1
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Abdelrazak Morsy MH, Lilienthal I, Lord M, Merrien M, Wasik AM, Sureda-Gómez M, Amador V, Johansson HJ, Lehtiö J, Garcia-Torre B, Martin-Subero JI, Tsesmetzis N, Tao S, Schinazi RF, Kim B, Sorteberg AL, Wickström M, Sheppard D, Rassidakis GZ, Taylor IA, Christensson B, Campo E, Herold N, Sander B. SOX11 is a novel binding partner and endogenous inhibitor of SAMHD1 ara-CTPase activity in mantle cell lymphoma. Blood 2024; 143:1953-1964. [PMID: 38237141 PMCID: PMC11103171 DOI: 10.1182/blood.2023022241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
ABSTRACT Sterile alpha motif and histidine-aspartate (HD) domain-containing protein 1 (SAMHD1) is a deoxynucleoside triphosphate triphosphohydrolase with ara-CTPase activity that confers cytarabine (ara-C) resistance in several hematological malignancies. Targeting SAMHD1's ara-CTPase activity has recently been demonstrated to enhance ara-C efficacy in acute myeloid leukemia. Here, we identify the transcription factor SRY-related HMG-box containing protein 11 (SOX11) as a novel direct binding partner and first known endogenous inhibitor of SAMHD1. SOX11 is aberrantly expressed not only in mantle cell lymphoma (MCL), but also in some Burkitt lymphomas. Coimmunoprecipitation of SOX11 followed by mass spectrometry in MCL cell lines identified SAMHD1 as the top SOX11 interaction partner, which was validated by proximity ligation assay. In vitro, SAMHD1 bound to the HMG box of SOX11 with low-micromolar affinity. In situ crosslinking studies further indicated that SOX11-SAMHD1 binding resulted in a reduced tetramerization of SAMHD1. Functionally, expression of SOX11 inhibited SAMHD1 ara-CTPase activity in a dose-dependent manner resulting in ara-C sensitization in cell lines and in a SOX11-inducible mouse model of MCL. In SOX11-negative MCL, SOX11-mediated ara-CTPase inhibition could be mimicked by adding the recently identified SAMHD1 inhibitor hydroxyurea. Taken together, our results identify SOX11 as a novel SAMHD1 interaction partner and its first known endogenous inhibitor with potentially important implications for clinical therapy stratification.
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Affiliation(s)
- Mohammad Hamdy Abdelrazak Morsy
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Applied Medical Chemistry, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ingrid Lilienthal
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Martin Lord
- Department of Pharmaceutical Biosciences, Immuno-oncology, Uppsala University Biomedical Centre, Uppsala, Sweden
| | - Magali Merrien
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Agata Magdalena Wasik
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Marta Sureda-Gómez
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
| | - Virginia Amador
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | | | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Raymond F. Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Agnes L. Sorteberg
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Georgios Z. Rassidakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Birger Christensson
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clinic Barcelona, University of Barcelona, Barcelona, Spain
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
- Paediatric Oncology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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2
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Zhang SM, Paulin CB, Shu H, Yagüe-Capilla M, Michel M, Marttila P, Ortis F, Bwanika HC, Dirks C, Venkatram RP, Wiita E, Jemth AS, Almlöf I, Loseva O, Hormann FM, Koolmeister T, Linde E, Lee S, Llona-Minguez S, Haraldsson M, Axelsson H, Strömberg K, Homan EJ, Scobie M, Lundbäck T, Helleday T, Rudd SG. Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel. iScience 2024; 27:108907. [PMID: 38318365 PMCID: PMC10839966 DOI: 10.1016/j.isci.2024.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 09/05/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase governing nucleotide pool homeostasis and can detoxify chemotherapy metabolites controlling their clinical responses. To understand SAMHD1 biology and investigate the potential of targeting SAMHD1 as neoadjuvant to current chemotherapies, we set out to discover selective small-molecule inhibitors. Here, we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for rigorous characterization of the screen output. The identified small molecules, TH6342 and analogs, accompanied by inactive control TH7126, demonstrated specific, low μM potency against both physiological and oncology-drug-derived substrates. By coupling kinetic studies with thermal shift assays, we reveal the inhibitory mechanism of TH6342 and analogs, which engage pre-tetrameric SAMHD1 and deter oligomerization and allosteric activation without occupying nucleotide-binding pockets. Altogether, our study diversifies inhibitory modes against SAMHD1, and the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development.
