1
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Ferrari M, Righi M, Baldan V, Wawrzyniecka P, Bulek A, Kinna A, Ma B, Bughda R, Akbar Z, Srivastava S, Gannon I, Robson M, Sillibourne J, Jha R, El-Kholy M, Amin OM, Kokalaki E, Banani MA, Hussain R, Day W, Lim WC, Ghongane P, Hopkins JR, Jungherz D, Herling M, Welin M, Surade S, Dyson M, McCafferty J, Logan D, Cordoba S, Thomas S, Sewell A, Maciocia P, Onuoha S, Pule M. Structure-guided engineering of immunotherapies targeting TRBC1 and TRBC2 in T cell malignancies. Nat Commun 2024; 15:1583. [PMID: 38383515 PMCID: PMC10881500 DOI: 10.1038/s41467-024-45854-3] [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: 03/21/2022] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Peripheral T cell lymphomas are typically aggressive with a poor prognosis. Unlike other hematologic malignancies, the lack of target antigens to discriminate healthy from malignant cells limits the efficacy of immunotherapeutic approaches. The T cell receptor expresses one of two highly homologous chains [T cell receptor β-chain constant (TRBC) domains 1 and 2] in a mutually exclusive manner, making it a promising target. Here we demonstrate specificity redirection by rational design using structure-guided computational biology to generate a TRBC2-specific antibody (KFN), complementing the antibody previously described by our laboratory with unique TRBC1 specificity (Jovi-1) in targeting broader spectrum of T cell malignancies clonally expressing either of the two chains. This permits generation of paired reagents (chimeric antigen receptor-T cells) specific for TRBC1 and TRBC2, with preclinical evidence to support their efficacy in T cell malignancies.
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Affiliation(s)
| | | | | | | | | | | | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | | | | | | | | | - Ram Jha
- Autolus Therapeutics, London, UK
| | | | | | | | | | | | | | | | | | - Jade R Hopkins
- Cardiff University School of Medicine; Heath Park, Cardiff, UK
| | - Dennis Jungherz
- Department of Hematology, Cell Therapy, Hemostaseology, and Infectious Diseases, University of Leipzig Medical Centre, Leipzig, Germany
| | - Marco Herling
- Department of Hematology, Cell Therapy, Hemostaseology, and Infectious Diseases, University of Leipzig Medical Centre, Leipzig, Germany
| | | | | | | | | | | | | | | | - Andrew Sewell
- Cardiff University School of Medicine; Heath Park, Cardiff, UK
| | - Paul Maciocia
- Cancer Institute; University College London, London, UK
| | | | - Martin Pule
- Autolus Therapeutics, London, UK.
- Cancer Institute; University College London, London, UK.
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2
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Billiald P, Slater A, Welin M, Clark JC, Loyau S, Pugnière M, Jiacomini IG, Rose N, Lebozec K, Toledano E, François D, Watson SP, Jandrot-Perrus M. Targeting platelet GPVI with glenzocimab: a novel mechanism for inhibition. Blood Adv 2023; 7:1258-1268. [PMID: 36375047 PMCID: PMC10119634 DOI: 10.1182/bloodadvances.2022007863] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Platelet glycoprotein VI (GPVI) is attracting interest as a potential target for the development of new antiplatelet molecules with a low bleeding risk. GPVI binding to vascular collagen initiates thrombus formation and GPVI interactions with fibrin promote the growth and stability of the thrombus. In this study, we show that glenzocimab, a clinical stage humanized antibody fragment (Fab) with a high affinity for GPVI, blocks the binding of both ligands through a combination of steric hindrance and structural change. A cocrystal of glenzocimab with an extracellular domain of monomeric GPVI was obtained and its structure determined to a resolution of 1.9 Å. The data revealed that (1) glenzocimab binds to the D2 domain of GPVI, GPVI dimerization was not observed in the crystal structure because glenzocimab prevented D2 homotypic interactions and the formation of dimers that have a high affinity for collagen and fibrin; and (2) the light variable domain of the GPVI-bound Fab causes steric hindrance that is predicted to prevent the collagen-related peptide (CRP)/collagen fibers from extending out of their binding site and preclude GPVI clustering and downstream signaling. Glenzocimab did not bind to a truncated GPVI missing loop residues 129 to 136, thus validating the epitope identified in the crystal structure. Overall, these findings demonstrate that the binding of glenzocimab to the D2 domain of GPVI induces steric hindrance and structural modifications that drive the inhibition of GPVI interactions with its major ligands.
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Affiliation(s)
- Philippe Billiald
- Laboratory for Vascular Translational Science, UMR_S1148 INSERM, Université Paris Cité, Hôpital Bichat, Paris, France
- School of Pharmacy, Université Paris-Saclay, Orsay, France
| | - Alexandre Slater
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Lund, Sweden
| | - Joanne C. Clark
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Stéphane Loyau
- Laboratory for Vascular Translational Science, UMR_S1148 INSERM, Université Paris Cité, Hôpital Bichat, Paris, France
| | - Martine Pugnière
- Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer, Montpellier, France
| | - Isabella G. Jiacomini
- Departamento de Patologia Básica, Laboratório de Imunoquímica, Universidade Federal do Paraná, Curitiba, Brazil
| | - Nadia Rose
- SARomics Biostructures, Medicon Village, Lund, Sweden
| | | | | | | | - Steve P. Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Martine Jandrot-Perrus
- Laboratory for Vascular Translational Science, UMR_S1148 INSERM, Université Paris Cité, Hôpital Bichat, Paris, France
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3
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Liu CY, Ahonen CL, Brown ME, Zhou L, Welin M, Krauland EM, Pejchal R, Widboom PF, Battles MB. Structure-based engineering of a novel CD3ε-targeting antibody for reduced polyreactivity. MAbs 2023; 15:2189974. [PMID: 36991534 PMCID: PMC10072072 DOI: 10.1080/19420862.2023.2189974] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Bispecific antibodies continue to represent a growth area for antibody therapeutics, with roughly a third of molecules in clinical development being T-cell engagers that use an anti-CD3 binding arm. CD3 antibodies possessing cross-reactivity with cynomolgus monkey typically recognize a highly electronegative linear epitope at the extreme N-terminus of CD3 epsilon (CD3ε). Such antibodies have high isoelectric points and display problematic polyreactivity (correlated with poor pharmacokinetics for monospecific antibodies). Using insights from the crystal structure of anti-Hu/Cy CD3 antibody ADI-26906 in complex with CD3ε and antibody engineering using a yeast-based platform, we have derived high-affinity CD3 antibody variants with very low polyreactivity and significantly improved biophysical developability. Comparison of these variants with CD3 antibodies in the clinic (as part of bi- or multi-specifics) shows that affinity for CD3 is correlated with polyreactivity. Our engineered CD3 antibodies break this correlation, forming a broad affinity range with no to low polyreactivity. Such antibodies will enable bispecifics with improved pharmacokinetic and safety profiles and suggest engineering solutions that will benefit the large and growing sector of T-cell engagers.
