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Petruk G, Puthia M, Samsudin F, Petrlova J, Olm F, Mittendorfer M, Hyllén S, Edström D, Strömdahl AC, Diehl C, Ekström S, Walse B, Kjellström S, Bond PJ, Lindstedt S, Schmidtchen A. Publisher Correction: Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs. Nat Commun 2023; 14:6436. [PMID: 37833291 PMCID: PMC10575983 DOI: 10.1038/s41467-023-42294-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023] Open
Affiliation(s)
- Ganna Petruk
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden.
| | - Manoj Puthia
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Firdaus Samsudin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Franziska Olm
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | | | - Snejana Hyllén
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Department of Cardiothoracic Surgery, Anesthesia and Intensive Care, Skåne University Hospital, SE-22185, Lund, Sweden
| | - Dag Edström
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Department of Cardiothoracic Surgery, Anesthesia and Intensive Care, Skåne University Hospital, SE-22185, Lund, Sweden
| | - Ann-Charlotte Strömdahl
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Carl Diehl
- SARomics Biostructures AB, Medicon Village, SE-22381, Lund, Sweden
| | - Simon Ekström
- BioMS - Swedish National Infrastructure for Biological Mass Spectrometry, SE-22184, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-22381, Lund, Sweden
| | - Sven Kjellström
- Division of Mass Spectrometry, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Sandra Lindstedt
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Department of Cardiothoracic Surgery, Anesthesia and Intensive Care, Skåne University Hospital, SE-22185, Lund, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Dermatology, Skane University Hospital, SE-22185, Lund, Sweden
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2
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Petruk G, Puthia M, Samsudin F, Petrlova J, Olm F, Mittendorfer M, Hyllén S, Edström D, Strömdahl AC, Diehl C, Ekström S, Walse B, Kjellström S, Bond PJ, Lindstedt S, Schmidtchen A. Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs. Nat Commun 2023; 14:6097. [PMID: 37773180 PMCID: PMC10541425 DOI: 10.1038/s41467-023-41702-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023] Open
Abstract
There is a clinical need for conceptually new treatments that target the excessive activation of inflammatory pathways during systemic infection. Thrombin-derived C-terminal peptides (TCPs) are endogenous anti-infective immunomodulators interfering with CD14-mediated TLR-dependent immune responses. Here we describe the development of a peptide-based compound for systemic use, sHVF18, expressing the evolutionarily conserved innate structural fold of natural TCPs. Using a combination of structure- and in silico-based design, nuclear magnetic resonance spectroscopy, biophysics, mass spectrometry, cellular, and in vivo studies, we here elucidate the structure, CD14 interactions, protease stability, transcriptome profiling, and therapeutic efficacy of sHVF18. The designed peptide displays a conformationally stabilized, protease resistant active innate fold and targets the LPS-binding groove of CD14. In vivo, it shows therapeutic efficacy in experimental models of endotoxin shock in mice and pigs and increases survival in mouse models of systemic polymicrobial infection. The results provide a drug class based on Nature´s own anti-infective principles.
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Affiliation(s)
- Ganna Petruk
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden.
| | - Manoj Puthia
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Firdaus Samsudin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Franziska Olm
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | | | - Snejana Hyllén
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Department of Cardiothoracic Surgery, Anesthesia and Intensive Care, Skåne University Hospital, SE-22185, Lund, Sweden
| | - Dag Edström
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Department of Cardiothoracic Surgery, Anesthesia and Intensive Care, Skåne University Hospital, SE-22185, Lund, Sweden
| | - Ann-Charlotte Strömdahl
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Carl Diehl
- SARomics Biostructures AB, Medicon Village, SE-22381, Lund, Sweden
| | - Simon Ekström
- BioMS - Swedish National Infrastructure for Biological Mass Spectrometry, SE-22184, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-22381, Lund, Sweden
| | - Sven Kjellström
- Division of Mass Spectrometry, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Sandra Lindstedt
- Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Department of Cardiothoracic Surgery, Anesthesia and Intensive Care, Skåne University Hospital, SE-22185, Lund, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184, Lund, Sweden
- Dermatology, Skane University Hospital, SE-22185, Lund, Sweden
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3
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Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Fernández AP, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun 2023; 14:5019. [PMID: 37596290 PMCID: PMC10439212 DOI: 10.1038/s41467-023-40764-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023] Open
Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ingeborg M M van Leeuwen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catherine J Drummond
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Su Chu
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Andrés Pastor Fernández
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Saikiran K Sedimbi
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Marta Nekulova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Marijke C C Sachweh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Johanna Campbell
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Maureen Higgins
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Chloe Tuck
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Mireia Mayoral Safont
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Pascal Gelebart
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Zinayida Fandalyuk
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Center, Holcombe Boulevard, Houston, TX, 77030, USA
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Ulrika Yngve
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Aljona Saleh
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Agathe C A D'Hollander
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Yan Zhao
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Karin Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Emma M Peat
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Mar Carmena
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - William C Earnshaw
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Anna R McCarthy
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
- Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden.
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4
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Maurer MF, Lewis KE, Kuijper JL, Ardourel D, Gudgeon CJ, Chandrasekaran S, Mudri SL, Kleist KN, Navas C, Wolfson MF, Rixon MW, Swanson R, Dillon SR, Levin SD, Kimbung YR, Akutsu M, Logan DT, Walse B, Swiderek KM, Peng SL. The engineered CD80 variant fusion therapeutic davoceticept combines checkpoint antagonism with conditional CD28 costimulation for anti-tumor immunity. Nat Commun 2022; 13:1790. [PMID: 35379805 PMCID: PMC8980021 DOI: 10.1038/s41467-022-29286-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractDespite the recent clinical success of T cell checkpoint inhibition targeting the CTLA-4 and PD-1 pathways, many patients either fail to achieve objective responses or they develop resistance to therapy. In some cases, poor responses to checkpoint blockade have been linked to suboptimal CD28 costimulation and the inability to generate and maintain a productive adaptive anti-tumor immune response. To address this, here we utilize directed evolution to engineer a CD80 IgV domain with increased PD-L1 affinity and fuse this to an immunoglobulin Fc domain, creating a therapeutic (ALPN-202, davoceticept) capable of providing CD28 costimulation in a PD-L1-dependent fashion while also antagonizing PD-1 - PD-L1 and CTLA-4–CD80/CD86 interactions. We demonstrate that by combining CD28 costimulation and dual checkpoint inhibition, ALPN-202 enhances T cell activation and anti-tumor efficacy in cell-based assays and mouse tumor models more potently than checkpoint blockade alone and thus has the potential to generate potent, clinically meaningful anti-tumor immunity in humans.
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5
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Hassan M, van Klaveren S, Håkansson M, Diehl C, Kovačič R, Baussière F, Sundin AP, Dernovšek J, Walse B, Zetterberg F, Leffler H, Anderluh M, Tomašič T, Jakopin Ž, Nilsson UJ. Benzimidazole-galactosides bind selectively to the Galectin-8 N-Terminal domain: Structure-based design and optimisation. Eur J Med Chem 2021; 223:113664. [PMID: 34225180 DOI: 10.1016/j.ejmech.2021.113664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/13/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
We have obtained the X-ray crystal structure of the galectin-8 N-terminal domain (galectin-8N) with a previously reported quinoline-galactoside ligand at a resolution of 1.6 Å. Based on this X-ray structure, a collection of galactosides derivatised at O3 with triazole, benzimidazole, benzothiazole, and benzoxazole moieties were designed and synthesised. This led to the discovery of a 3-O-(N-methylbenzimidazolylmethyl)-galactoside with a Kd of 1.8 μM for galectin-8N, the most potent selective synthetic galectin-8N ligand to date. Molecular dynamics simulations showed that benzimidazole-galactoside derivatives bind the non-conserved amino acid Gln47, accounting for the higher selectivity for galectin-8N. Galectin-8 is a carbohydrate-binding protein that plays a key role in pathological lymphangiogenesis, modulation of the immune system, and autophagy. Thus, the benzimidazole-derivatised galactosides represent promising compounds for studies of the pathological implications of galectin-8, as well as a starting point for the development of anti-tumour and anti-inflammatory therapeutics targeting galectin-8.
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Affiliation(s)
- Mujtaba Hassan
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden; University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Sjors van Klaveren
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden; University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carl Diehl
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Rebeka Kovačič
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Floriane Baussière
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Anders P Sundin
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Jaka Dernovšek
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Fredrik Zetterberg
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8 A, SE-413 46, Gothenburg, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84, Lund, Sweden
| | - Marko Anderluh
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Žiga Jakopin
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden.
