1
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Swift LP, Lagerholm BC, Henderson LR, Ratnaweera M, Baddock HT, Sengerova B, Lee S, Cruz-Migoni A, Waithe D, Renz C, Ulrich HD, Newman JA, Schofield CJ, McHugh PJ. SNM1A is crucial for efficient repair of complex DNA breaks in human cells. Nat Commun 2024; 15:5392. [PMID: 38918391 PMCID: PMC11199599 DOI: 10.1038/s41467-024-49583-5] [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: 07/18/2023] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
DNA double-strand breaks (DSBs), such as those produced by radiation and radiomimetics, are amongst the most toxic forms of cellular damage, in part because they involve extensive oxidative modifications at the break termini. Prior to completion of DSB repair, the chemically modified termini must be removed. Various DNA processing enzymes have been implicated in the processing of these dirty ends, but molecular knowledge of this process is limited. Here, we demonstrate a role for the metallo-β-lactamase fold 5'-3' exonuclease SNM1A in this vital process. Cells disrupted for SNM1A manifest increased sensitivity to radiation and radiomimetic agents and show defects in DSB damage repair. SNM1A is recruited and is retained at the sites of DSB damage via the concerted action of its three highly conserved PBZ, PIP box and UBZ interaction domains, which mediate interactions with poly-ADP-ribose chains, PCNA and the ubiquitinated form of PCNA, respectively. SNM1A can resect DNA containing oxidative lesions induced by radiation damage at break termini. The combined results reveal a crucial role for SNM1A to digest chemically modified DNA during the repair of DSBs and imply that the catalytic domain of SNM1A is an attractive target for potentiation of radiotherapy.
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Affiliation(s)
- Lonnie P Swift
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Cell Imaging and Cytometry Core, Turku Bioscience Centre, University of Turku and Åbo Akademi, ku, Finland
| | - Lucy R Henderson
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Malitha Ratnaweera
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hannah T Baddock
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Calico Life Sciences, South San Francisco, CA, USA
| | - Blanka Sengerova
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sook Lee
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Abimael Cruz-Migoni
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dominic Waithe
- Wolfson Imaging Centre, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Christian Renz
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Peter J McHugh
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom.
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2
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Bielinski M, Henderson LR, Yosaatmadja Y, Swift LP, Baddock HT, Bowen MJ, Brem J, Jones PS, McElroy SP, Morrison A, Speake M, van Boeckel S, van Doornmalen E, van Groningen J, van den Hurk H, Gileadi O, Newman JA, McHugh PJ, Schofield CJ. Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target. Chem Sci 2024; 15:8227-8241. [PMID: 38817593 PMCID: PMC11134331 DOI: 10.1039/d4sc00367e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/30/2024] [Indexed: 06/01/2024] Open
Abstract
The three human SNM1 metallo-β-lactamase fold nucleases (SNM1A-C) play key roles in DNA damage repair and in maintaining telomere integrity. Genetic studies indicate that they are attractive targets for cancer treatment and to potentiate chemo- and radiation-therapy. A high-throughput screen for SNM1A inhibitors identified diverse pharmacophores, some of which were shown by crystallography to coordinate to the di-metal ion centre at the SNM1A active site. Structure and turnover assay-guided optimization enabled the identification of potent quinazoline-hydroxamic acid containing inhibitors, which bind in a manner where the hydroxamic acid displaces the hydrolytic water and the quinazoline ring occupies a substrate nucleobase binding site. Cellular assays reveal that SNM1A inhibitors cause sensitisation to, and defects in the resolution of, cisplatin-induced DNA damage, validating the tractability of MBL fold nucleases as cancer drug targets.