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4
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Boonkrai C, Cotrone TS, Chaisuriyong W, Tantawichien T, Thisyakorn U, Fernandez S, Hunsawong T, Reed M, Wongtangprasert T, Audomsun T, Phakham T, Attakitbancha C, Saelao P, Focht D, Kimbung R, Welin M, Malik AA, Pisitkun T, Srisawat N. Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants. PLoS One 2023; 18:e0284173. [PMID: 37141227 PMCID: PMC10159178 DOI: 10.1371/journal.pone.0284173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/25/2023] [Indexed: 05/05/2023] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the biggest healthcare issue worldwide. This study aimed to develop a monoclonal antibody against SARS-CoV-2 from B cells of recovered COVID-19 patients, which might have beneficial therapeutic purposes for COVID-19 patients. We successfully generated human monoclonal antibodies (hmAbs) against the receptor binding domain (RBD) protein of SARS-CoV-2 using developed hybridoma technology. The isolated hmAbs against the RBD protein (wild-type) showed high binding activity and neutralized the interaction between the RBD and the cellular receptor angiotensin-converting enzyme 2 (ACE2) protein. Epitope binning and crystallography results displayed target epitopes of these antibodies in distinct regions beneficial in the mix as a cocktail. The 3D2 binds to conserved epitopes among multi-variants. Pseudovirion-based neutralization results revealed that the antibody cocktail, 1D1 and 3D2, showed high potency in multiple variants of SARS-CoV-2 infection. In vivo studies showed the ability of the antibody cocktail treatment (intraperitoneal (i.p.) administration) to reduce viral load (Beta variant) in blood and various tissues. While the antibody cocktail treatment (intranasal (i.n.) administration) could not significantly reduce the viral load in nasal turbinate and lung tissue, it could reduce the viral load in blood, kidney, and brain tissue. These findings revealed that the efficacy of the antibody cocktail, 1D1 and 3D2, should be further studied in animal models in terms of timing of administration, optimal dose, and efficacy to mitigate inflammation in targeted tissue such as nasal turbinate and lung.
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Affiliation(s)
- Chatikorn Boonkrai
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
| | - Thomas S Cotrone
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Watchadaporn Chaisuriyong
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Faculty of Medicine, Center of Excellence in Critical Care Nephrology, Chulalongkorn University, Bangkok, Thailand
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Terapong Tantawichien
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand
- Faculty of Medicine, Department of Medicine, Division of Infectious Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Usa Thisyakorn
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Taweewun Hunsawong
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Matthew Reed
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Tossapon Wongtangprasert
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
- The Excellence Chulalongkorn Comprehensive Cancer Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Thittaya Audomsun
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
| | - Tanapati Phakham
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
| | - Chadaporn Attakitbancha
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
| | - Pijitra Saelao
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
| | - Dorota Focht
- SARomics Biostructures AB, Medicon Village, Lund, Sweden
| | | | - Martin Welin
- SARomics Biostructures AB, Medicon Village, Lund, Sweden
| | - Aijaz Ahmad Malik
- Faculty of Medicine, Center of Excellence in Computational Molecular Biology, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Faculty of Medicine, Center of Excellence in Systems Biology, Chulalongkorn University, Bangkok, Thailand
| | - Nattachai Srisawat
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Faculty of Medicine, Center of Excellence in Critical Care Nephrology, Chulalongkorn University, Bangkok, Thailand
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand
- Faculty of Medicine, Department of Medicine, Division of Nephrology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Department of Critical Care Medicine, Center for Critical Care Nephrology, The CRISMA Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States of America
- Academy of Science, Royal Society of Thailand, Bangkok, Thailand
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5
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Ahlqvist J, Linares-Pastén JA, Jasilionis A, Welin M, Håkansson M, Svensson LA, Wang L, Watzlawick H, Ævarsson A, Friðjónsson ÓH, Hreggviðsson GÓ, Ketelsen Striberny B, Glomsaker E, Lanes O, Al-Karadaghi S, Nordberg Karlsson E. Crystal structure of DNA polymerase I from Thermus phage G20c. Acta Cryst Sect D Struct Biol 2022; 78:1384-1398. [DOI: 10.1107/s2059798322009895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3′–5′ exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5′–3′ exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SβαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SβαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3′–5′ exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SβαR motif, was first determined to 2.19 Å resolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Å resolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.
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6
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Składanowska K, Bloch Y, Strand J, White KF, Hua J, Aldridge D, Welin M, Logan DT, Soete A, Merceron R, Murphy C, Provost M, Bazan JF, Hunter CA, Hill JA, Savvides SN. Structural basis of activation and antagonism of receptor signaling mediated by interleukin-27. Cell Rep 2022; 41:111490. [PMID: 36261006 PMCID: PMC9597551 DOI: 10.1016/j.celrep.2022.111490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/14/2022] [Accepted: 09/21/2022] [Indexed: 11/19/2022] Open
Abstract
Interleukin-27 (IL-27) uniquely assembles p28 and EBI3 subunits to a heterodimeric cytokine that signals via IL-27Rα and gp130. To provide the structural framework for receptor activation by IL-27 and its emerging therapeutic targeting, we report here crystal structures of mouse IL-27 in complex with IL-27Rα and of human IL-27 in complex with SRF388, a monoclonal antibody undergoing clinical trials with oncology indications. One face of the helical p28 subunit interacts with EBI3, while the opposite face nestles into the interdomain elbow of IL-27Rα to juxtapose IL-27Rα to EBI3. This orients IL-27Rα for paired signaling with gp130, which only uses its immunoglobulin domain to bind to IL-27. Such a signaling complex is distinct from those mediated by IL-12 and IL-23. The SRF388 binding epitope on IL-27 overlaps with the IL-27Rα interaction site explaining its potent antagonistic properties. Collectively, our findings will facilitate the mechanistic interrogation, engineering, and therapeutic targeting of IL-27.