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6
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Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Átlasson ÚÁ, Brandt D, Cichowicz-Cieślak M, Cornish KAS, Courtin J, Dabrowski S, Dahle H, Djeffane S, Dorawa S, Dusaucy J, Enault F, Fedøy AE, Freitag-Pohl S, Fridjonsson OH, Galiez C, Glomsaker E, Guérin M, Gundesø SE, Gudmundsdóttir EE, Gudmundsson H, Håkansson M, Henke C, Helleux A, Henriksen JR, Hjörleifdóttir S, Hreggvidsson GO, Jasilionis A, Jochheim A, Jónsdóttir I, Jónsdóttir LB, Jurczak-Kurek A, Kaczorowski T, Kalinowski J, Kozlowski LP, Krupovic M, Kwiatkowska-Semrau K, Lanes O, Lange J, Lebrat J, Linares-Pastén J, Liu Y, Lorentsen SA, Lutterman T, Mas T, Merré W, Mirdita M, Morzywołek A, Ndela EO, Karlsson EN, Olgudóttir E, Pedersen C, Perler F, Pétursdóttir SK, Plotka M, Pohl E, Prangishvili D, Ray JL, Reynisson B, Róbertsdóttir T, Sandaa RA, Sczyrba A, Skírnisdóttir S, Söding J, Solstad T, Steen IH, Stefánsson SK, Steinegger M, Overå KS, Striberny B, Svensson A, Szadkowska M, Tarrant EJ, Terzian P, Tourigny M, Bergh TVD, Vanhalst J, Vincent J, Vroling B, Walse B, Wang L, Watzlawick H, Welin M, Werbowy O, Wons E, Zhang R. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett 2021; 368:6296640. [PMID: 34114607 DOI: 10.1093/femsle/fnab067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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Affiliation(s)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Josefin Ahlqvist
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Joseph Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hasan Arsin
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - David Brandt
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Magdalena Cichowicz-Cieślak
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katy A S Cornish
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,Department of Informatics, University of Bergen, PO Box 7803, Thormøhlens gate 53 A/B, N-5020 Bergen, Norway
| | | | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Francois Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | - Clovis Galiez
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eirin Glomsaker
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | - Sigurd E Gundesø
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | | | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | | | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Askja-Sturlugata 7, Reykjavik, Iceland
| | - Andrius Jasilionis
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Agata Jurczak-Kurek
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Lukasz P Kozlowski
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Mart Krupovic
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Karolina Kwiatkowska-Semrau
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olav Lanes
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Joanna Lange
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | | | - Javier Linares-Pastén
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Ying Liu
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | - Tobias Lutterman
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Thibaud Mas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agnieszka Morzywołek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Eric Olo Ndela
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Cathrine Pedersen
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Francine Perler
- Perls of Wisdom Biotech Consulting, 74 Fuller Street, Brookline, MA 02446, USA
| | | | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - David Prangishvili
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jessica L Ray
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | | | | | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Terese Solstad
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - Martin Steinegger
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Bernd Striberny
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Anders Svensson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Emma J Tarrant
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Paul Terzian
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | | | | | - Jonathan Vincent
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Bas Vroling
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Lei Wang
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ruoshi Zhang
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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7
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Ladds MJGW, Popova G, Pastor-Fernández A, Kannan S, van Leeuwen IMM, Håkansson M, Walse B, Tholander F, Bhatia R, Verma CS, Lane DP, Laín S. Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology. J Biol Chem 2020; 295:17935-17949. [PMID: 32900849 PMCID: PMC7939445 DOI: 10.1074/jbc.ra119.012056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 08/18/2020] [Indexed: 01/17/2023] Open
Abstract
The tenovins are a frequently studied class of compounds capable of inhibiting sirtuin activity, which is thought to result in increased acetylation and protection of the tumor suppressor p53 from degradation. However, as we and other laboratories have shown previously, certain tenovins are also capable of inhibiting autophagic flux, demonstrating the ability of these compounds to engage with more than one target. In this study, we present two additional mechanisms by which tenovins are able to activate p53 and kill tumor cells in culture. These mechanisms are the inhibition of a key enzyme of the de novo pyrimidine synthesis pathway, dihydroorotate dehydrogenase (DHODH), and the blockage of uridine transport into cells. These findings hold a 3-fold significance: first, we demonstrate that tenovins, and perhaps other compounds that activate p53, may activate p53 by more than one mechanism; second, that work previously conducted with certain tenovins as SirT1 inhibitors should additionally be viewed through the lens of DHODH inhibition as this is a major contributor to the mechanism of action of the most widely used tenovins; and finally, that small changes in the structure of a small molecule can lead to a dramatic change in the target profile of the molecule even when the phenotypic readout remains static.
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Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrés Pastor-Fernández
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | - Fredrik Tholander
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, O'Neal Comprehensive Cancer Center, University of Alabama, Birmingham, Alabama, USA
| | - Chandra S Verma
- Bioinformatics Institute (BII), A*STAR, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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8
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Schneider P, Welin M, Svensson B, Walse B, Schneider G. Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors. Mol Inform 2020; 39:e2000109. [PMID: 33448694 PMCID: PMC7539333 DOI: 10.1002/minf.202000109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022]
Abstract
Ligand-based virtual screening of large compound collections, combined with fast bioactivity determination, facilitate the discovery of bioactive molecules with desired properties. Here, chemical similarity based machine learning and label-free differential scanning fluorimetry were used to rapidly identify new ligands of the anticancer target Pim-1 kinase. The three-dimensional crystal structure complex of human Pim-1 with ligand bound revealed an ATP-competitive binding mode. Generative de novo design with a recurrent neural network additionally suggested innovative molecular scaffolds. Results corroborate the validity of the chemical similarity principle for rapid ligand prototyping, suggesting the complementarity of similarity-based and generative computational approaches.
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Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.,inSili.com GmbH, Segantinisteig 3, 8049, Zurich, Switzerland
| | - Martin Welin
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Bo Svensson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
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9
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Freitag-Pohl S, Jasilionis A, Håkansson M, Svensson LA, Kovačič R, Welin M, Watzlawick H, Wang L, Altenbuchner J, Płotka M, Kaczorowska AK, Kaczorowski T, Nordberg Karlsson E, Al-Karadaghi S, Walse B, Aevarsson A, Pohl E. Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS. Acta Crystallogr D Struct Biol 2019; 75:1028-1039. [PMID: 31692476 PMCID: PMC6834076 DOI: 10.1107/s2059798319013330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022] Open
Abstract
As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.
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Affiliation(s)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Rebeka Kovačič
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Hildegard Watzlawick
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lei Wang
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Magdalena Płotka
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Anna Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | | | | | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, England
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10
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Ruggieri F, van Langen LM, Logan DT, Walse B, Berglund P. Transaminase-Catalyzed Racemization with Potential for Dynamic Kinetic Resolutions. ChemCatChem 2018; 10:5012-5018. [PMID: 30546495 PMCID: PMC6282829 DOI: 10.1002/cctc.201801049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Indexed: 11/11/2022]
Abstract
Dynamic kinetic resolution (DKR) reactions in which a stereoselective enzyme and a racemization step are coupled in one pot would represent powerful tools for the production of enantiopure amines through enantioconvergence of racemates. The exploitation of DKR strategies is currently hampered by the lack of effective, enzyme-compatible and scalable racemization strategies for amines. In the present work, the proof of concept of a fully biocatalytic method for amine racemization is presented. Both enantiomers of the model compound 1-methyl-3-phenylpropylamine could be racemized in water and at room temperature using a couple of wild-type, non-proprietary, enantiocomplementary amine transaminases and a minimum amount of pyruvate/alanine as a co-substrate couple. The biocatalytic simultaneous parallel cascade reaction presented here poses itself as a customizable amine racemization system with potential for the chemical industry in competition with traditional transition-metal catalysis.
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Affiliation(s)
- Federica Ruggieri
- Department of Industrial Biotechnology KTH Royal Institute of TechnologyAlbaNova University CenterStockholmSE-106 91Sweden
- SARomics Biostructures AB Medicon VillageLundSE-223 81Sweden
| | | | - Derek T. Logan
- SARomics Biostructures AB Medicon VillageLundSE-223 81Sweden
| | - Björn Walse
- SARomics Biostructures AB Medicon VillageLundSE-223 81Sweden
| | - Per Berglund
- Department of Industrial Biotechnology KTH Royal Institute of TechnologyAlbaNova University CenterStockholmSE-106 91Sweden
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11
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Cordeiro RS, Håkansson M, Logan D, Walse B, Kourist R. Structural characterization of a novel amino acid decarboxylase. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318095739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Abdillahi SM, Maaß T, Kasetty G, Strömstedt AA, Baumgarten M, Tati R, Nordin SL, Walse B, Wagener R, Schmidtchen A, Mörgelin M. Collagen VI Contains Multiple Host Defense Peptides with Potent In Vivo Activity. J Immunol 2018; 201:1007-1020. [PMID: 29925677 DOI: 10.4049/jimmunol.1700602] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/01/2018] [Indexed: 11/19/2022]
Abstract
Collagen VI is a ubiquitous extracellular matrix component that forms extensive microfibrillar networks in most connective tissues. In this study, we describe for the first time, to our knowledge, that the collagen VI von Willebrand factor type A-like domains exhibit a broad-spectrum antimicrobial activity against Gram-positive and Gram-negative bacteria in human skin infections in vivo. In silico sequence and structural analysis of VWA domains revealed that they contain cationic and amphipathic peptide sequence motifs, which might explain the antimicrobial nature of collagen VI. In vitro and in vivo studies show that these peptides exhibited significant antibacterial activity against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa through membrane disruption. Our findings shed new light on the role of collagen VI-derived peptides in innate host defense and provide templates for development of peptide-based antibacterial therapies.