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Affiliation(s)
- Si Min Zhang
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Cynthia B.J. Paulin
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Huazhang Shu
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Miriam Yagüe-Capilla
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Florian Ortis
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Henri Colyn Bwanika
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Christopher Dirks
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Rajagopal Papagudi Venkatram
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Femke M. Hormann
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Erika Linde
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sun Lee
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Kia Strömberg
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Evert J. Homan
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Sean G. Rudd
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
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3
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Morsy MHA, Lilienthal I, Lord M, Merrien M, Wasik AM, Sureda-Gómez M, Amador V, Johansson HJ, Lehtiö J, Garcia-Torre B, Martin-Subero JI, Tsesmetzis N, Tao S, Schinazi RF, Kim B, Sorteberg AL, Wickström M, Sheppard D, Rassidakis GZ, Taylor IA, Christensson B, Campo E, Herold N, Sander B. SOX11 is a novel binding partner and endogenous inhibitor of SAMHD1 ara-CTPase activity in mantle cell lymphoma. Blood 2024; 143:1953-1964. [PMID: 38774451 PMCID: PMC7615944 DOI: 10.1182/blood.2023022241/2210808/blood.2023022241.pdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024] Open
Abstract
The sterile alpha motif and histidine-aspartate (HD) domain containing protein 1 (SAMHD1) is a deoxynucleoside triphosphate triphosphohydrolase with ara-CTPase activity that confers cytarabine (ara-C) resistance in several haematological malignancies. Targeting SAMHD1's ara-CTPase activity has recently been demonstrated to enhance ara-C efficacy in acute myeloid leukemia. Here, we identify the transcription factor SRY-related HMG-box containing protein 11 (SOX11) as a novel direct binding partner and first known endogenous inhibitor of SAMHD1. SOX11 is aberrantly expressed not only in mantle cell lymphoma (MCL), but also in some Burkitt lymphomas. Co-immunoprecipitation of SOX11 followed by mass spectrometry in MCL cell lines identified SAMHD1 as the top SOX11 interaction partner which was validated by proximity ligation assay. In vitro, SAMHD1 bound to the HMG box of SOX11 with low-micromolar affinity. In situ crosslinking studies further indicated that SOX11-SAMHD1 binding resulted in a reduced tetramerization of SAMHD1. Functionally, expression of SOX11 inhibited SAMHD1 ara-CTPase activity in a dose-dependent manner resulting in ara-C sensitization in cell lines and in a SOX11-inducible mouse model of MCL. In SOX11-negative MCL, SOX11-mediated ara-CTPase inhibition could be mimicked by adding the recently identified SAMHD1 inhibitor hydroxyurea. Taken together, our results identify SOX11 as a novel SAMHD1 interaction partner and its first known endogenous inhibitor with potentially important implications for clinical therapy stratification.
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Affiliation(s)
- Mohammad Hamdy Abdelrazak Morsy
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
- Department of Applied Medical Chemistry, Medical Research Institute, Alexandria University, 21561, Alexandria, Egypt
| | - Ingrid Lilienthal
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Martin Lord
- Department of Pharmaceutical Biosciences, Immuno-oncology, Uppsala University Biomedical Centre (BMC), SE-751 24, Uppsala, Sweden
| | - Magali Merrien
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| | - Agata Magdalena Wasik
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| | - Marta Sureda-Gómez
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Virginia Amador
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, USA
| | - Agnes L Sorteberg
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Georgios Z Rassidakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Birger Christensson
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clinic Barcelona, University of Barcelona, Barcelona, Spain
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women’s, and Children’s Health, Karolinska Institutet, Solna, Sweden
- Paediatric Oncology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, SE14186, Stockholm, Sweden
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4
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Tsai MHC, Caswell SJ, Morris ER, Mann MC, Pennell S, Kelly G, Groom HCT, Taylor IA, Bishop KN. Attenuation of reverse transcriptase facilitates SAMHD1 restriction of HIV-1 in cycling cells. Retrovirology 2023; 20:5. [PMID: 37127613 PMCID: PMC10150492 DOI: 10.1186/s12977-023-00620-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND SAMHD1 is a deoxynucleotide triphosphohydrolase that restricts replication of HIV-1 in differentiated leucocytes. HIV-1 is not restricted in cycling cells and it has been proposed that this is due to phosphorylation of SAMHD1 at T592 in these cells inactivating the enzymatic activity. To distinguish between theories for how SAMHD1 restricts HIV-1 in differentiated but not cycling cells, we analysed the effects of substitutions at T592 on restriction and dNTP levels in both cycling and differentiated cells as well as tetramer stability and enzymatic activity in vitro. RESULTS We first showed that HIV-1 restriction was not due to SAMHD1 nuclease activity. We then characterised a panel of SAMHD1 T592 mutants and divided