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Affiliation(s)
- Katarzyna Składanowska
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Jamie Strand
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Kerry F White
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Jing Hua
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Daniel Aldridge
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin Welin
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 63 Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 63 Lund, Sweden
| | - Arne Soete
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium; Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Romain Merceron
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Casey Murphy
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Mathias Provost
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium; ħ Bioconsulting, Stillwater, MN, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A Hill
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA.
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium.
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7
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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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8
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Nyerges A, Tomašič T, Durcik M, Revesz T, Szili P, Draskovits G, Bogar F, Skok Ž, Zidar N, Ilaš J, Zega A, Kikelj D, Daruka L, Kintses B, Vasarhelyi B, Foldesi I, Kata D, Welin M, Kimbung R, Focht D, Mašič LP, Pal C. Rational design of balanced dual-targeting antibiotics with limited resistance. PLoS Biol 2020; 18:e3000819. [PMID: 33017402 PMCID: PMC7561186 DOI: 10.1371/journal.pbio.3000819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 02/28/2020] [Revised: 10/15/2020] [Accepted: 08/26/2020] [Indexed: 12/02/2022] Open
Abstract
Antibiotics that inhibit multiple bacterial targets offer a promising therapeutic strategy against resistance evolution, but developing such antibiotics is challenging. Here we demonstrate that a rational design of balanced multitargeting antibiotics is feasible by using a medicinal chemistry workflow. The resultant lead compounds, ULD1 and ULD2, belonging to a novel chemical class, almost equipotently inhibit bacterial DNA gyrase and topoisomerase IV complexes and interact with multiple evolutionary conserved amino acids in the ATP-binding pockets of their target proteins. ULD1 and ULD2 are excellently potent against a broad range of gram-positive bacteria. Notably, the efficacy of these compounds was tested against a broad panel of multidrug-resistant Staphylococcus aureus clinical strains. Antibiotics with clinical relevance against staphylococcal infections fail to inhibit a significant fraction of these isolates, whereas both ULD1 and ULD2 inhibit all of them (minimum inhibitory concentration [MIC] ≤1 μg/mL). Resistance mutations against these compounds are rare, have limited impact on compound susceptibility, and substantially reduce bacterial growth. Based on their efficacy and lack of toxicity demonstrated in murine infection models, these compounds could translate into new therapies against multidrug-resistant bacterial infections.
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Affiliation(s)
- Akos Nyerges
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Tamas Revesz
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Petra Szili
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Gabor Draskovits
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Ferenc Bogar
- MTA-SZTE Biomimetic Systems Research Group, Department of Medical Chemistry, University of Szeged, Hungary
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Balint Kintses
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
- HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary
| | - Balint Vasarhelyi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Imre Foldesi
- Department of Laboratory Medicine, University of Szeged, Szeged, Hungary
| | - Diána Kata
- Department of Laboratory Medicine, University of Szeged, Szeged, Hungary
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Lund, Sweden
| | | | - Dorota Focht
- SARomics Biostructures, Medicon Village, Lund, Sweden
| | | | - Csaba Pal
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
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9
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Shilova A, Lebrette H, Aurelius O, Nan J, Welin M, Kovacic R, Ghosh S, Safari C, Friel RJ, Milas M, Matej Z, Högbom M, Brändén G, Kloos M, Shoeman RL, Doak B, Ursby T, Håkansson M, Logan DT, Mueller U. Current status and future opportunities for serial crystallography at MAX IV Laboratory. J Synchrotron Radiat 2020; 27:1095-1102. [PMID: 32876583 PMCID: PMC7467353 DOI: 10.1107/s1600577520008735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.
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Affiliation(s)
- Anastasya Shilova
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Rebeka Kovacic
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Ross J. Friel
- School of Information Technology, Halmstad University, Halmstad 30118, Sweden
| | - Mirko Milas
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Derek T. Logan
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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10
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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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11
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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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12
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Casaletto JB, Geddie ML, Abu-Yousif AO, Masson K, Fulgham A, Boudot A, Maiwald T, Kearns JD, Kohli N, Su S, Razlog M, Raue A, Kalra A, Håkansson M, Logan DT, Welin M, Chattopadhyay S, Harms BD, Nielsen UB, Schoeberl B, Lugovskoy AA, MacBeath G. MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM. Proc Natl Acad Sci U S A 2019; 116:7533-7542. [PMID: 30898885 PMCID: PMC6462049 DOI: 10.1073/pnas.1819085116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Activation of the Met receptor tyrosine kinase, either by its ligand, hepatocyte growth factor (HGF), or via ligand-independent mechanisms, such as MET amplification or receptor overexpression, has been implicated in driving tumor proliferation, metastasis, and resistance to therapy. Clinical development of Met-targeted antibodies has been challenging, however, as bivalent antibodies exhibit agonistic properties, whereas monovalent antibodies lack potency and the capacity to down-regulate Met. Through computational modeling, we found that the potency of a monovalent antibody targeting Met could be dramatically improved by introducing a second binding site that recognizes an unrelated, highly expressed antigen on the tumor cell surface. Guided by this prediction, we engineered MM-131, a bispecific antibody that is monovalent for both Met and epithelial cell adhesion molecule (EpCAM). MM-131 is a purely antagonistic antibody that blocks ligand-dependent and ligand-independent Met signaling by inhibiting HGF binding to Met and inducing receptor down-regulation. Together, these mechanisms lead to inhibition of proliferation in Met-driven cancer cells, inhibition of HGF-mediated cancer cell migration, and inhibition of tumor growth in HGF-dependent and -independent mouse xenograft models. Consistent with its design, MM-131 is more potent in EpCAM-high cells than in EpCAM-low cells, and its potency decreases when EpCAM levels are reduced by RNAi. Evaluation of Met, EpCAM, and HGF levels in human tumor samples reveals that EpCAM is expressed at high levels in a wide range of Met-positive tumor types, suggesting a broad opportunity for clinical development of MM-131.
