that IR have a competent ATP-binding site and kinase activation loop. IR-TM also activates mutated receptors from patients with severe insulin resistance, which do not respond to insulin. These results show that IR can be activated through a pathway that bypasses its canonical ligand-binding domain.
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Affiliation(s)
- Jongsoon Lee
- From the Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Masaya Miyazaki
- From the Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Giulio R Romeo
- From the Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Steven E Shoelson
- From the Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
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45
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Del Vecchio L, Locatelli F. New treatment approaches in chronic kidney disease-associated anaemia. Expert Opin Biol Ther 2014; 14:687-96. [PMID: 24579747 DOI: 10.1517/14712598.2014.892577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Erythropoiesis-stimulating agents (ESA) and iron are the main tools for treating anaemia associated with chronic kidney disease (CKD). Pharmaceutical research has focused on modified epoetins or different strategies to stimulate erythropoiesis with the idea of improving relative disadvantages of the molecules already available in the market. AREAS COVERED Following a literature search on PubMed using anaemia, haemoglobin, erythropoietin (EPO), hypoxia-inducible transcription factor (HIF) inhibitors and chronic kidney disease as keywords, we critically analysed new strategies for increasing erythropoiesis, looking in depth at their peculiar characteristics and possible advantages in the clinical setting. EXPERT OPINION In recent years the ESA market is facing a number of hurdles making it less appealing than before. Economic recession or stagnation has raised the need of sustainability of medical treatment. New treatments must bring clear benefits compared to existing drugs. In addition to this, ESA consumption has been progressively reduced, fearing possible risks of increased cardiovascular events especially when given at excessive doses. New drugs may also undergo premature stopping because of unexpected adverse reactions as for peginesatide. At present, the most promising approach to anaemia treatment in CKD patients is the manipulation of the HIF system. The regulation of activin A pathway is another option with good potential, also considering the additional advantage of increasing bone mass.
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Affiliation(s)
- Lucia Del Vecchio
- A Manzoni Hospital, Department of Nephrology, Dialysis, and Renal Transplant , Via dell'Eremo 9, 23900 Lecco , Italy
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46
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Längle D, Halver J, Rathmer B, Willems E, Schade D. Small molecules targeting in vivo tissue regeneration. ACS Chem Biol 2014; 9:57-71. [PMID: 24372447 DOI: 10.1021/cb4008277] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of regenerative medicine has boomed in recent years thanks to milestone discoveries in stem cell biology and tissue engineering, which has been driving paradigm shifts in the pharmacotherapy of degenerative and ischemic diseases. Small molecule-mediated replenishment of lost and/or dysfunctional tissue in vivo, however, is still in its infancy due to a limited understanding of mechanisms that control such endogenous processes of tissue homeostasis or regeneration. Here, we discuss current progress using small molecules targeting in vivo aspects of regeneration, including adult stem cells, stem cell niches, and mechanisms of homing, mobilization, and engraftment as well as somatic cell proliferation. Many of these compounds derived from both knowledge-based design and screening campaigns, illustrating the feasibility of translating in vitro discovery to in vivo regeneration. These early examples of drug-mediated in vivo regeneration provide a glimpse of the future directions of in vivo regenerative medicine approaches.
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Affiliation(s)
- Daniel Längle
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Jonas Halver
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Bernd Rathmer
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Erik Willems
- Muscle
Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis Schade
- Faculty of Chemistry & Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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47
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Moraga I, Spangler J, Mendoza JL, Garcia KC. Multifarious determinants of cytokine receptor signaling specificity. Adv Immunol 2014; 121:1-39. [PMID: 24388212 DOI: 10.1016/b978-0-12-800100-4.00001-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytokines play crucial roles in regulating immune homeostasis. Two important characteristics of most cytokines are pleiotropy, defined as the ability of one cytokine to exhibit diverse functionalities, and redundancy, defined as the ability of multiple cytokines to exert overlapping activities. Identifying the determinants for unique cellular responses to cytokines in the face of shared receptor usage, pleiotropy, and redundancy will be essential in order to harness the potential of cytokines as therapeutics. Here, we discuss the biophysical (ligand-receptor geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters that contribute to the specificity of cytokine bioactivities. Whereas the role of extracellular ternary complex geometry in cytokine-induced signaling is still not completely elucidated, cytokine-receptor affinity is known to impact signaling through modulation of the stability and kinetics of ternary complex formation. Receptor trafficking also plays an important and likely underappreciated role in the diversification of cytokine bioactivities but it has been challenging to experimentally probe trafficking effects. We also review recent efforts to quantify levels of intracellular signaling components, as second messenger abundance can affect cytokine-induced bioactivities both quantitatively and qualitatively. We conclude by discussing the application of protein engineering to develop therapeutically relevant cytokines with reduced pleiotropy and redirected biological functionalities.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jamie Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Juan L Mendoza
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA.