them into three classes. We found that a subset of mutants lost their ability to restrict HIV-1 in differentiated cells which generally corresponded with a decrease in triphosphohydrolase activity and/or tetramer stability in vitro. Interestingly, no T592 mutants were able to restrict WT HIV-1 in cycling cells, despite not being regulated by phosphorylation and retaining their ability to hydrolyse dNTPs. Lowering dNTP levels by addition of hydroxyurea did not give rise to restriction. Compellingly however, HIV-1 RT mutants with reduced affinity for dNTPs were significantly restricted by wild-type and T592 mutant SAMHD1 in both cycling U937 cells and Jurkat T-cells. Restriction correlated with reverse transcription levels. CONCLUSIONS Altogether, we found that the amino acid at residue 592 has a strong effect on tetramer formation and, although this is not a simple "on/off" switch, this does correlate with the ability of SAMHD1 to restrict HIV-1 replication in differentiated cells. However, preventing phosphorylation of SAMHD1 and/or lowering dNTP levels by adding hydroxyurea was not enough to restore restriction in cycling cells. Nonetheless, lowering the affinity of HIV-1 RT for dNTPs, showed that restriction is mediated by dNTP levels and we were able to observe for the first time that SAMHD1 is active and capable of inhibiting HIV-1 replication in cycling cells, if the affinity of RT for dNTPs is reduced. This suggests that the very high affinity of HIV-1 RT for dNTPs prevents HIV-1 restriction by SAMHD1 in cycling cells.
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Affiliation(s)
- Ming-Han C Tsai
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK
- LabGenius, London, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
- AstraZeneca, Granta Park, Cambridge, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
- Department of Biosciences, University of Durham, Durham, UK
| | - Melanie C Mann
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK
- Sartorius, Ulm, Germany
| | - Simon Pennell
- Structural Biology of DNA-Damage Signalling Laboratory, The Francis Crick Institute, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, London, UK
| | - Harriet C T Groom
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Kate N Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK.
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5
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Helleday T, Rudd SG. Targeting the DNA damage response and repair in cancer through nucleotide metabolism. Mol Oncol 2022; 16:3792-3810. [PMID: 35583750 PMCID: PMC9627788 DOI: 10.1002/1878-0261.13227] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
The exploitation of the DNA damage response and DNA repair proficiency of cancer cells is an important anticancer strategy. The replication and repair of DNA are dependent upon the supply of deoxynucleoside triphosphate (dNTP) building blocks, which are produced and maintained by nucleotide metabolic pathways. Enzymes within these pathways can be promising targets to selectively induce toxic DNA lesions in cancer cells. These same pathways also activate antimetabolites, an important group of chemotherapies that disrupt both nucleotide and DNA metabolism to induce DNA damage in cancer cells. Thus, dNTP metabolic enzymes can also be targeted to refine the use of these chemotherapeutics, many of which remain standard of care in common cancers. In this review article, we will discuss both these approaches exemplified by the enzymes MTH1, MTHFD2 and SAMHD1. © 2022 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
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Affiliation(s)
- Thomas Helleday
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetStockholmSweden,Department of Oncology and Metabolism, Weston Park Cancer CentreUniversity of SheffieldUK
| | - Sean G. Rudd
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetStockholmSweden
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6
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Orris B, Huynh KW, Ammirati M, Han S, Bolaños B, Carmody J, Petroski MD, Bosbach B, Shields DJ, Stivers JT. Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics. Nucleic Acids Res 2022; 50:7545-7559. [PMID: 35801923 PMCID: PMC9303311 DOI: 10.1093/nar/gkac573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/24/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023] Open
Abstract
SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) is driven into its activated tetramer form by binding of GTP activator and dNTP activators/substrates. In addition, the inactive monomeric and dimeric forms of the enzyme bind to single-stranded (ss) nucleic acids. During DNA replication SAMHD1 can be phosphorylated by CDK1 and CDK2 at its C-terminal threonine 592 (pSAMHD1), localizing the enzyme to stalled replication forks (RFs) to promote their restart. Although phosphorylation has only a small effect on the dNTPase activity and ssDNA binding affinity of SAMHD1, perturbation of the native T592 by phosphorylation decreased the thermal stability of tetrameric SAMHD1 and accelerated tetramer dissociation in the absence and presence of ssDNA (∼15-fold). In addition, we found that ssDNA binds competitively with GTP to the A1 site. A full-length SAMHD1 cryo-EM structure revealed substantial dynamics in the C-terminal domain (which contains T592), which could be modulated by phosphorylation. We propose that T592 phosphorylation increases tetramer dynamics and allows invasion of ssDNA into the A1 site and the previously characterized DNA binding surface at the dimer-dimer interface. These features are consistent with rapid and regiospecific inactivation of pSAMHD1 dNTPase at RFs or other sites of free ssDNA in cells.