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Affiliation(s)
- Suado M Abdillahi
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden;
| | - Tobias Maaß
- Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Gopinath Kasetty
- Division of Respiratory Medicine and Allergology, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden
| | - Adam A Strömstedt
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, 751 23 Uppsala, Sweden
| | - Maria Baumgarten
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden
| | - Ramesh Tati
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden
| | - Sara L Nordin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden
| | - Björn Walse
- Saromics Biostructures AB, 223 63 Lund, Sweden
| | - Raimund Wagener
- Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden.,Copenhagen Wound Healing Center, Bispebjerg Hospital, Department of Biomedical Sciences, University of Copenhagen, 2400 Copenhagen, Denmark and
| | - Matthias Mörgelin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 221 84 Lund, Sweden.,Colzyx AB, 223 81 Lund, Sweden
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13
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Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun 2018; 9:2071. [PMID: 29789663 PMCID: PMC5964109 DOI: 10.1038/s41467-018-04198-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ingeborg M M van Leeuwen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catherine J Drummond
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Su Chu
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Andrés Pastor Fernández
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Saikiran K Sedimbi
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Marta Nekulova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Marijke C C Sachweh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Johanna Campbell
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Maureen Higgins
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Chloe Tuck
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Mireia Mayoral Safont
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Pascal Gelebart
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Zinayida Fandalyuk
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Center, Holcombe Boulevard, Houston, 77030, USA
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Ulrika Yngve
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Aljona Saleh
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Agathe C A D'Hollander
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Yan Zhao
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Karin Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Emma M Peat
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Mar Carmena
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - William C Earnshaw
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Anna R McCarthy
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway.,Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden. .,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden.
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14
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Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun 2018; 9:1107. [PMID: 29549331 PMCID: PMC5856786 DOI: 10.1038/s41467-018-03441-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/13/2018] [Indexed: 01/29/2023] Open
Abstract
The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidate the mechanism of action of a chiral tetrahydroindazole (HZ00), and through target deconvolution, we deduce that its active enantiomer (R)-HZ00, inhibits dihydroorotate dehydrogenase (DHODH). The chiral specificity of HZ05, a more potent analog, is revealed by the crystal structure of the (R)-HZ05/DHODH complex. Twelve other DHODH inhibitor chemotypes are detailed among the p53 activators, which identifies DHODH as a frequent target for structurally diverse compounds. We observe that HZ compounds accumulate cancer cells in S-phase, increase p53 synthesis, and synergize with an inhibitor of p53 degradation to reduce tumor growth in vivo. We, therefore, propose a strategy to promote cancer cell killing by p53 instead of its reversible cell cycle arresting effect.
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Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ingeborg M M van Leeuwen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catherine J Drummond
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Su Chu
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Andrés Pastor Fernández
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Saikiran K Sedimbi
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Marta Nekulova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Marijke C C Sachweh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Johanna Campbell
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Maureen Higgins
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Chloe Tuck
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Mireia Mayoral Safont
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Pascal Gelebart
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Zinayida Fandalyuk
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Center, Holcombe Boulevard, Houston, 77030, USA
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Ulrika Yngve
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Aljona Saleh
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Agathe C A D'Hollander
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Yan Zhao
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Karin Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Emma M Peat
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Mar Carmena
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - William C Earnshaw
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Anna R McCarthy
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
- Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden.
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15
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Anderson LC, Håkansson M, Walse B, Nilsson CL. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). J Am Soc Mass Spectrom 2017; 28:1796-1804. [PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/16/2023]
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carol L Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX, 77555-1074, USA.
- Institute of Clinical Sciences-Lund, Lund University, SE-221 85, Lund, Sweden.
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16
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Nilsson LM, Green LC, Muralidharan SV, Demir D, Welin M, Bhadury J, Logan DT, Walse B, Nilsson JA. Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits BET Bromodomain Proteins. Cancer Res 2016; 76:2376-83. [PMID: 26941288 DOI: 10.1158/0008-5472.can-15-2721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/18/2016] [Indexed: 11/16/2022]
Abstract
Agents that trigger cell differentiation are highly efficacious in treating certain cancers, but such approaches are not generally effective in most malignancies. Compounds such as DMSO and hexamethylene bisacetamide (HMBA) have been used to induce differentiation in experimental systems, but their mechanisms of action and potential range of uses on that basis have not been developed. Here, we show that HMBA, a compound first tested in the oncology clinic over 25 years ago, acts as a selective bromodomain inhibitor. Biochemical and structural studies revealed an affinity of HMBA for the second bromodomain of BET proteins. Accordingly, both HMBA and the prototype BET inhibitor JQ1 induced differentiation of mouse erythroleukemia cells. As expected of a BET inhibitor, HMBA displaced BET proteins from chromatin, caused massive transcriptional changes, and triggered cell-cycle arrest and apoptosis in Myc-induced B-cell lymphoma cells. Furthermore, HMBA exerted anticancer effects in vivo in mouse models of Myc-driven B-cell lymphoma. This study illuminates the function of an early anticancer agent and suggests an intersection with ongoing clinical trials of BET inhibitor, with several implications for predicting patient selection and response rates to this therapy and starting points for generating BD2-selective BET inhibitors. Cancer Res; 76(8); 2376-83. ©2016 AACR.
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Affiliation(s)
- Lisa M Nilsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Lydia C Green
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Somsundar Veppil Muralidharan
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Dağsu Demir
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | | | - Joydeep Bhadury
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | | | | | - Jonas A Nilsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden.
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17
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Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P, Walse B, Schneider G. De Novo Fragment Design for Drug Discovery and Chemical Biology. Angew Chem Int Ed Engl 2015; 54:15079-83. [DOI: 10.1002/anie.201508055] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 01/08/2023]
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18
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Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P, Walse B, Schneider G. De-novo-Fragmententwurf für die Wirkstoffforschung und chemische Biologie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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von Schantz L, Håkansson M, Logan DT, Walse B, Österlin J, Nordberg-Karlsson E, Ohlin M. Structural basis for carbohydrate-binding specificity—A comparative assessment of two engineered carbohydrate-binding modules. Glycobiology 2012; 22:948-61. [DOI: 10.1093/glycob/cws063] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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21
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Humble MS, Cassimjee KE, Håkansson M, Kimbung YR, Walse B, Abedi V, Federsel HJ, Berglund P, Logan DT. Crystal structures of the Chromobacterium violaceumω-transaminase reveal major structural rearrangements upon binding of coenzyme PLP. FEBS J 2012; 279:779-92. [PMID: 22268978 DOI: 10.1111/j.1742-4658.2012.08468.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UNLABELLED The bacterial ω-transaminase from Chromobacterium violaceum (Cv-ωTA, EC2.6.1.18) catalyses industrially important transamination reactions by use of the coenzyme pyridoxal 5'-phosphate (PLP). Here, we present four crystal structures of Cv-ωTA: two in the apo form, one in the holo form and one in an intermediate state, at resolutions between 1.35 and 2.4 Å. The enzyme is a homodimer with a molecular mass of ∼ 100 kDa. Each monomer has an active site at the dimeric interface that involves amino acid residues from both subunits. The apo-Cv-ωTA structure reveals unique 'relaxed' conformations of three critical loops involved in structuring the active site that have not previously been seen in a transaminase. Analysis of the four crystal structures reveals major structural rearrangements involving elements of the large and small domains of both monomers that reorganize the active site in the presence of PLP. The conformational change appears to be triggered by binding of the phosphate group of PLP. Furthermore, one of the apo structures shows a disordered 'roof ' over the PLP-binding site, whereas in the other apo form and the holo form the 'roof' is ordered. Comparison with other known transaminase crystal structures suggests that ordering of the 'roof' structure may be associated with substrate binding in Cv-ωTA and some other transaminases. DATABASE The atomic coordinates and structure factors for the Chromobacterium violaceumω-transaminase crystal structures can be found in the RCSB Protein Data Bank (http://www.rcsb.org) under the accession codes 4A6U for the holoenzyme, 4A6R for the apo1 form, 4A6T for the apo2 form and 4A72 for the mixed form STRUCTURED DIGITAL ABSTRACT • -transaminases and -transaminases bind by dynamic light scattering (View interaction) • -transaminase and -transaminase bind by x-ray crystallography (View interaction) • -transaminase and -transaminase bind by x-ray crystallography (View interaction).