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Affiliation(s)
| | - Melissa L Geddie
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Adnan O Abu-Yousif
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Kristina Masson
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Aaron Fulgham
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Antoine Boudot
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Tim Maiwald
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Jeffrey D Kearns
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Neeraj Kohli
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Stephen Su
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Maja Razlog
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Andreas Raue
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139;
| | - Ashish Kalra
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81 Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, SE-223 81 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures AB, Medicon Village, SE-223 81 Lund, Sweden
| | | | - Brian D Harms
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Ulrik B Nielsen
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Birgit Schoeberl
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Alexey A Lugovskoy
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Gavin MacBeath
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139;
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13
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Badarau A, Rouha H, Malafa S, Battles MB, Walker L, Nielson N, Dolezilkova I, Teubenbacher A, Banerjee S, Maierhofer B, Weber S, Stulik L, Logan DT, Welin M, Mirkina I, Pleban C, Zauner G, Gross K, Jägerhofer M, Magyarics Z, Nagy E. Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. MAbs 2016; 8:1347-1360. [PMID: 27467113 PMCID: PMC5058624 DOI: 10.1080/19420862.2016.1215791] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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] [Indexed: 12/31/2022] Open
Abstract
LukGH (LukAB) is a potent leukocidin of Staphylococcus aureus that lyses human phagocytic cells and is thought to contribute to immune evasion. Unlike the other bi-component leukocidins of S. aureus, LukGH forms a heterodimer before binding to its receptor, CD11b expressed on professional phagocytic cells, and displays significant sequence variation. We employed a high diversity human IgG1 library presented on yeast cells to discover monoclonal antibodies (mAbs) neutralizing the cytolytic activity of LukGH. Recombinant LukG and LukH monomers or a LukGH dimer were used as capture antigens in the library selections. We found that mAbs identified with LukG or LukH as bait had no or very low toxin neutralization potency. In contrast, LukGH dimer-selected antibodies proved to be highly potent, and several mAbs were able to neutralize even the most divergent LukGH variants. Based on biolayer interferometry and mesoscale discovery, the high affinity antibody binding site on the LukGH complex was absent on the individual monomers, suggesting that it was generated upon formation of the LukG-LukH dimer. X-ray crystallography analysis of the complex between the LukGH dimer and the antigen-binding fragment of a very potent mAb (PDB code 5K59) indicated that the epitope is located in the predicted cell binding region (rim domain) of LukGH. The corresponding IgG inhibited the binding of LukGH dimer to target cells. Our data suggest that knowledge of the native conformation of target molecules is essential to generate high affinity and functional mAbs.
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Affiliation(s)
- Adriana Badarau
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Harald Rouha
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Stefan Malafa
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | | | | | | | | | - Srijib Banerjee
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Susanne Weber
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Lukas Stulik
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Derek T Logan
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Martin Welin
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Irina Mirkina
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Clara Pleban
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Gerhild Zauner
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Karin Gross
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Zoltán Magyarics
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Eszter Nagy
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
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14
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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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15
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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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16
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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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17
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Trésaugues L, Lundbäck T, Welin M, Flodin S, Nyman T, Silvander C, Gräslund S, Nordlund P. Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate. PLoS One 2015; 10:e0131507. [PMID: 26121039 PMCID: PMC4485890 DOI: 10.1371/journal.pone.0131507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
Human NUDT16 is a member of the NUDIX hydrolase superfamily. After having been initially described as an mRNA decapping enzyme, recent studies conferred it a role as an “housecleaning” enzyme specialized in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. Here we present the crystal structure of human NUDT16 both in its apo-form and in complex with its product inosine monophosphate (IMP). NUDT16 appears as a dimer whose formation generates a positively charged trench to accommodate substrate-binding. Complementation of the structural data with detailed enzymatic and biophysical studies revealed the determinants of substrate recognition and particularly the importance of the substituents in position 2 and 6 on the purine ring. The affinity for the IMP product, harboring a carbonyl in position 6 on the base, compared to purine monophosphates lacking a H-bond acceptor in this position, implies a catalytic cycle whose rate is primarily regulated by the product-release step. Finally, we have also characterized a phenomenon of inhibition by the product of the reaction, IMP, which might exclude non-deleterious nucleotides from NUDT16-mediated hydrolysis regardless of their cellular concentration. Taken together, this study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16.
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Affiliation(s)
- Lionel Trésaugues
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (PN); (LT)
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Flodin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Nyman
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Silvander
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PN); (LT)
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18
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Trésaugues L, Silvander C, Flodin S, Welin M, Nyman T, Gräslund S, Hammarström M, Berglund H, Nordlund P. Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases. Structure 2014; 22:744-55. [PMID: 24704254 DOI: 10.1016/j.str.2014.01.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/15/2022]
Abstract
SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phophatases is still poorly understood. We determined the crystal structures of human SHIP2, OCRL, and INPP5B, the latter in complex with phosphoinositide substrate analogs, which revealed a membrane interaction patch likely to assist in sequestering substrates from the lipid bilayer. Residues recognizing the 1-phosphate of the substrates are highly conserved among human family members, suggesting similar substrate binding modes. However, 3- and 4-phosphate recognition varies and determines individual substrate specificity profiles. The high conservation of the environment of the scissile 5-phosphate suggests a common reaction geometry for all members of the human 5-phosphatase family.
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Affiliation(s)
- Lionel Trésaugues
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Camilla Silvander
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden.