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Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | | | | | - Seungil Han
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Ben Bolaños
- Oncology Research and Development, Pfizer, San Diego, CA 92121, USA
| | - Jason Carmody
- Oncology Research and Development, Pfizer, San Diego, CA 92121, USA
| | | | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, NY, NY 10016, USA
| | - David J Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, NY, NY 10016, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
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7
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Oleksy B, Mierzewska H, Tryfon J, Wypchło M, Wasilewska K, Zalewska-Miszkurka Z, Płoski R, Rydzanicz M, Szczepanik E. Aicardi-Goutières Syndrome due to a SAMHD1 Mutation Presenting with Deep White Matter Cysts. Mol Syndromol 2021; 13:132-138. [DOI: 10.1159/000518941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/07/2021] [Indexed: 11/19/2022] Open
Abstract
We report on the first Polish patient diagnosed with the Aicardi-Goutières syndrome 5 (AGS5). AGS is caused by mutations in one of 9 genes (<i>TREX1</i>, <i>RNASEH2A</i>, <i>RNASEH2B</i>, <i>RNASEH2C</i>, <i>SAMHD1</i>, <i>ADAR</i>, <i>IFIH</i>, <i>LSM11</i>, <i>RNU7-1</i>) which stimulate the type I interferon response. The diagnosis was confirmed by identifying a compound heterozygous mutation p.(Phe165Ser)/p.(Gln235*) in the <i>SAMHD1</i> gene using whole-exome sequencing. The cystic lesions in the temporal lobes are an uncommon finding in the presented patient carrying a <i>SAMHD1</i> mutation. Reporting new cases expands the range of phenotypes and plays the crucial role in understanding the AGS pathogenesis and creates new therapy approaches.
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8
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Banchenko S, Krupp F, Gotthold C, Bürger J, Graziadei A, O’Reilly FJ, Sinn L, Ruda O, Rappsilber J, Spahn CMT, Mielke T, Taylor IA, Schwefel D. Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses. PLoS Pathog 2021; 17:e1009775. [PMID: 34339457 PMCID: PMC8360603 DOI: 10.1371/journal.ppat.1009775] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/12/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
Viruses have evolved means to manipulate the host's ubiquitin-proteasome system, in order to down-regulate antiviral host factors. The Vpx/Vpr family of lentiviral accessory proteins usurp the substrate receptor DCAF1 of host Cullin4-RING ligases (CRL4), a family of modular ubiquitin ligases involved in DNA replication, DNA repair and cell cycle regulation. CRL4DCAF1 specificity modulation by Vpx and Vpr from certain simian immunodeficiency viruses (SIV) leads to recruitment, poly-ubiquitylation and subsequent proteasomal degradation of the host restriction factor SAMHD1, resulting in enhanced virus replication in differentiated cells. To unravel the mechanism of SIV Vpr-induced SAMHD1 ubiquitylation, we conducted integrative biochemical and structural analyses of the Vpr protein from SIVs infecting Cercopithecus cephus (SIVmus). X-ray crystallography reveals commonalities between SIVmus Vpr and other members of the Vpx/Vpr family with regard to DCAF1 interaction, while cryo-electron microscopy and cross-linking mass spectrometry highlight a divergent molecular mechanism of SAMHD1 recruitment. In addition, these studies demonstrate how SIVmus Vpr exploits the dynamic architecture of the multi-subunit CRL4DCAF1 assembly to optimise SAMHD1 ubiquitylation. Together, the present work provides detailed molecular insight into variability and species-specificity of the evolutionary arms race between host SAMHD1 restriction and lentiviral counteraction through Vpx/Vpr proteins.