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Affiliation(s)
- Marcin Bielinski
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Lucy R Henderson
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Yuliana Yosaatmadja
- Centre for Medicines Discovery, NDM Research Building, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Lonnie P Swift
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Matthew J Bowen
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Philip S Jones
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | - Stuart P McElroy
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | - Angus Morrison
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | - Michael Speake
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | | | | | | | | | - Opher Gileadi
- Centre for Medicines Discovery, NDM Research Building, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Joseph A Newman
- Centre for Medicines Discovery, NDM Research Building, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
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3
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Sonmez C, Toia B, Eickhoff P, Matei AM, El Beyrouthy M, Wallner B, Douglas ME, de Lange T, Lottersberger F. DNA-PK controls Apollo's access to leading-end telomeres. Nucleic Acids Res 2024; 52:4313-4327. [PMID: 38407308 PMCID: PMC11077071 DOI: 10.1093/nar/gkae105] [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: 05/19/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
The complex formed by Ku70/80 and DNA-PKcs (DNA-PK) promotes the synapsis and the joining of double strand breaks (DSBs) during canonical non-homologous end joining (c-NHEJ). In c-NHEJ during V(D)J recombination, DNA-PK promotes the processing of the ends and the opening of the DNA hairpins by recruiting and/or activating the nuclease Artemis/DCLRE1C/SNM1C. Paradoxically, DNA-PK is also required to prevent the fusions of newly replicated leading-end telomeres. Here, we describe the role for DNA-PK in controlling Apollo/DCLRE1B/SNM1B, the nuclease that resects leading-end telomeres. We show that the telomeric function of Apollo requires DNA-PKcs's kinase activity and the binding of Apollo to DNA-PK. Furthermore, AlphaFold-Multimer predicts that Apollo's nuclease domain has extensive additional interactions with DNA-PKcs, and comparison to the cryo-EM structure of Artemis bound to DNA-PK phosphorylated on the ABCDE/Thr2609 cluster suggests that DNA-PK can similarly grant Apollo access to the DNA end. In agreement, the telomeric function of DNA-PK requires the ABCDE/Thr2609 cluster. These data reveal that resection of leading-end telomeres is regulated by DNA-PK through its binding to Apollo and its (auto)phosphorylation-dependent positioning of Apollo at the DNA end, analogous but not identical to DNA-PK dependent regulation of Artemis at hairpins.
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Affiliation(s)
- Ceylan Sonmez
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58 183, Sweden
| | - Beatrice Toia
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58 183, Sweden
| | - Patrik Eickhoff
- Chester Beatty Laboratories, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Andreea Medeea Matei
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58 183, Sweden
| | - Michael El Beyrouthy
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58 183, Sweden
| | - Björn Wallner
- Department of Physics, Chemistry and Biology, Linköping University, Linköping 58 183, Sweden
| | - Max E Douglas
- Chester Beatty Laboratories, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, NY, NY 10021, USA
| | - Francisca Lottersberger
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58 183, Sweden
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4
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Ratto A, Honek JF. Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry. Curr Med Chem 2024; 31:1172-1213. [PMID: 36915986 DOI: 10.2174/0929867330666230313141452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/15/2023]
Abstract
The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.
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Affiliation(s)
- Amanda Ratto
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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5
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El-Khoury R, Roman M, Assi HA, Moye AL, Bryan T, Damha M. Telomeric i-motifs and C-strands inhibit parallel G-quadruplex extension by telomerase. Nucleic Acids Res 2023; 51:10395-10410. [PMID: 37742080 PMCID: PMC10602923 DOI: 10.1093/nar/gkad764] [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: 05/29/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/25/2023] Open
Abstract
Telomeric C-rich repeated DNA sequences fold into tetrahelical i-motif structures in vitro at acidic pH. While studies have suggested that i-motifs may form in cells, little is known about their potential role in human telomere biology. In this study, we explore the effect of telomeric C-strands and i-motifs on the ability of human telomerase to extend G-rich substrates. To promote i-motif formation at neutral pH, we use telomeric sequences where the cytidines have been substituted with 2'-fluoroarabinocytidine. Using FRET-based studies, we show that the stabilized i-motifs resist hybridization to concomitant parallel G-quadruplexes, implying that both structures could exist simultaneously at telomeric termini. Moreover, through telomerase activity assays, we show that both unstructured telomeric C-strands and telomeric i-motifs can inhibit the activity and processivity of telomerase extension of parallel G-quadruplexes and linear telomeric DNA. The data suggest at least three modes of inhibition by C-strands and i-motifs: direct hybridization to the substrate DNA, hybridization to nascent product DNA resulting in early telomerase dissociation, and interference with the unique mechanism of telomerase unwinding and extension of a G-quadruplex. Overall, this study highlights a potential inhibitory role for the telomeric C-strand in telomere maintenance.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Morgane Roman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Aaron L Moye
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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6
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Arbour CA, Fay EM, McGouran JF, Imperiali B. Deploying solid-phase synthesis to access thymine-containing nucleoside analogs that inhibit DNA repair nuclease SNM1A. Org Biomol Chem 2023; 21:5873-5879. [PMID: 37417819 PMCID: PMC10529636 DOI: 10.1039/d3ob00836c] [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] [Indexed: 07/08/2023]
Abstract
Nucleoside analogs show useful bioactive properties. A versatile solid-phase synthesis that readily enables the diversification of thymine-containing nucleoside analogs is presented. The utility of the approach is demonstrated with the preparation of a library of compounds for analysis with SNM1A, a DNA damage repair enzyme that contributes to cytotoxicity. This exploration provided the most promising nucleoside-derived inhibitor of SNM1A to date with an IC50 of 12.3 μM.