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Affiliation(s)
- Maria S Humble
- Division of Biochemistry, KTH Royal Institute of Technology, Stockholm, Sweden
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22
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Papareddy P, Mörgelin M, Walse B, Schmidtchen A, Malmsten M. Antimicrobial activity of peptides derived from human ß-amyloid precursor protein. J Pept Sci 2012; 18:183-91. [PMID: 22249992 DOI: 10.1002/psc.1439] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/03/2011] [Accepted: 11/15/2011] [Indexed: 11/07/2022]
Abstract
Antimicrobial peptides are important effector molecules of the innate immune system. Here, we describe that peptides derived from the heparin-binding disulfide-constrained loop region of human ß-amyloid precursor protein are antimicrobial. The peptides investigated were linear and cyclic forms of NWCKRGRKQCKTHPH (NWC15) as well as the cyclic form comprising the C-terminal hydrophobic amino acid extension FVIPY (NWCKRGRKQCKTHPHFVIPY; NWC20c). Compared with the benchmark antimicrobial peptide LL-37, these peptides efficiently killed the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, the Gram-positive Staphylococcus aureus and Bacillus subtilis, and the fungi Candida albicans and Candida parapsilosis. Correspondingly, fluorescence and electron microscopy demonstrated that the peptides caused defects in bacterial membranes. Analogously, the peptides permeabilised negatively charged liposomes. Despite their bactericidal effect, the peptides displayed very limited hemolytic activities within the concentration range investigated and exerted very small membrane permeabilising effects on human epithelial cells. The efficiency of the peptides with respect to bacterial killing and liposome membrane leakage was in the order NWC20c > NWC15c > NWC15l, which also correlated to the adsorption density for these peptides at the model lipid membrane. Thus, whereas the cationic sequence is a minimum determinant for antimicrobial action, a constrained loop-structure as well as a hydrophobic extension further contributes to membrane permeabilising activity of this region of amyloid precursor protein.
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Affiliation(s)
- Praveen Papareddy
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Tornavägen 10, SE-221 84, Lund, Sweden
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23
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Kasetty G, Papareddy P, Kalle M, Rydengård V, Walse B, Svensson B, Mörgelin M, Malmsten M, Schmidtchen A. The C-terminal sequence of several human serine proteases encodes host defense functions. J Innate Immun 2011; 3:471-82. [PMID: 21576923 DOI: 10.1159/000327016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 02/17/2011] [Indexed: 12/21/2022] Open
Abstract
Serine proteases of the S1 family have maintained a common structure over an evolutionary span of more than one billion years, and evolved a variety of substrate specificities and diverse biological roles, involving digestion and degradation, blood clotting, fibrinolysis and epithelial homeostasis. We here show that a wide range of C-terminal peptide sequences of serine proteases, particularly from the coagulation and kallikrein systems, share characteristics common with classical antimicrobial peptides of innate immunity. Under physiological conditions, these peptides exert antimicrobial effects as well as immunomodulatory functions by inhibiting macrophage responses to bacterial lipopolysaccharide. In mice, selected peptides are protective against lipopolysaccharide-induced shock. Moreover, these S1-derived host defense peptides exhibit helical structures upon binding to lipopolysaccharide and also permeabilize liposomes. The results uncover new and fundamental aspects on host defense functions of serine proteases present particularly in blood and epithelia, and provide tools for the identification of host defense molecules of therapeutic interest.
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Affiliation(s)
- Gopinath Kasetty
- Division of Dermatology and Venereology, Lund University, Biomedical Center, Lund, Sweden
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24
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Fritzson I, Svensson B, Al-Karadaghi S, Walse B, Wellmar U, Nilsson UJ, da Graça Thrige D, Jönsson S. Inhibition of human DHODH by 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids identified by structure-guided fragment selection. ChemMedChem 2010; 5:608-17. [PMID: 20183850 DOI: 10.1002/cmdc.200900454] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A strategy that combines virtual screening and structure-guided selection of fragments was used to identify three unexplored classes of human DHODH inhibitor compounds: 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids. Structure-guided selection of fragments targeting the inner subsite of the DHODH ubiquinone binding site made these findings possible with screening of fewer than 300 fragments in a DHODH assay. Fragments from the three inhibitor classes identified were subsequently chemically expanded to target an additional subsite of hydrophobic character. All three classes were found to exhibit distinct structure-activity relationships upon expansion. The novel N-(alkylcarbonyl)anthranilic acid class shows the most promising potency against human DHODH, with IC(50) values in the low nanomolar range. The structure of human DHODH in complex with an inhibitor of this class is presented.
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Svensson SL, Pasupuleti M, Walse B, Malmsten M, Mörgelin M, Sjögren C, Olin AI, Collin M, Schmidtchen A, Palmer R, Egesten A. Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution. J Biol Chem 2010; 285:16105-15. [PMID: 20308059 PMCID: PMC2871479 DOI: 10.1074/jbc.m109.081232] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 03/16/2010] [Indexed: 12/17/2022] Open
Abstract
Antibacterial peptides of the innate immune system combat pathogenic microbes, but often have additional roles in promoting inflammation and as growth factors during tissue repair. Midkine (MK) and pleiotrophin (PTN) are the only two members of a family of heparin-binding growth factors. They show restricted expression during embryogenesis and are up-regulated in neoplasia. In addition, MK shows constitutive and inflammation-dependent expression in some non-transformed tissues of the adult. In the present study, we show that both MK and PTN display strong antibacterial activity, present at physiological salt concentrations. Electron microscopy of bacteria and experiments using artificial lipid bilayers suggest that MK and PTN exert their antibacterial action via a membrane disruption mechanism. The predicted structure of PTN, employing the previously solved MK structure as a template, indicates that both molecules consist of two domains, each containing three antiparallel beta-sheets. The antibacterial activity was mapped to the unordered C-terminal tails of both molecules and the last beta-sheets of the N-terminals. Analysis of the highly conserved MK and PTN orthologues from the amphibian Xenopus laevis and the fish Danio rerio suggests that they also harbor antibacterial activity in the corresponding domains. In support of an evolutionary conserved function it was found that the more distant orthologue, insect Miple2 from Drosophila melanogaster, also displays strong antibacterial activity. Taken together, the findings suggest that MK and PTN, in addition to their earlier described activities, may have previously unrealized important roles as innate antibiotics.
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Affiliation(s)
| | | | - Björn Walse
- SARomics AB, P. O. Box 724, SE-220 07 Lund, Sweden
| | - Martin Malmsten
- the Department of Pharmacy, Uppsala University, SE-751 23 Uppsala, Sweden, and
| | - Matthias Mörgelin
- Infection Medicine, Department of Clinical Sciences Lund, Lund University, University Hospital, SE-221 85 Lund, Sweden
| | - Camilla Sjögren
- the Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Anders I. Olin
- From the Sections for Respiratory Medicine & Allergology
- Infection Medicine, Department of Clinical Sciences Lund, Lund University, University Hospital, SE-221 85 Lund, Sweden
| | - Mattias Collin
- Infection Medicine, Department of Clinical Sciences Lund, Lund University, University Hospital, SE-221 85 Lund, Sweden
| | | | - Ruth Palmer
- the Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Arne Egesten
- From the Sections for Respiratory Medicine & Allergology
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Papareddy P, Rydengård V, Pasupuleti M, Walse B, Mörgelin M, Chalupka A, Malmsten M, Schmidtchen A. Proteolysis of human thrombin generates novel host defense peptides. PLoS Pathog 2010; 6:e1000857. [PMID: 20421939 PMCID: PMC2858699 DOI: 10.1371/journal.ppat.1000857] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/15/2010] [Indexed: 11/25/2022] Open
Abstract
The coagulation system is characterized by the sequential and highly localized activation of a series of serine proteases, culminating in the conversion of fibrinogen into fibrin, and formation of a fibrin clot. Here we show that C-terminal peptides of thrombin, a key enzyme in the coagulation cascade, constitute a novel class of host defense peptides, released upon proteolysis of thrombin in vitro, and detected in human wounds in vivo. Under physiological conditions, these peptides exert antimicrobial effects against Gram-positive and Gram-negative bacteria, mediated by membrane lysis, as well as immunomodulatory functions, by inhibiting macrophage responses to bacterial lipopolysaccharide. In mice, they are protective against P. aeruginosa sepsis, as well as lipopolysaccharide-induced shock. Moreover, the thrombin-derived peptides exhibit helical structures upon binding to lipopolysaccharide and can also permeabilize liposomes, features typical of “classical” helical antimicrobial peptides. These findings provide a novel link between the coagulation system and host-defense peptides, two fundamental biological systems activated in response to injury and microbial invasion. Wounding of the skin and other epithelial barriers represents an ever-present challenge and poses a potential threat for invasive infection and sepsis. Therefore, it is not surprising that evolutionary pressure has maintained and developed multiple host defense systems, involving initial hemostasis and fibrin formation, and the subsequent action of multiple proteins and peptides of our innate immune system. In humans, the coagulation pathways and those mediating innate immune responses to infections have so far been seen as separate entities. This view is challenged by the present study, which discloses novel host defense functions of C-terminal peptides of thrombin, a key enzyme in the coagulation cascade. The thrombin-derived peptides, which are detected in human wounds and fibrin, effectively kill microbes by membrane lysis, but also exert potent immunomodulatory and anti-endotoxic functions. Importantly, these peptides protect against P. aeruginosa sepsis, as well as lipopolysaccharide-induced shock in animal models. Thus, from the perspective of wounding and infection, thrombin, after fulfilling its primary function by generating a first line of defense, the fibrin clot, serves an additional role by the generation of antimicrobial and anti-endotoxic host-defense peptides.