| | - Susanne Flodin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Tomas Nyman
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Hammarström
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Helena Berglund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden; Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
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19
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Welin M, Lehtiö L, Johansson A, Flodin S, Nyman T, Trésaugues L, Hammarström M, Gräslund S, Nordlund P. Substrate specificity and oligomerization of human GMP synthetase. J Mol Biol 2013; 425:4323-33. [PMID: 23816837 DOI: 10.1016/j.jmb.2013.06.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 10/26/2022]
Abstract
Guanine monophosphate (GMP) synthetase is a bifunctional two-domain enzyme. The N-terminal glutaminase domain generates ammonia from glutamine and the C-terminal synthetase domain aminates xanthine monophosphate (XMP) to form GMP. Mammalian GMP synthetases (GMPSs) contain a 130-residue-long insert in the synthetase domain in comparison to bacterial proteins. We report here the structure of a eukaryotic GMPS. Substrate XMP was bound in the crystal structure of the human GMPS enzyme. XMP is bound to the synthetase domain and covered by a LID motif. The enzyme forms a dimer in the crystal structure with subunit orientations entirely different from the bacterial counterparts. The inserted sub-domain is shown to be involved in substrate binding and dimerization. Furthermore, the structural basis for XMP recognition is revealed as well as a potential allosteric site. Enzymes in the nucleotide metabolism typically display an increased activity in proliferating cells due to the increased need for nucleotides. Many drugs used as immunosuppressants and for treatment of cancer and viral diseases are indeed nucleobase- and nucleoside-based compounds, which are acting on or are activated by enzymes in this pathway. The information obtained from the crystal structure of human GMPS might therefore aid in understanding interactions of nucleoside-based drugs with GMPS and in structure-based design of GMPS-specific inhibitors.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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20
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Egeblad L, Welin M, Flodin S, Gräslund S, Wang L, Balzarini J, Eriksson S, Nordlund P. Pan-pathway based interaction profiling of FDA-approved nucleoside and nucleobase analogs with enzymes of the human nucleotide metabolism. PLoS One 2012; 7:e37724. [PMID: 22662200 PMCID: PMC3360617 DOI: 10.1371/journal.pone.0037724] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [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: 02/23/2012] [Accepted: 04/23/2012] [Indexed: 11/24/2022] Open
Abstract
To identify interactions a nucleoside analog library (NAL) consisting of 45 FDA-approved nucleoside analogs was screened against 23 enzymes of the human nucleotide metabolism using a thermal shift assay. The method was validated with deoxycytidine kinase; eight interactions known from the literature were detected and five additional interactions were revealed after the addition of ATP, the second substrate. The NAL screening gave relatively few significant hits, supporting a low rate of “off target effects.” However, unexpected ligands were identified for two catabolic enzymes guanine deaminase (GDA) and uridine phosphorylase 1 (UPP1). An acyclic guanosine prodrug analog, valaciclovir, was shown to stabilize GDA to the same degree as the natural substrate, guanine, with a ΔTagg around 7°C. Aciclovir, penciclovir, ganciclovir, thioguanine and mercaptopurine were also identified as ligands for GDA. The crystal structure of GDA with valaciclovir bound in the active site was determined, revealing the binding of the long unbranched chain of valaciclovir in the active site of the enzyme. Several ligands were identified for UPP1: vidarabine, an antiviral nucleoside analog, as well as trifluridine, idoxuridine, floxuridine, zidovudine, telbivudine, fluorouracil and thioguanine caused concentration-dependent stabilization of UPP1. A kinetic study of UPP1 with vidarabine revealed that vidarabine was a mixed-type competitive inhibitor with the natural substrate uridine. The unexpected ligands identified for UPP1 and GDA imply further metabolic consequences for these nucleoside analogs, which could also serve as a starting point for future drug design.
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Affiliation(s)
- Louise Egeblad
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Flodin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Balzarini
- Rega Institute for Medical Research, Leuven, Belgium
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Pär Nordlund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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21
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Welin M, Egeblad L, Johansson A, Stenmark P, Wang L, Flodin S, Nyman T, Trésaugues L, Kotenyova T, Johansson I, Eriksson S, Eklund H, Nordlund P. Structural and functional studies of the human phosphoribosyltransferase domain containing protein 1. FEBS J 2010; 277:4920-30. [PMID: 21054786 DOI: 10.1111/j.1742-4658.2010.07897.x] [Citation(s) in RCA: 8] [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: 11/28/2022]
Abstract
Human hypoxanthine-guanine phosphoribosyltransferase (HPRT) (EC 2.4.2.8) catalyzes the conversion of hypoxanthine and guanine to their respective nucleoside monophosphates. Human HPRT deficiency as a result of genetic mutations is linked to both Lesch-Nyhan disease and gout. In the present study, we have characterized phosphoribosyltransferase domain containing protein 1 (PRTFDC1), a human HPRT homolog of unknown function. The PRTFDC1 structure has been determined at 1.7 Å resolution with bound GMP. The overall structure and GMP binding mode are very similar to that observed for HPRT. Using a thermal-melt assay, a nucleotide metabolome library was screened against PRTFDC1 and revealed that hypoxanthine and guanine specifically interacted with the enzyme. It was subsequently confirmed that PRTFDC1 could convert these two bases into their corresponding nucleoside monophosphate. However, the catalytic efficiency (k(cat)/K(m)) of PRTFDC1 towards hypoxanthine and guanine was only 0.26% and 0.09%, respectively, of that of HPRT. This low activity could be explained by the fact that PRTFDC1 has a Gly in the position of the proposed catalytic Asp of HPRT. In PRTFDC1, a water molecule at the position of the aspartic acid side chain position in HPRT might be responsible for the low activity observed by acting as a weak base. The data obtained in the present study indicate that PRTFDC1 does not have a direct catalytic role in the nucleotide salvage pathway.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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22
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Nyman T, Trésaugues L, Welin M, Lehtiö L, Flodin S, Persson C, Johansson I, Hammarström M, Nordlund P. The crystal structure of the Dachshund domain of human SnoN reveals flexibility in the putative protein interaction surface. PLoS One 2010; 5:e12907. [PMID: 20957027 PMCID: PMC2944819 DOI: 10.1371/journal.pone.0012907] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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: 05/19/2010] [Accepted: 08/30/2010] [Indexed: 11/18/2022] Open
Abstract
The human SnoN is an oncoprotein that interacts with several transcription-regulatory proteins such as the histone-deacetylase, N-CoR containing co-repressor complex and Smad proteins. This study presents the crystal structure of the Dachshund homology domain of human SnoN. The structure reveals a groove composed of conserved residues with characteristic properties of a protein-interaction surface. A comparison of the 12 monomers in the asymmetric unit reveals the presence of two major conformations: an open conformation with a well accessible groove and a tight conformation with a less accessible groove. The variability in the backbone between the open and the tight conformations matches the differences seen in previously determined structures of individual Dachshund homology domains, suggesting a general plasticity within this fold family. The flexibility observed in the putative protein binding groove may enable SnoN to recognize multiple interaction partners.