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Affiliation(s)
- Christine A Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ellen M Fay
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin 2, Ireland
| | - Joanna F McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin 2, Ireland
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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7
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Fay EM, Newton A, Berney M, El‐Sagheer AH, Brown T, McGouran JF. Two-Step Validation Approach for Tools To Study the DNA Repair Enzyme SNM1A. Chembiochem 2023; 24:e202200756. [PMID: 36917742 PMCID: PMC10962688 DOI: 10.1002/cbic.202200756] [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: 12/16/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
We report a two-step validation approach to evaluate the suitability of metal-binding groups for targeting DNA damage-repair metalloenzymes using model enzyme SNM1A. A fragment-based screening approach was first used to identify metal-binding fragments suitable for targeting the enzyme. Effective fragments were then incorporated into oligonucleotides using the copper-catalysed azide-alkyne cycloaddition reaction. These modified oligonucleotides were recognised by SNM1A at >1000-fold lower concentrations than their fragment counterparts. The exonuclease SNM1A is a key enzyme involved in the repair of interstrand crosslinks, a highly cytotoxic form of DNA damage. However, SNM1A and other enzymes of this class are poorly understood, as there is a lack of tools available to facilitate their study. Our novel approach of incorporating functional fragments into oligonucleotides is broadly applicable to generating modified oligonucleotide structures with high affinity for DNA damage-repair enzymes.
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Affiliation(s)
- Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Ailish Newton
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Mark Berney
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Tom Brown
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
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8
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Zhang T, Rawal Y, Jiang H, Kwon Y, Sung P, Greenberg RA. Break-induced replication orchestrates resection-dependent template switching. Nature 2023; 619:201-208. [PMID: 37316655 PMCID: PMC10937050 DOI: 10.1038/s41586-023-06177-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Break-induced telomere synthesis (BITS) is a RAD51-independent form of break-induced replication that contributes to alternative lengthening of telomeres1,2. This homology-directed repair mechanism utilizes a minimal replisome comprising proliferating cell nuclear antigen (PCNA) and DNA polymerase-δ to execute conservative DNA repair synthesis over many kilobases. How this long-tract homologous recombination repair synthesis responds to complex secondary DNA structures that elicit replication stress remains unclear3-5. Moreover, whether the break-induced replisome orchestrates additional DNA repair events to ensure processivity is also unclear. Here we combine synchronous double-strand break induction with proteomics of isolated chromatin segments (PICh) to capture the telomeric DNA damage response proteome during BITS1,6. This approach revealed a replication stress-dominated response, highlighted by repair synthesis-driven DNA damage tolerance signalling through RAD18-dependent PCNA ubiquitination. Furthermore, the SNM1A nuclease was identified as the major effector of ubiquitinated PCNA-dependent DNA damage tolerance. SNM1A recognizes the ubiquitin-modified break-induced replisome at damaged telomeres, and this directs its nuclease activity to promote resection. These findings show that break-induced replication orchestrates resection-dependent lesion bypass, with SNM1A nuclease activity serving as a critical effector of ubiquitinated PCNA-directed recombination in mammalian cells.