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Affiliation(s)
- Praveen Papareddy
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Lund, Sweden
| | - Victoria Rydengård
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Lund, Sweden
| | - Mukesh Pasupuleti
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Lund, Sweden
| | | | - Matthias Mörgelin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Biomedical Center, Lund, Sweden
| | - Anna Chalupka
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Lund, Sweden
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Martin Malmsten
- Department of Pharmacy, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Biomedical Center, Lund, Sweden
- * E-mail:
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Gustafsson E, Rosén A, Barchan K, van Kessel KPM, Haraldsson K, Lindman S, Forsberg C, Ljung L, Bryder K, Walse B, Haas PJ, van Strijp JAG, Furebring C. Directed evolution of chemotaxis inhibitory protein of Staphylococcus aureus generates biologically functional variants with reduced interaction with human antibodies. Protein Eng Des Sel 2009; 23:91-101. [PMID: 19959567 DOI: 10.1093/protein/gzp062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chemotaxis inhibitory protein of Staphylococcus aureus (CHIPS) is a protein that binds and blocks the C5a receptor (C5aR) and formylated peptide receptor, thereby inhibiting the immune cell recruitment associated with inflammation. If CHIPS was less reactive with existing human antibodies, it would be a promising anti-inflammatory drug candidate. Therefore, we applied directed evolution and computational/rational design to the CHIPS gene in order to generate new CHIPS variants displaying lower interaction with human IgG, yet retaining biological function. The optimization was performed in four rounds: one round of random mutagenesis to add diversity into the CHIPS gene and three rounds of DNA recombination by Fragment INduced Diversity (FIND). Every round was screened by phage selection and/or ELISA for decreased interaction with human IgG and retained C5aR binding. The mean binding of human anti-CHIPS IgG decreased with every round of evolution. For further optimization, new amino acid substitutions were introduced by rational design, based on the mutations identified during directed evolution. Finally, seven CHIPS variants with low interaction with human IgG and retained C5aR blocking capacity could be identified.
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Gustafsson E, Haas PJ, Walse B, Hijnen M, Furebring C, Ohlin M, van Strijp JAG, van Kessel KPM. Identification of conformational epitopes for human IgG on Chemotaxis inhibitory protein of Staphylococcus aureus. BMC Immunol 2009; 10:13. [PMID: 19284584 PMCID: PMC2662796 DOI: 10.1186/1471-2172-10-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 03/11/2009] [Indexed: 11/17/2022] Open
Abstract
Background The Chemotaxis inhibitory protein of Staphylococcus aureus (CHIPS) blocks the Complement fragment C5a receptor (C5aR) and formylated peptide receptor (FPR) and is thereby a potent inhibitor of neutrophil chemotaxis and activation of inflammatory responses. The majority of the healthy human population has antibodies against CHIPS that have been shown to interfere with its function in vitro. The aim of this study was to define potential epitopes for human antibodies on the CHIPS surface. We also initiate the process to identify a mutated CHIPS molecule that is not efficiently recognized by preformed anti-CHIPS antibodies and retains anti-inflammatory activity. Results In this paper, we panned peptide displaying phage libraries against a pool of CHIPS specific affinity-purified polyclonal human IgG. The selected peptides could be divided into two groups of sequences. The first group was the most dominant with 36 of the 48 sequenced clones represented. Binding to human affinity-purified IgG was verified by ELISA for a selection of peptide sequences in phage format. For further analysis, one peptide was chemically synthesized and antibodies affinity-purified on this peptide were found to bind the CHIPS molecule as studied by ELISA and Surface Plasmon Resonance. Furthermore, seven potential conformational epitopes responsible for antibody recognition were identified by mapping phage selected peptide sequences on the CHIPS surface as defined in the NMR structure of the recombinant CHIPS31–121 protein. Mapped epitopes were verified by in vitro mutational analysis of the CHIPS molecule. Single mutations introduced in the proposed antibody epitopes were shown to decrease antibody binding to CHIPS. The biological function in terms of C5aR signaling was studied by flow cytometry. A few mutations were shown to affect this biological function as well as the antibody binding. Conclusion Conformational epitopes recognized by human antibodies have been mapped on the CHIPS surface and amino acid residues involved in both antibody and C5aR interaction could be defined. This information has implications for the development of an effective anti-inflammatory agent based on a functional CHIPS molecule with low interaction with human IgG.
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Dahlén E, Barchan K, Herrlander D, Höjman P, Karlsson M, Ljung L, Andersson M, Bäckman E, Hager ACM, Walse B, Joosten L, van den Berg W. Development of Interleukin-1 Receptor Antagonist Mutants with Enhanced Antagonistic ActivityIn Vitroand Improved Therapeutic Efficacy in Collagen-Induced Arthritis. J Immunotoxicol 2008; 5:189-99. [DOI: 10.1080/15476910802131477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Walse B, Dufe VT, Svensson B, Fritzson I, Dahlberg L, Khairoullina A, Wellmar U, Al-Karadaghi S. The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites. Biochemistry 2008; 47:8929-36. [PMID: 18672895 DOI: 10.1021/bi8003318] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inhibitors of dihydroorotate dehydrogenase (DHODH) have been suggested for the treatment of rheumatoid arthritis, psoriasis, autoimmune diseases, Plasmodium, and bacterial and fungal infections. Here we present the structures of N-terminally truncated (residues Met30-Arg396) DHODH in complex with two inhibitors: a brequinar analogue (6) and a novel inhibitor (a fenamic acid derivative) (7), as well as the first structure of the enzyme to be characterized without any bound inhibitor. It is shown that 7 uses the "standard" brequinar binding mode and, in addition, interacts with Tyr356, a residue conserved in most class 2 DHODH proteins. Compared to the inhibitor-free structure, some of the amino acid side chains in the tunnel in which brequinar binds and which was suggested to be the binding site of ubiquinone undergo changes in conformation upon inhibitor binding. Using our data, the loop regions of residues Leu68-Arg72 and Asn212-Leu224, which were disordered in previously studied human DHODH structures, could be built into the electron density. The first of these loops, which is located at the entrance to the inhibitor-binding pocket, shows different conformations in the three structures, suggesting that it may interfere with inhibitor/cofactor binding. The second loop has been suggested to control the access of dihydroorotate to the active site of the enzyme and may be an important player in the enzymatic reaction. These observations provide new insights into the dynamic features of the DHODH reaction and suggest new approaches to the design of inhibitors against DHODH.
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Affiliation(s)
- Björn Walse
- SARomics AB, P.O. Box 724, SE-220 07 Lund, Sweden.
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31
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Pumphrey N, Vuidepot A, Jakobsen B, Forsberg G, Walse B, Lindkvist-Petersson K. Cutting Edge: Evidence of Direct TCR α-Chain Interaction with Superantigen. J Immunol 2007; 179:2700-4. [PMID: 17709482 DOI: 10.4049/jimmunol.179.5.2700] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Superantigens are known to activate a large number of T cells. The SAg is presented by MHC class II on the APC and its classical feature is that it recognizes the variable region of the beta-chain of the TCR. In this article, we report, by direct binding studies, that staphylococcal enterotoxin (SE) H (SEH), a bacterial SAg secreted by Staphylococcus aureus, instead recognizes the variable alpha-chain (TRAV27) of TCR. Furthermore, we show that different SAgs (e.g., SEH and SEA) can simultaneously bind to one TCR by binding the alpha-chain and the beta-chain, respectively. Theoretical three-dimensional models of the penta complexes are presented. Hence, these findings open up a new dimension of the biology of the staphylococcal enterotoxins.