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Affiliation(s)
- Sofia Banchenko
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Ferdinand Krupp
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Christine Gotthold
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Francis J. O’Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ludwig Sinn
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Olga Ruda
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Christian M. T. Spahn
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David Schwefel
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
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9
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Morris ER, Kunzelmann S, Caswell SJ, Purkiss AG, Kelly G, Taylor IA. Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p- and S p-dNTPαS Diastereomers. Biochemistry 2021; 60:1682-1698. [PMID: 33988981 PMCID: PMC8173608 DOI: 10.1021/acs.biochem.0c00944] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in CD4+ myeloid lineage and resting T-cells. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome (AGS) and certain cancers. More recently, SAMHD1 has been linked to anticancer drug resistance and the suppression of the interferon response to cytosolic nucleic acids after DNA damage. Here, we probe dNTP hydrolysis and inhibition of SAMHD1 using the Rp and Sp diastereomers of dNTPαS nucleotides. Our biochemical and enzymological data show that the α-phosphorothioate substitution in Sp-dNTPαS but not Rp-dNTPαS diastereomers prevents Mg2+ ion coordination at both the allosteric and catalytic sites, rendering SAMHD1 unable to form stable, catalytically active homotetramers or hydrolyze substrate dNTPs at the catalytic site. Furthermore, we find that Sp-dNTPαS diastereomers competitively inhibit dNTP hydrolysis, while Rp-dNTPαS nucleotides stabilize tetramerization and are hydrolyzed with similar kinetic parameters to cognate dNTPs. For the first time, we present a cocrystal structure of SAMHD1 with a substrate, Rp-dGTPαS, in which an Fe-Mg-bridging water species is poised for nucleophilic attack on the Pα. We conclude that it is the incompatibility of Mg2+, a hard Lewis acid, and the α-phosphorothioate thiol, a soft Lewis base, that prevents the Sp-dNTPαS nucleotides coordinating in a catalytically productive conformation. On the basis of these data, we present a model for SAMHD1 stereospecific hydrolysis of Rp-dNTPαS nucleotides and for a mode of competitive inhibition by Sp-dNTPαS nucleotides that competes with formation of the enzyme-substrate complex.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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10
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De Meo S, Dell'Oste V, Molfetta R, Tassinari V, Lotti LV, Vespa S, Pignoloni B, Covino DA, Fantuzzi L, Bona R, Zingoni A, Nardone I, Biolatti M, Coscia A, Paolini R, Benkirane M, Edfors F, Sandalova T, Achour A, Hiscott J, Landolfo S, Santoni A, Cerboni C. SAMHD1 phosphorylation and cytoplasmic relocalization after human cytomegalovirus infection limits its antiviral activity. PLoS Pathog 2020; 16:e1008855. [PMID: 32986788 PMCID: PMC7544099 DOI: 10.1371/journal.ppat.1008855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 10/08/2020] [Accepted: 08/03/2020] [Indexed: 12/16/2022] Open
Abstract
SAMHD1 is a host restriction factor that functions to restrict both retroviruses and DNA viruses, based on its nuclear deoxynucleotide triphosphate (dNTP) hydrolase activity that limits availability of intracellular dNTP pools. In the present study, we demonstrate that SAMHD1 expression was increased following human cytomegalovirus (HCMV) infection, with only a modest effect on infectious virus production. SAMHD1 was rapidly phosphorylated at residue T592 after infection by cellular cyclin-dependent kinases, especially Cdk2, and by the viral kinase pUL97, resulting in a significant fraction of phosho-SAMHD1 being relocalized to the cytoplasm of infected fibroblasts, in association with viral particles and dense bodies. Thus, our findings indicate that HCMV-dependent SAMHD1 cytoplasmic delocalization and inactivation may represent a potential novel mechanism of HCMV evasion from host antiviral restriction activities.
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Affiliation(s)
- Simone De Meo
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Rosa Molfetta
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Tassinari
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Simone Vespa
- Laboratory of General Pathology, Center of Aging Science and Translational Medicine (CeSI-MeT) and Department of Medical, Oral and Biotechnological Sciences G. d'Annunzio University, Chieti, Italy
| | - Benedetta Pignoloni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Laura Fantuzzi
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta Bona
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Zingoni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Ilaria Nardone
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Alessandra Coscia
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Rossella Paolini
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Monsef Benkirane
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, CNRS-Université de Montpellier, Montpellier, France
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - John Hiscott
- Istituto Pasteur Italia-Cenci Bolognetti Foundation, Rome, Italy
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Angela Santoni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
- IRCCS, Neuromed, Pozzilli, Isernia, Italy
| | - Cristina Cerboni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
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11
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Morris ER, Caswell SJ, Kunzelmann S, Arnold LH, Purkiss AG, Kelly G, Taylor IA. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nat Commun 2020; 11:3165. [PMID: 32576829 PMCID: PMC7311409 DOI: 10.1038/s41467-020-16983-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,AstraZeneca, 50F49, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Laurence H Arnold
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Pelago Bioscience, Banvaktsvägen 20, 171 48, Solna, Sweden
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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