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Affiliation(s)
- Tomas Nyman
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (TN); (PN)
| | - Lionel Trésaugues
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Lari Lehtiö
- Pharmaceutical Sciences, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Susanne Flodin
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Persson
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Ida Johansson
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Martin Hammarström
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (TN); (PN)
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23
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Welin M, Grossmann JG, Flodin S, Nyman T, Stenmark P, Trésaugues L, Kotenyova T, Johansson I, Nordlund P, Lehtiö L. Structural studies of tri-functional human GART. Nucleic Acids Res 2010; 38:7308-19. [PMID: 20631005 PMCID: PMC2978367 DOI: 10.1093/nar/gkq595] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [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] [Indexed: 11/16/2022] Open
Abstract
Human purine de novo synthesis pathway contains several multi-functional enzymes, one of which, tri-functional GART, contains three enzymatic activities in a single polypeptide chain. We have solved structures of two domains bearing separate catalytic functions: glycinamide ribonucleotide synthetase and aminoimidazole ribonucleotide synthetase. Structures are compared with those of homologous enzymes from prokaryotes and analyzed in terms of the catalytic mechanism. We also report small angle X-ray scattering models for the full-length protein. These models are consistent with the enzyme forming a dimer through the middle domain. The protein has an approximate seesaw geometry where terminal enzyme units display high mobility owing to flexible linker segments. This resilient seesaw shape may facilitate internal substrate/product transfer or forwarding to other enzymes in the pathway.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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24
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Welin M, Nordlund P. Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism. Biochem Biophys Res Commun 2010; 396:157-63. [PMID: 20494131 DOI: 10.1016/j.bbrc.2010.04.054] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 04/08/2010] [Indexed: 10/19/2022]
Abstract
Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
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25
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Herman MD, Moche M, Flodin S, Welin M, Trésaugues L, Johansson I, Nilsson M, Nordlund P, Nyman T. Structures of BIR domains from human NAIP and cIAP2. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1091-6. [PMID: 19923725 DOI: 10.1107/s1744309109038597] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 09/23/2009] [Indexed: 11/11/2022]
Abstract
The inhibitor of apoptosis (IAP) family of proteins contains key modulators of apoptosis and inflammation that interact with caspases through baculovirus IAP-repeat (BIR) domains. Overexpression of IAP proteins frequently occurs in cancer cells, thus counteracting the activated apoptotic program. The IAP proteins have therefore emerged as promising targets for cancer therapy. In this work, X-ray crystallography was used to determine the first structures of BIR domains from human NAIP and cIAP2. Both structures harbour an N-terminal tetrapeptide in the conserved peptide-binding groove. The structures reveal that these two proteins bind the tetrapeptides in a similar mode as do other BIR domains. Detailed interactions are described for the P1'-P4' side chains of the peptide, providing a structural basis for peptide-specific recognition. An arginine side chain in the P3' position reveals favourable interactions with its hydrophobic moiety in the binding pocket, while hydrophobic residues in the P2' and P4' pockets make similar interactions to those seen in other BIR domain-peptide complexes. The structures also reveal how a serine in the P1' position is accommodated in the binding pockets of NAIP and cIAP2. In addition to shedding light on the specificity determinants of these two proteins, the structures should now also provide a framework for future structure-based work targeting these proteins.
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Affiliation(s)
- Maria Dolores Herman
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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26
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Trésaugues L, Stenmark P, Schüler H, Flodin S, Welin M, Nyman T, Hammarström M, Moche M, Gräslund S, Nordlund P. The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site. Proteins 2008; 73:1047-52. [PMID: 18767156 DOI: 10.1002/prot.22198] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lionel Trésaugues
- Department of Medical Biochemistry and Biophysics, Structural Genomics Consortium, Karolinska Institute, Stockholm, Sweden
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27
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Herman MD, Nyman T, Welin M, Lehtiö L, Flodin S, Trésaugues L, Kotenyova T, Flores A, Nordlund P. Completing the family portrait of the anti-apoptotic Bcl-2 proteins: crystal structure of human Bfl-1 in complex with Bim. FEBS Lett 2008; 582:3590-4. [PMID: 18812174 DOI: 10.1016/j.febslet.2008.09.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 08/20/2008] [Accepted: 09/02/2008] [Indexed: 11/16/2022]
Abstract
Evasion of apoptosis is recognized as a characteristic of malignant growth. Anti-apoptotic B-cell lymphoma-2 (Bcl-2) family members have therefore emerged as potential therapeutic targets due to their critical role in proliferating cancer cells. Here, we present the crystal structure of Bfl-1, the last anti-apoptotic Bcl-2 family member to be structurally characterized, in complex with a peptide corresponding to the BH3 region of the pro-apoptotic protein Bim. The structure reveals distinct features at the peptide-binding site, likely to define the binding specificity for pro-apoptotic proteins. Superposition of the Bfl-1:Bim complex with that of Mcl-1:Bim reveals a significant local plasticity of hydrophobic interactions contributed by the Bim peptide, likely to be the basis for the multi specificity of Bim for anti-apoptotic proteins.
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Affiliation(s)
- Maria Dolores Herman
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Pär Nordlund, 17177 Stockholm, Sweden
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28
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Egeblad-Welin L, Welin M, Wang L, Eriksson S. Structural and functional investigations of Ureaplasma parvum UMP kinase--a potential antibacterial drug target. FEBS J 2007; 274:6403-14. [PMID: 18021254 DOI: 10.1111/j.1742-4658.2007.06157.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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
The crystal structure of uridine monophosphate kinase (UMP kinase, UMPK) from the opportunistic pathogen Ureaplasma parvum was determined and showed similar three-dimensional fold as other bacterial and archaeal UMPKs that all belong to the amino acid kinase family. Recombinant UpUMPK exhibited Michaelis-Menten kinetics with UMP, with K(m) and V(max) values of 214 +/- 4 microm and 262 +/- 24 micromol.min(-1).mg(-1), respectively, but with ATP as variable substrate the kinetic analysis showed positive cooperativity, with an n value of 1.5 +/- 0.1. The end-product UTP was a competitive inhibitor against UMP and a noncompetitive inhibitor towards ATP. Unlike UMPKs from other bacteria, which are activated by GTP, GTP had no detectable effect on UpUMPK activity. An attempt to create a GTP-activated enzyme was made using site-directed mutagenesis. The mutant enzyme F133N (F133 corresponds to the residue in Escherichia coli that is involved in GTP activation), with F133A as a control, were expressed, purified and characterized. Both enzymes exhibited negative cooperativity with UMP, and GTP had no effect on enzyme activity, demonstrating that F133 is involved in subunit interactions but apparently not in GTP activation. The physiological role of UpUMPK in bacterial nucleic acid synthesis and its potential as target for development of antimicrobial agents are discussed.
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Affiliation(s)
- Louise Egeblad-Welin
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Sweden
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Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H. In situ proteolysis for protein crystallization and structure determination. Nat Methods 2007; 4:1019-21. [PMID: 17982461 DOI: 10.1038/nmeth1118] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 10/03/2007] [Indexed: 11/09/2022]
Abstract
We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.