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32
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Abstract
Protein-protein interactions are widely found in biological systems controlling diverse cellular events. Because these interactions are implicated in many diseases such as autoimmunity and cancer, regulation of protein-protein interactions provides ideal targets for drug intervention. The CD80-CD28 costimulatory pathway plays a critical role in regulation of the immune response and thus constitutes an attractive target for therapeutic manipulation of autoimmune diseases. The objective of this study is to identify small compounds disrupting these pivotal protein-protein interactions. Compounds that specifically blocked binding of CD80 to CD28 were identified using a strategy involving a cell-based scintillation proximity assay as the initial step. Secondary screening (e.g., by analyzing the direct binding of these compounds to the target immobilized on a biosensor surface) revealed that these compounds are highly selective CD80 binders. Screening of structurally related derivatives led to the identification of the chemical features required for inhibition of the CD80-CD28 interaction. In addition, the optimization process led to a 10-fold increase in binding affinity of the CD80 inhibitors. Using this approach, the authors identify low-molecular-weight compounds that specifically and with high potency inhibit the interaction between CD80 and CD28. These compounds serve as promising starting points for further development of CD80 inhibitors as potential immunomodulatory drugs. ( Journal of Biomolecular Screening 2007:464-472)
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33
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Abstract
Growth factors, comprising diverse protein and peptide families, are involved in a multitude of developmental processes, including embryogenesis, angiogenesis, and wound healing. Here we show that peptides derived from HB-EGF, amphiregulin, hepatocyte growth factor, PDGF-A and PDGF-B, as well as various FGFs are antimicrobial, demonstrating a previously unknown activity of growth factor-derived peptides. The peptides killed the Gram-negative bacteria Escherichia coli, Pseudomonas aeruginosa, and the Gram-positive Bacillus subtilis, as well as the fungus Candida albicans. Several peptides were also active against the Gram-positive S. aureus. Electron microscopy analysis of peptide-treated bacteria, paired with analysis of peptide effects on liposomes, showed that the peptides exerted membrane-breaking effects similar to those seen after treatment with the "classical" human antimicrobial peptide LL-37. Furthermore, HB-EGF was antibacterial per se, and its epitope GKRKKKGKGLGKKRDPCLRKYK retained its activity in presence of physiological salt and plasma. No discernible hemolysis was noted for the growth factor-derived peptides. Besides providing novel templates for design of peptide-based antimicrobials, our findings demonstrate a previously undisclosed link between the family of growth factors and antimicrobial peptides, both of which are induced during tissue remodelling and repair.
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Affiliation(s)
- Martin Malmsten
- Department of Pharmacy, Uppsala University, Uppsala, SE-751 23, Sweden
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34
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Pasupuleti M, Walse B, Nordahl EA, Mörgelin M, Malmsten M, Schmidtchen A. Preservation of antimicrobial properties of complement peptide C3a, from invertebrates to humans. J Biol Chem 2006; 282:2520-8. [PMID: 17132627 DOI: 10.1074/jbc.m607848200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human anaphylatoxin peptide C3a, generated during complement activation, exerts antimicrobial effects. Phylogenetic analysis, sequence analyses, and structural modeling studies paired with antimicrobial assays of peptides from known C3a sequences showed that, in particular in vertebrate C3a, crucial structural determinants governing antimicrobial activity have been conserved during the evolution of C3a. Thus, regions of the ancient C3a from Carcinoscorpius rotundicauda as well as corresponding parts of human C3a exhibited helical structures upon binding to bacterial lipopolysaccharide permeabilized liposomes and were antimicrobial against gram-negative and gram-positive bacteria. Human C3a and C4a (but not C5a) were antimicrobial, in concert with the separate evolutionary development of the chemotactic C5a. Thus, the results demonstrate that, notwithstanding a significant sequence variation, functional and structural constraints imposed on C3a during evolution have preserved critical properties governing antimicrobial activity.
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Affiliation(s)
- Mukesh Pasupuleti
- Section of Dermatology and Venereology, Department of Clinical Sciences, Biomedical Center, Lund University, Tornavägen 10, SE-221 84 Lund, Sweden
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35
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Evans EJ, Esnouf RM, Manso-Sancho R, Gilbert RJC, James JR, Yu C, Fennelly JA, Vowles C, Hanke T, Walse B, Hünig T, Sørensen P, Stuart DI, Davis SJ. Crystal structure of a soluble CD28-Fab complex. Nat Immunol 2005; 6:271-9. [PMID: 15696168 DOI: 10.1038/ni1170] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Accepted: 01/19/2005] [Indexed: 11/08/2022]
Abstract
Naive T cell activation requires signaling by the T cell receptor and by nonclonotypic cell surface receptors. The most important costimulatory protein is the monovalent homodimer CD28, which interacts with CD80 and CD86 expressed on antigen-presenting cells. Here we present the crystal structure of a soluble form of CD28 in complex with the Fab fragment of a mitogenic antibody. Structural comparisons redefine the evolutionary relationships of CD28-related proteins, antigen receptors and adhesion molecules and account for the distinct ligand-binding and stoichiometric properties of CD28 and the related, inhibitory homodimer CTLA-4. Cryo-electron microscopy-based comparisons of complexes of CD28 with mitogenic and nonmitogenic antibodies place new constraints on models of antibody-induced receptor triggering. This work completes the initial structural characterization of the CD28-CTLA-4-CD80-CD86 signaling system.
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Affiliation(s)
- Edward J Evans
- Nuffield Department of Clinical Medicine, The University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
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36
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Sørensen P, Kussmann M, Rosén A, Bennett KL, Thrige DDG, Uvebrant K, Walse B, Roepstorff P, Björk P. Identification of Protein-Protein Interfaces Implicated in CD80-CD28 Costimulatory Signaling. J Immunol 2004; 172:6803-9. [PMID: 15153498 DOI: 10.4049/jimmunol.172.11.6803] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The B7 ligands CD80 and CD86 on APCs deliver either costimulatory or inhibitory signals to the T cell when interacting with their counter-receptors CD28 and CD152 (CTLA-4) on the T cell surface. Although crucial for lymphocyte regulation, the structural basis of these interactions is still not completely understood. Using multivalent presentation and conditions mimicking clustering, believed to be essential for signaling through these receptors, and by applying a combined differential mass spectrometry and structural mapping approach to these conditions, we were able to identify a putative contact area involving hydrophilic regions on both CD28 and CD80 as well as a putative CD28 oligomerization interface induced by B7 ligation. Analysis of the CD80-CD28 interaction site reveals a well-defined interface structurally distinct from that of CD80 and CD152 and thus provides valuable information for therapeutic intervention targeted at this pathway, suggesting a general approach for other receptors.
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37
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Abstract
Superantigens (SAGs) cause a massive T-cell proliferation by simultaneously binding to major histocompatibility complex (MHC) class II on antigen-presenting cells and T-cell receptors (TCRs) on T cells. These T-cell mitogens can cause disease in host, such as food poisoning or toxic shock. The best characterized groups of SAGs are the bacterial SAGs secreted by Staphylococcus aureus and Streptococcus pyogenes. Despite a common overall three-dimensional fold of these SAGs, they have been shown to bind to MHC class II in different ways. Recently, it has also been shown that SAGs have individual preferences in their binding to the TCRs. They can interact with various regions of the variable beta-chain of TCRs and at least one SAG seems to bind to the alpha-chain of TCRs. In this review, different subclasses of SAGs are classified based upon their binding mode to MHC class II, and models of trimolecular complexes of MHC-SAG-TCR molecules are described in order to reveal and understand the complexity of SAG-mediated T-cell activation.
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38
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Erlandsson E, Andersson K, Cavallin A, Nilsson A, Larsson-Lorek U, Niss U, Sjöberg A, Wallén-Ohman M, Antonsson P, Walse B, Forsberg G. Identification of the antigenic epitopes in staphylococcal enterotoxins A and E and design of a superantigen for human cancer therapy. J Mol Biol 2003; 333:893-905. [PMID: 14583188 DOI: 10.1016/j.jmb.2003.09.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monoclonal antibodies have a potential for cancer therapy that may be further improved by linking them to effector molecules such as superantigens. Tumor targeting of a superantigen leads to a powerful T cell attack against the tumour tissue. Encouraging results have been observed preclinically and in patients using the superantigen staphylococcal enterotoxin A, SEA. To further improve the concept, we have reduced the reactivity to antibodies against superantigens, which is found in all individuals. Using epitope mapping, antibody binding sites in SEA and SEE were found around their MHC class II binding sites. These epitopes were removed genetically and a large number of synthetic superantigens were produced in an iterative engineering procedure. Properties such as decreased binding to anti-SEA as well as higher selectivity to induce killing of tumour cells compared to MHC class II expressing cells, were sequentially improved. The lysine residues 79, 81, 83 and 84 are all part of major antigenic epitopes, Gln204, Lys74, Asp75 and Asn78 are important for optimal killing of tumour cells while Asp45 affects binding to MHC class II. The production properties were optimised by further engineering and a novel synthetic superantigen, SEA/E-120, was designed. It is recognised by approximately 15% of human anti-SEA antibodies and have more potent tumour cell killing properties than SEA. SEA/E-120 is likely to have a low toxicity due to its reduced capacity to mediate killing of MHC class II expressing cells. It is produced as a Fab fusion protein at approximately 35 mg/l in Escherichia coli.