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Affiliation(s)
- Tianpeng Zhang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Haoyang Jiang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Baddock HT, Brolih S, Yosaatmadja Y, Ratnaweera M, Bielinski M, Swift L, Cruz-Migoni A, Fan H, Keown JR, Walker AP, Morris G, Grimes J, Fodor E, Schofield C, Gileadi O, McHugh P. Characterization of the SARS-CoV-2 ExoN (nsp14ExoN-nsp10) complex: implications for its role in viral genome stability and inhibitor identification. Nucleic Acids Res 2022; 50:1484-1500. [PMID: 35037045 PMCID: PMC8860572 DOI: 10.1093/nar/gkab1303] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
The SARS-CoV-2 coronavirus is the causal agent of the current global pandemic. SARS-CoV-2 belongs to an order, Nidovirales, with very large RNA genomes. It is proposed that the fidelity of coronavirus (CoV) genome replication is aided by an RNA nuclease complex, comprising the non-structural proteins 14 and 10 (nsp14-nsp10), an attractive target for antiviral inhibition. Our results validate reports that the SARS-CoV-2 nsp14-nsp10 complex has RNase activity. Detailed functional characterization reveals nsp14-nsp10 is a versatile nuclease capable of digesting a wide variety of RNA structures, including those with a blocked 3'-terminus. Consistent with a role in maintaining viral genome integrity during replication, we find that nsp14-nsp10 activity is enhanced by the viral RNA-dependent RNA polymerase complex (RdRp) consisting of nsp12-nsp7-nsp8 (nsp12-7-8) and demonstrate that this stimulation is mediated by nsp8. We propose that the role of nsp14-nsp10 in maintaining replication fidelity goes beyond classical proofreading by purging the nascent replicating RNA strand of a range of potentially replication-terminating aberrations. Using our developed assays, we identify drug and drug-like molecules that inhibit nsp14-nsp10, including the known SARS-CoV-2 major protease (Mpro) inhibitor ebselen and the HIV integrase inhibitor raltegravir, revealing the potential for multifunctional inhibitors in COVID-19 treatment.
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Affiliation(s)
- Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sanja Brolih
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Yuliana Yosaatmadja
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Malitha Ratnaweera
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Marcin Bielinski
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Lonnie P Swift
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Abimael Cruz-Migoni
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jeremy R Keown
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Alexander P Walker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford OX1 3LB, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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10
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Wu HY, Zheng Y, Laciak AR, Huang NN, Koszelak-Rosenblum M, Flint AJ, Carr G, Zhu G. Structure and Function of SNM1 Family Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:1-26. [PMID: 35708844 DOI: 10.1007/5584_2022_724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Three human nucleases, SNM1A, SNM1B/Apollo, and SNM1C/Artemis, belong to the SNM1 gene family. These nucleases are involved in various cellular functions, including homologous recombination, nonhomologous end-joining, cell cycle regulation, and telomere maintenance. These three proteins share a similar catalytic domain, which is characterized as a fused metallo-β-lactamase and a CPSF-Artemis-SNM1-PSO2 domain. SNM1A and SNM1B/Apollo are exonucleases, whereas SNM1C/Artemis is an endonuclease. This review contains a summary of recent research on SNM1's cellular and biochemical functions, as well as structural biology studies. In addition, protein structure prediction by the artificial intelligence program AlphaFold provides a different view of the proteins' non-catalytic domain features, which may be used in combination with current results from X-ray crystallography and cryo-EM to understand their mechanism more clearly.
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11
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Berney M, T Manoj M, Fay EM, McGouran JF. 5'-Phosphorylation Increases the Efficacy of Nucleoside Inhibitors of the DNA Repair Enzyme SNM1A. ChemMedChem 2021; 17:e202100603. [PMID: 34905656 DOI: 10.1002/cmdc.202100603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/07/2021] [Indexed: 11/11/2022]
Abstract
Certain cancers exhibit upregulation of DNA interstrand crosslink repair pathways, which contributes to resistance to crosslinking chemotherapy drugs and poor prognoses. Inhibition of enzymes implicated in interstrand crosslink repair is therefore a promising strategy for improving the efficacy of cancer treatment. One such target enzyme is SNM1A, a zinc co-ordinating 5'-3' exonuclease. Previous studies have demonstrated the feasibility of inhibiting SNM1A using modified nucleosides appended with zinc-binding groups. In this work, we sought to develop more effective SNM1A inhibitors by exploiting interactions with the phosphate-binding pocket adjacent to the enzyme's active site, in addition to the catalytic zinc ions. A series of nucleoside derivatives bearing phosphate moieties at the 5'-position, as well as zinc-binding groups at the 3'-position, were prepared and tested in gel-electrophoresis and real-time fluorescence assays. As well as investigating novel zinc-binding groups, we found that incorporation of a 5'-phosphate dramatically increased the potency of the inhibitors.