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Affiliation(s)
- Aiping Dong
- Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada
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Welin M, Wang L, Eriksson S, Eklund H. Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity. J Mol Biol 2006; 366:1615-23. [PMID: 17229440 DOI: 10.1016/j.jmb.2006.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 11/29/2006] [Accepted: 12/05/2006] [Indexed: 11/26/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.
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Affiliation(s)
- Martin Welin
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S-751 24 Uppsala, Sweden
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Welin M, Skovgaard T, Knecht W, Zhu C, Berenstein D, Munch-Petersen B, Piskur J, Eklund H. Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D. FEBS J 2005; 272:3733-42. [PMID: 16008571 DOI: 10.1111/j.1742-4658.2005.04803.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 12/01/2022]
Abstract
The Drosophila melanogaster deoxyribonucleoside kinase (Dm-dNK) double mutant N45D/N64D was identified during a previous directed evolution study. This mutant enzyme had a decreased activity towards the natural substrates and decreased feedback inhibition with dTTP, whereas the activity with 3'-modified nucleoside analogs like 3'-azidothymidine (AZT) was nearly unchanged. Here, we identify the mutation N64D as being responsible for these changes. Furthermore, we crystallized the mutant enzyme in the presence of one of its substrates, thymidine, and the feedback inhibitor, dTTP. The introduction of the charged Asp residue appears to destabilize the LID region (residues 167-176) of the enzyme by electrostatic repulsion and no hydrogen bond to the 3'-OH is made in the substrate complex by Glu172 of the LID region. This provides a binding space for more bulky 3'-substituents like the azido group in AZT but influences negatively the interactions between Dm-dNK, substrates and feedback inhibitors based on deoxyribose. The detailed picture of the structure-function relationship provides an improved background for future development of novel mutant suicide genes for Dm-dNK-mediated gene therapy.
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Affiliation(s)
- Martin Welin
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Center, Uppsala, Sweden
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Welin M, Kosinska U, Mikkelsen NE, Carnrot C, Zhu C, Wang L, Eriksson S, Munch-Petersen B, Eklund H. Structures of thymidine kinase 1 of human and mycoplasmic origin. Proc Natl Acad Sci U S A 2004; 101:17970-5. [PMID: 15611477 PMCID: PMC539776 DOI: 10.1073/pnas.0406332102] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Indexed: 11/18/2022] Open
Abstract
Cytosolic thymidine kinase 1, TK1, is a well known cell-cycle-regulated enzyme of importance in nucleotide metabolism as well as an activator of antiviral and anticancer drugs such as 3'-azido-3'-deoxythymidine (AZT). We have now determined the structures of the TK1 family, the human and Ureaplasma urealyticum enzymes, in complex with the feedback inhibitor dTTP. The TK1s have a tetrameric structure in which each subunit contains an alpha/beta-domain that is similar to ATPase domains of members of the RecA structural family and a domain containing a structural zinc. The zinc ion connects beta-structures at the root of a beta-ribbon that forms a stem that widens to a lasso-type loop. The thymidine of dTTP is hydrogen-bonded to main-chain atoms predominantly coming from the lasso loop. This binding is in contrast to other deoxyribonucleoside kinases where specific interactions occur with side chains. The TK1 structure differs fundamentally from the structures of the other deoxyribonucleoside kinases, indicating a different evolutionary origin.
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Affiliation(s)
- Martin Welin
- Department of Molecular Biology, Swedish University of Agricultural Sciences, S-751 24 Uppsala, Sweden
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Pastoret PP, Sitrin R, Merten OW, Vincent Falquet JC, Schwanig M, Welin M, Hegger I, Neeleman R, van der Velden T, Urital A, Rene S, Behr-Gross ME, Smith M, McArdle J, Prior S, Schmidt C, Krell T, Chevalier M, Klein H, Rosskopf-Streicher U, Jaekel C. New vaccine production technologies and their impact on the use of animals. Dev Biol (Basel) 2003; 111:219-20. [PMID: 12678245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Abstract
BACKGROUND The bacterium Helicobacter pylori is associated with a number of gastrointestinal diseases, such as gastric ulcer, duodenal ulcer and gastric cancer. Several histological changes may be observed during the course of infection; some may influence the progression towards cancer. The aim of this study was to build a statistical model to discover direct interactions between H. pylori and different precancerous changes of the gastric mucosa, and in what order and to what degree those may influence the development of the intestinal type of gastric cancer. METHODS To find direct and indirect interactions between H. pylori and different histological variables, log-linear analyses were used on a case-control study. To generate mathematically and biologically relevant statistical models, a designed algorithm and observed frequency tables were used. RESULTS The results show that patients with H. pylori infection need to present with proliferation and intestinal metaplasia to develop gastric cancer of the intestinal type. Proliferation and intestinal metaplasia interacted with the variables atrophy and foveolar hyperplasia. Intestinal metaplasia was the only variable with direct interaction with gastric cancer. Gender had no effect on the variables examined. CONCLUSION The direct interactions observed in the final statistical model between H. pylori, changes of the mucosa and gastric cancer strengthens and supports previous theories about the progression towards gastric cancer. The results suggest that gastric cancer of the intestinal type may develop from H. pylori infection, proliferation and intestinal metaplasia, while atrophy and foveolar hyperplasia interplay with the other histological variables in the disease process.
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Affiliation(s)
- Martin Welin
- Department of Natural Science, University of Skövde, Sweden
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Abstract
This study reports an improved approach for the determination of neuropeptide levels in human cerebrospinal fluid (CSF). The method is based on sample acidification followed by liquid-liquid extraction (LLE) combined with radioimmunoassay. It was applied to study the recovery and level of some opioid peptides (Met-enkephalin-Arg(6)-Phe(7) and Leu-enkephalin-Arg(6)), substance P and the substance P(1-7) fragment, which are all compounds known to be present in human CSF. The results indicated that the use of LLE highly improved the recovery of these peptides compared to current liquid-solid-phase extraction methods by using silica gel cartridges or mini-columns for ion-exchange chromatography. Peptides added to CSF in concentrations down to 10 fmol/ml were recovered in yields exceeding 80%. The mean recovery of synthetic peptides as recorded by radioimmunoassay in the LLE procedure was significantly improved when HCl was added to the sample. In contrast, when the (125)I-labeled analogues of the peptides were added to CSF samples, the mean recovery of the four labeled peptides using the LLE procedure was markedly reduced in acidified samples. We also found that the inclusion of HCl effectively improved the removal of proteins present in the samples. As an application the levels of substance P and Met-enkephalin-Arg(6)-Phe(7) in CSF samples from patients with chronic pain (fibromyalgia syndrome) were measured using the new procedure. It was possible to confirm a significant difference in the CSF levels of both peptides when comparing patients and controls.