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48
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CD28: direct and critical receptor for superantigen toxins. Toxins (Basel) 2013; 5:1531-42. [PMID: 24022021 PMCID: PMC3798871 DOI: 10.3390/toxins5091531] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/30/2013] [Accepted: 09/05/2013] [Indexed: 01/16/2023] Open
Abstract
Every adaptive immune response requires costimulation through the B7/CD28 axis, with CD28 on T-cells functioning as principal costimulatory receptor. Staphylococcal and streptococcal superantigen toxins hyperstimulate the T-cell-mediated immune response by orders of magnitude, inducing a lethal cytokine storm. We show that to elicit an inflammatory cytokine storm and lethality, superantigens must bind directly to CD28. Blocking access of the superantigen to its CD28 receptor with peptides mimicking the contact domains in either toxin or CD28 suffices to protect mice effectively from lethal shock. Our finding that CD28 is a direct receptor of superantigen toxins broadens the scope of microbial pathogen recognition mechanisms.
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49
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Chen P, Li J, Wong L, Kuwahara H, Huang JZ, Gao X. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins 2013; 81:1351-62. [DOI: 10.1002/prot.24278] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 02/07/2013] [Accepted: 02/23/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Peng Chen
- Computer, Electrical and Mathematical Sciences and Engineering Division; King Abdullah University of Science and Technology (KAUST); Thuwal 23955-6900 Saudi Arabia
| | - Jinyan Li
- Advanced Analytics Institute; University of Technology; Sydney New South Wales Australia
| | - Limsoon Wong
- School of Computing; National University of Singapore; Singapore 117417
| | - Hiroyuki Kuwahara
- Computer, Electrical and Mathematical Sciences and Engineering Division; King Abdullah University of Science and Technology (KAUST); Thuwal 23955-6900 Saudi Arabia
| | - Jianhua Z. Huang
- Department of Statistics; Texas A&M University; College Station Texas 77843-3143
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division; King Abdullah University of Science and Technology (KAUST); Thuwal 23955-6900 Saudi Arabia
- Computational Bioscience Research Center; King Abdullah University of Science and Technology (KAUST); Thuwal 23955-6900 Saudi Arabia
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50
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Pasquato A, Burri DJ, Kunz S. Current drug discovery strategies against arenavirus infections. Expert Rev Anti Infect Ther 2013; 10:1297-309. [PMID: 23241187 DOI: 10.1586/eri.12.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Arenaviruses are a large group of emerging viruses including several causative agents of severe hemorrhagic fevers with high mortality in man. Considering the number of people affected and the currently limited therapeutic options, novel efficacious therapeutics against arenaviruses are urgently needed. Over the past decade, significant advances in knowledge about the basic virology of arenaviruses have been accompanied by the development of novel therapeutics targeting different steps of the arenaviral life cycle. High-throughput, small-molecule screens identified potent and broadly active inhibitors of arenavirus entry that were instrumental for the dissection of unique features of arenavirus fusion. Novel inhibitors of arenavirus replication have been successfully tested in animal models and hold promise for application in humans. Late in the arenavirus life cycle, the proteolytic processing of the arenavirus envelope glycoprotein precursor and cellular factors critically involved virion assembly and budding provide further promising 'druggable' targets for novel therapeutics to combat human arenavirus infection.
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Affiliation(s)
- Antonella Pasquato
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
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