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Affiliation(s)
- Eva Erlandsson
- Active Biotech Research AB, Box 724, 220 07 Lund, Sweden
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39
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Petersson K, Pettersson H, Skartved NJ, Walse B, Forsberg G. Staphylococcal enterotoxin H induces V alpha-specific expansion of T cells. J Immunol 2003; 170:4148-54. [PMID: 12682246 DOI: 10.4049/jimmunol.170.8.4148] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Staphylococcal enterotoxin H (SEH) is a bacterial superantigen secreted by Staphylococcus aureus. Superantigens are presented on the MHC class II and activate large amounts of T cells by cross-linking APC and T cells. In this study, RT-PCR was used to show that SEH stimulates human T cells via the Valpha domain of TCR, in particular Valpha10 (TRAV27), while no TCR Vbeta-specific expansion was seen. This is in sharp contrast to all other studied bacterial superantigens, which are highly specific for TCR Vbeta. It was further confirmed by flow cytometry that SEH stimulation does not alter the levels of certain TCR Vbeta. In a functional assay addressing cross-reactivity, Vbeta binding superantigens were found to form one group, whereas SEH has different properties that fit well with Valpha reactivity. As SEH binds on top of MHC class II, an interaction between MHC and TCR upon SEH binding is not likely. This concludes that the specific expansion of TCR Valpha is not due to contacts between MHC and TCR, instead we suggest that SEH directly interacts with the TCR Valpha domain.
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MESH Headings
- Binding, Competitive/immunology
- Cell Communication/immunology
- Cell Line
- Cytotoxicity, Immunologic/genetics
- Enterotoxins/metabolism
- Enterotoxins/pharmacology
- Epitopes, T-Lymphocyte/immunology
- Gene Expression Regulation/immunology
- Genes, T-Cell Receptor alpha/physiology
- Humans
- Immunoglobulin Variable Region/biosynthesis
- Immunoglobulin Variable Region/genetics
- Lymphocyte Activation/immunology
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Staphylococcus aureus/immunology
- Superantigens/metabolism
- Superantigens/pharmacology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/microbiology
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40
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Petersson K, Thunnissen M, Forsberg G, Walse B. Crystal structure of a SEA variant in complex with MHC class II reveals the ability of SEA to crosslink MHC molecules. Structure 2002; 10:1619-26. [PMID: 12467569 DOI: 10.1016/s0969-2126(02)00895-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although the biological properties of staphylococcal enterotoxin A (SEA) have been well characterized, structural insights into the interaction between SEA and major histocompatibilty complex (MHC) class II have only been obtained by modeling. Here, the crystal structure of the D227A variant of SEA in complex with human MHC class II has been determined by X-ray crystallography. SEA(D227A) exclusively binds with its N-terminal domain to the alpha chain of HLA-DR1. The ability of one SEA molecule to crosslink two MHC molecules was modeled. It shows that this SEA molecule cannot interact with the T cell receptor (TCR) while a second SEA molecule interacts with MHC. Because of its relatively low toxicity, the D227A variant of SEA is used in tumor therapy.
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Affiliation(s)
- Karin Petersson
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
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41
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Collins AV, Brodie DW, Gilbert RJC, Iaboni A, Manso-Sancho R, Walse B, Stuart DI, van der Merwe PA, Davis SJ. The interaction properties of costimulatory molecules revisited. Immunity 2002; 17:201-10. [PMID: 12196291 DOI: 10.1016/s1074-7613(02)00362-x] [Citation(s) in RCA: 485] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
B7-1 and B7-2 are generally thought to have comparable structures and affinities for their receptors, CD28 and CTLA-4, each of which is assumed to be bivalent. We show instead (1) that B7-2 binds the two receptors more weakly than B7-1, (2) that, relative to its CTLA-4 binding affinity, B7-2 binds CD28 2- to 3-fold more effectively than B7-1, (3) that, unlike B7-1, B7-2 does not self-associate, and (4) that, in contrast to CTLA-4 homodimers, which are bivalent, CD28 homodimers are monovalent. Our results indicate that B7-1 markedly favors CTLA-4 over CD28 engagement, whereas B7-2 exhibits much less bias. We propose that the distinct structures and binding properties of B7-1 and B7-2 account for their overlapping but distinct effects on T cell responses.
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Affiliation(s)
- Alison V Collins
- Nuffield Department of Clinical Medicine, The University of Oxford, John Radcliffe Hospital, Headington, United Kingdom
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42
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Petersson K, Håkansson M, Nilsson H, Forsberg G, Svensson L, Liljas A, Walse B. Crystal structure of a superantigen bound to MHC class II displays zinc and peptide dependence. EMBO J 2001; 20:3306-12. [PMID: 11432818 PMCID: PMC125526 DOI: 10.1093/emboj/20.13.3306] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The three-dimensional structure of a bacterial superantigen, Staphylococcus aureus enterotoxin H (SEH), bound to human major histocompatibility complex (MHC) class II (HLA-DR1) has been determined by X-ray crystallography to 2.6 A resolution (1HXY). The superantigen binds on top of HLA-DR1 in a completely different way from earlier co-crystallized superantigens from S.aureus. SEH interacts with high affinity through a zinc ion with the beta1 chain of HLA-DR1 and also with the peptide presented by HLA-DR1. The structure suggests that all superantigens interacting with MHC class II in a zinc-dependent manner present the superantigen in a common way. This suggests a new model for ternary complex formation with the T-cell receptor (TCR), in which a contact between the TCR and the MHC class II is unlikely.
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Affiliation(s)
- Karin Petersson
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
| | - Maria Håkansson
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
| | - Helen Nilsson
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
| | - Göran Forsberg
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
| | - L.Anders Svensson
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
| | - Anders Liljas
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
| | - Björn Walse
- Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, PO Box 124, S-221 00 Lund and Active Biotech Research AB, PO Box 724, S-220 07 Lund, Sweden Present address: NovoNordisk A/S, Novo Allé, DK-2880 Bagsvaerd, Denmark Corresponding author e-mail:
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43
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Karlsson KF, Walse B, Drakenberg T, Roy S, Bergquist KE, Pinkner JS, Hultgren SJ, Kihlberg J. Binding of peptides in solution by the Escherichia coli chaperone PapD as revealed using an inhibition ELISA and NMR spectroscopy. Bioorg Med Chem 1998; 6:2085-101. [PMID: 9881099 DOI: 10.1016/s0968-0896(98)00162-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
PapD is the prototype member of a family of periplasmic chaperones which are required for assembly of virulence associated pili in pathogenic, gram-negative bacteria. In the present investigation, an ELISA has been developed for evaluation of compounds as inhibitors of PapD. Synthetic peptides, including an octamer, derived from the C-terminus of the pilus adhesin PapG were able to inhibit PapD in the ELISA. Evaluation of a panel of octapeptides in the ELISA, in combination with NMR studies, showed that the peptides were bound as extended beta-strands by PapD in aqueous solution. The PapD-peptide complex was stabilized by backbone to backbone hydrogen bonds and interactions involving three hydrophobic peptide side chains. This structural information, together with previous crystal structure data, provides a starting point in efforts to design and synthesize compounds which bind to chaperones and interfere with pilus assembly in pathogenic bacteria.