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Affiliation(s)
- Z Liu
- Department of Pharmaceutical Biosciences, Divison of Biological Research on Drug Dependence, Uppsala University, P.O. Box 591, S-751 24, Uppsala, Sweden
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Abstract
Cerebrospinal fluid (CSF) levels of calcitonin gene-related peptide-like activity (CGRP-LI), were determined in 35 patients with painful orthopaedic disorders and the activity was compared to that of 12 healthy controls without pain. Fourteen patients had pain from osteoarthritis of the hip or the knee, 11 had rhizopathic pain due to a herniated lumbar disc and 10 had pain from a hip fracture. In all patients, decreased CGRP-LI was observed in CSF compared to the controls. The lowest values were found in the patients with osteoarthritis, while there was less, but still significant, reduction of CGRP-LI in the patients with herniated lumbar disc and those with a hip fracture. In most of the patients, CGRP-LI was also analysed at a second lumbar puncture after operative treatment, when pain had subsided or was reduced. However, the CGRP-LI remained low after treatment, which may suggest the influence of factors other than pain.
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Affiliation(s)
- C Lindh
- Department of Orthopedics, University Hospital, Uppsala, Sweden
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Svensson BA, Welin M, Gordh T, Westman J. Chronic subarachnoid midazolam (Dormicum) in the rat. Morphologic evidence of spinal cord neurotoxicity. Reg Anesth 1995; 20:426-34. [PMID: 8519721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND AND OBJECTIVES In humans, the benzodiazepine midazolam has been reported to exert an antinociceptive action after subarachnoid injections. It has been shown that subarachnoid midazolam given to rabbits produces significant pathology in spinal cord morphology, as detected with light microscopy. In order to further characterize these changes, this study was performed, using a more sensitive histologic technique, including electron microscopy as well as unbiased morphometry. METHODS The histopathology of the rat lumbar spinal cord was investigated after chronic subarachnoid administration of a commercially available preparation of midazolam. After daily injections of 100 micrograms of midazolam, the animals were transcardially perfused on the twentieth day with a mixture of formaldehyde and glutaraldehyde. RESULTS Morphometric evaluation of cell number and mean cell volume (MCV) by the disector method revealed a significant lower (P < .05) cell number and a tendency toward higher MCV in the midazolam-injected group (n = 6), compared to the rats injected with saline (n = 6). The higher MCV, in combination with a reduced number of nerve cells, indicated a loss of small neurons. The electron microscopic findings confirmed that midazolam caused neuronal death, since degenerated cell somata, fibers, and terminals were observed in most of the rats. Furthermore, an increased number of microglial cells phagocytosing nerve structures were also seen mainly in the dorsal horn. CONCLUSIONS The authors found that chronic subarachnoid administration of midazolam gives objective signs of neurotoxicity in the rat spinal cord. The authors' findings are in contrast to those of an earlier light microscopic study in the rat. The present results emphasize both the necessity of morphometric and ultrastructural studies before spinal administration of novel drugs to humans and the neurotoxic potential of midazolam. Since neurotoxicity of midazolam now has been demonstrated in both rats and rabbits, there may be reason to be sceptical of the use of subarachnoid midazolam in humans.
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Affiliation(s)
- B A Svensson
- Department of Human Anatomy, Uppsala University, Sweden
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Abstract
The effect of morphine treatment on cholecystokinin (CCK) receptor binding in rat cerebral cortex was investigated. Subcutaneous implantation and removal of Alzet miniosmotic pumps, releasing morphine, permitted us to establish the phases of initial analgesia, tolerance to the analgesic action of morphine, morphine withdrawal and abstinence. CCK receptor binding in rat cerebral cortex never differed from the values obtained from animals implanted with saline-releasing minipumps. The results of the present study suggest that the putative changes in the interaction between opioidergic and CCKergic neurotransmission at different stages of morphine treatment and withdrawal are not caused by changes of CCK receptor binding properties.
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Affiliation(s)
- M Welin
- Department of Medical Pharmacology, Uppsala University, Sweden
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Welin M. [rDNA technique in production of drugs. How endogenous are human proteins prepared with rDNA?]. Lakartidningen 1994; 91:1188-1191. [PMID: 8189847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- M Welin
- Bioteknologiska enheten, Läkemedelsverket, Uppsala
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Rutanen EM, Kärkkäinen T, Lundqvist C, Pekonen F, Ritvos O, Tanner P, Welin M, Weber T. Monoclonal antibodies to the 27-34K insulin-like growth factor binding protein. Biochem Biophys Res Commun 1988; 152:208-15. [PMID: 2451912 DOI: 10.1016/s0006-291x(88)80701-0] [Citation(s) in RCA: 33] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Monoclonal antibodies were prepared against the 27-34K insulin-like growth factor (IGF)-binding protein purified from human placenta/decidua and designated placental protein 12 (PP12). Four different antibodies were characterized. Each recognized the major band at 32K on immunoblots of the purified PP12 preparation and amniotic fluid. In liquid phase RIA, IGF-I did not affect the binding of [125I] PP12 to one antibody (Mab 6303), it slightly increased the binding to two antibodies (Mab 6301 and 6304), and it slightly decreased the binding to one antibody (Mab 6302). All antibodies immunoprecipitated the cross-linked PP12-[125I] IGF-I complex, but Mab 6302 considerably less effectively than the others. Preincubation of PP12 with Mab 6302 completely inhibited the binding of [125I] IGF-I to PP12, whereas preincubation with Mab 6303 had no effect, and Mab 6301 as well as Mab 6304 increased it. These results suggest that Mab 6302 binds to an epitope at or near to the IGF-binding site, whereas the other antibodies react at other sites of the PP12 molecule. Conformational changes in PP12 probably account for the IGF-I-induced increase in the binding of Mabs 6301 and 6304 to [125I] PP12, and vice versa, for Mabs 6301- and 6304-induced increase in the binding of [125I] IGF-I to PP12.
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