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Affiliation(s)
- K F Karlsson
- Center for Chemistry and Chemical Engineering, Lund University, Sweden
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44
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Walse B, Kihlberg J, Drakenberg T. Conformation of desmopressin, an analogue of the peptide hormone vasopressin, in aqueous solution as determined by NMR spectroscopy. Eur J Biochem 1998; 252:428-40. [PMID: 9546658 DOI: 10.1046/j.1432-1327.1998.2520428.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Desmopressin (1-desamino-[DArg8]vasopressin, is a synthetic analogue of the neurohypophyseal peptide hormone vasopressin which has high antidiuretic and antibleeding potency. The structure of desmopressin has been determined in aqueous solution by two-dimensional NMR techniques and molecular dynamics simulations. Both standard and time-averaged distance restraints were used in structure calculations because of the inherent flexibility in small peptides. 21 models calculated with standard restraints were compared with structures refined with time-averaged distance restraints and were found to be good representatives of the conformational ensemble of desmopressin. The macrocyclic ring forms an inverse gamma-turn centered around Gln4. Residues 1 and 2, the disulphide bridge and the three-residue acyclic tail were found to be flexible in solution. Residues 4-6 in the ensemble of calculated structures contain essentially the same backbone conformation as in the crystal structure of pressinoic acid, the cyclic moiety of vasopressin, whereas residues 2-6 superimpose on the NMR-derived conformation of oxytocin bound to neurophysin. The results presented in this work suggest that, in addition to the differences in sequence between desmopressin and vasopressin, differences in conformational and dynamic properties between the two compounds explain their pharmacological differences.
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Affiliation(s)
- B Walse
- Physical Chemistry 2, Center for Chemistry and Chemical Engineering, Lund University, Sweden
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45
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Walse B, Kihlberg J, Karlsson KF, Nilsson M, Wahlund KG, Pinkner JS, Hultgren SJ, Drakenberg T. Transferred nuclear Overhauser effect spectroscopy study of a peptide from the PapG pilus subunit bound by the Escherichia coli PapD chaperone. FEBS Lett 1997; 412:115-20. [PMID: 9257702 DOI: 10.1016/s0014-5793(97)00759-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Interaction of the Escherichia coli PapD chaperone with the synthetic peptide PapG308-314 (Thr-Met-Val-Leu-Ser-Phe-Pro), corresponding to the seven C-terminal residues of the PapG pilus subunit, was studied by transferred nuclear Overhauser effect (TRNOE) spectroscopy. The observation of cross-peaks corresponding to either intraresidue or sequential C(alpha)H/NH and C(beta)H/NH TRNOEs and the absence of sequential NH(i)/NH(i+1) TRNOEs indicate that the peptide binds to PapD in an extended conformation. In addition, line-broadening effects gave information of the peptide's mode of interaction with PapD. These observations were in excellent agreement with a recent crystal structure of a PapG peptide complexed with PapD.
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Affiliation(s)
- B Walse
- Physical Chemistry 2, Center for Chemistry and Chemical Engineering, Lund University, Sweden
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46
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Elofsson M, Walse B, Kihlberg J. Solid-phase synthesis and conformational studies of helper T cell immunogenic peptides that carry carbohydrate haptens linked to serine. Int J Pept Protein Res 1996; 47:340-7. [PMID: 8791156 DOI: 10.1111/j.1399-3011.1996.tb01082.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
N alpha-Fmoc serine and its corresponding pentafluorophenyl ester were glycosylated with the 1,2-trans peracetates of the disaccharides galabiose and cellobiose. Complete stereoselectivity and 52-75% yields were obtained under boron trifluoride etherate promotion. Lower yields and loss of stereoselectivity were obtained when thioglycosides, trichloroacetimidates or glycosyl bromides were employed as glycosyl donors. The glycosylated building blocks were used in solid-phase synthesis of derivatives of a helper T cell immunogenic peptide consisting of amino acids 52-61 from hen-egg lysozyme. 1H-NMR spectroscopy in DMSO-d6 showed that the peptide moiety of the glycopeptides assumed random conformations which were not influenced by glycosylation at different positions.
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Affiliation(s)
- M Elofsson
- Center for Chemistry and Chemical Engineering, Lund Institute of Technology, Lund University, Sweden
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47
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Walse B, Ullner M, Lindbladh C, Bülow L, Drakenberg T, Teleman O. Structure of a cyclic peptide with a catalytic triad, determined by computer simulation and NMR spectroscopy. J Comput Aided Mol Des 1996; 10:11-22. [PMID: 8786411 DOI: 10.1007/bf00124461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report the design of a cyclic, eight-residue peptide that possesses the catalytic triad residues of the serine proteases. A manually built model has been relaxed by 0.3 ns of molecular dynamics simulation at room temperature, during which no major changes occurred in the peptide. The molecule has been synthesised and purified. Two-dimensional NMR spectroscopy provided 35 distance and 7 torsion angle constraints, which were used to determine the three-dimensional structure. The experimental conformation agrees with the predicted one at the beta-turn, but deviates in the arrangement of the disulphide bridge that closes the backbone to a ring. A 1.2 ns simulation at 600 K provided extended sampling of conformation space. The disulphide bridge reoriented into the experimental arrangement, producing a minimum backbone rmsd from the experimental conformation of 0.8 A. At a later stage in the simulation, a transition at Ser3 produced more pronounced high-temperature behaviour. The peptide hydrolyses p-nitrophenyl acetate about nine times faster than free histidine.
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Affiliation(s)
- B Walse
- Departments of Physical Chemistry 2, Lund University, Sweden
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48
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Jämsä E, Holkeri H, Vihinen H, Wikström M, Simonen M, Walse B, Kalkkinen N, Paakkola J, Makarow M. Structural features of a polypeptide carrier promoting secretion of a beta-lactamase fusion protein in yeast. Yeast 1995; 11:1381-91. [PMID: 8585321 DOI: 10.1002/yea.320111406] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Escherichia coli beta-lactamase was secreted into the culture medium of Saccharomyces cerevisiae in biologically active form, when fused to the C-terminus of the hsp150 delta-carrier. The hsp150 delta-carrier is an N-terminal fragment of the yeast hsp150 protein, having a signal peptide and consisting mostly of a 19 amino acid peptide repeated 11 times in tandem. Here we expressed the hsp150 delta-carrier fragment alone in S. cerevisiae. Apparently due to a positional effect of the gene insertion, large amounts of the hsp150 delta-carrier were synthesized. About half of the de novo synthesized carrier molecules were secreted into the culture medium, the rest remaining mostly in the pre-Golgi compartment. The extensively O-glycosylated carrier fragment was purified from the culture medium under non-denaturing conditions. Circular dichroism spectroscopy showed that it had no regular secondary structure. Nuclear magnetic resonance spectroscopy showed that a non-glycosylated synthetic peptide, the consensus sequence of the repetitive 19 amino acid peptide, also lacked secondary structure. The unstructured carrier polypeptide may facilitate proper folding and secretion of heterologous proteins attached to it.
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Affiliation(s)
- E Jämsä
- Institute of Biotechnology, University of Helsinki, Finland
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49
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Kihlberg J, Ahman J, Walse B, Drakenberg T, Nilsson A, Söderberg-ahlm C, Bengtsson B, Olsson H. Glycosylated peptide hormones: pharmacological properties and conformational studies of analogues of [1-desamino,8-D-arginine]vasopressin. J Med Chem 1995; 38:161-9. [PMID: 7837227 DOI: 10.1021/jm00001a021] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two analogues of the antidiuretic drug [1-desamino,8-D-arginine]vasopressin (DDAVP), which have a glycosylated serine at position 4, have been prepared by Fmoc solid phase peptide synthesis. The glycosylated analogues had significantly higher bioavailabilities than the nonglycosylated [D-Tyr2,Ser4]DDAVP and DDAVP on intraintestinal administration in rat. The improved bioavailability resulted from an increased absorption from the small intestine and most likely from an increased stability toward enzymatic degradation, whereas plasma clearance was either unaffected or slightly increased by the glycosylation. The glycosylated analogues displayed only very low agonistic and antagonistic activities at the vasopressin V2-receptor. Conformational studies performed by 1H NMR spectroscopy did not reveal any major influence from glycosylation on the conformation of the peptide backbone. The lack of receptor binding displayed by the analogues is therefore most likely explained by steric repulsion between the carbohydrate moiety and the vasopressin receptor which prevents receptor binding.
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Affiliation(s)
- J Kihlberg
- Chemical Center, Lund Institute of Technology, University of Lund, Sweden
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50
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Elofsson M, Roy S, Walse B, Kihlberg J. Solid-phase synthesis and conformational studies of glycosylated derivatives of helper-T-cell immunogenic peptides from hen-egg lysozyme. Carbohydr Res 1993; 246:89-103. [PMID: 8370047 DOI: 10.1016/0008-6215(93)84026-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
3-Mercaptopropionic acid and N alpha-Fmoc serine, both with unprotected carboxyl groups, were stereospecifically glycosylated in 62-82% yields, using saccharide 1,2-trans peracetates and Lewis acid catalysis. The resulting glycosylated building blocks were used in the synthesis of derivatives of helper-T-cell stimulating peptides, with the carbohydrate moiety located at the amino terminus, or internally in the peptide chain. 1H NMR spectroscopy in Me2SO-d6 showed that the glycopeptides assumed random conformations, which were not influenced by the glycosylation or by single substitutions of amino acids in the peptide moiety.
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