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Affiliation(s)
- Mark Berney
- Trinity College Dublin: The University of Dublin Trinity College, Chemistry, IRELAND
| | - Manav T Manoj
- Trinity College Dublin: The University of Dublin Trinity College, Chemistry, IRELAND
| | - Ellen Mary Fay
- Trinity College Dublin: The University of Dublin Trinity College, Chemistry, IRELAND
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12
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Baddock H, Newman J, Yosaatmadja Y, Bielinski M, Schofield C, Gileadi O, McHugh P. A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family. Nucleic Acids Res 2021; 49:9294-9309. [PMID: 34387694 PMCID: PMC8450094 DOI: 10.1093/nar/gkab692] [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: 12/22/2020] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
The SNM1 nucleases which help maintain genome integrity are members of the metallo-β-lactamase (MBL) structural superfamily. Their conserved MBL-β-CASP-fold SNM1 core provides a molecular scaffold forming an active site which coordinates the metal ions required for catalysis. The features that determine SNM1 endo- versus exonuclease activity, and which control substrate selectivity and binding are poorly understood. We describe a structure of SNM1B/Apollo with two nucleotides bound to its active site, resembling the product state of its exonuclease reaction. The structure enables definition of key SNM1B residues that form contacts with DNA and identifies a 5' phosphate binding pocket, which we demonstrate is important in catalysis and which has a key role in determining endo- versus exonucleolytic activity across the SNM1 family. We probed the capacity of SNM1B to digest past sites of common endogenous DNA lesions and find that base modifications planar to the nucleobase can be accommodated due to the open architecture of the active site, but lesions axial to the plane of the nucleobase are not well tolerated due to constriction around the altered base. We propose that SNM1B/Apollo might employ its activity to help remove common oxidative lesions from telomeres.
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Affiliation(s)
- Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, ORCRB, OX3 7DQ, UK
| | | | - Marcin Bielinski
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, ORCRB, OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
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13
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Yosaatmadja Y, Baddock H, Newman J, Bielinski M, Gavard A, Mukhopadhyay SMM, Dannerfjord A, Schofield C, McHugh P, Gileadi O. Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition. Nucleic Acids Res 2021; 49:9310-9326. [PMID: 34387696 PMCID: PMC8450076 DOI: 10.1093/nar/gkab693] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 07/20/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
Artemis (SNM1C/DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in dsDNA break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Artemis deficiency leads to congenital radiosensitive severe acquired immune deficiency (RS-SCID). Artemis belongs to a superfamily of nucleases containing metallo-β-lactamase (MBL) and β-CASP (CPSF-Artemis-SNM1-Pso2) domains. We present crystal structures of the catalytic domain of wildtype and variant forms of Artemis, including one causing RS-SCID Omenn syndrome. The catalytic domain of the Artemis has similar endonuclease activity to the phosphorylated full-length protein. Our structures help explain the predominantly endonucleolytic activity of Artemis, which contrasts with the predominantly exonuclease activity of the closely related SNM1A and SNM1B MBL fold nucleases. The structures reveal a second metal binding site in its β-CASP domain unique to Artemis, which is amenable to inhibition by compounds including ebselen. By combining our structural data with that from a recently reported Artemis structure, we were able model the interaction of Artemis with DNA substrates. The structures, including one of Artemis with the cephalosporin ceftriaxone, will help enable the rational development of selective SNM1 nuclease inhibitors.
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Affiliation(s)
- Yuliana Yosaatmadja
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Hannah T Baddock
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Marcin Bielinski
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Angeline E Gavard
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | | | - Adam A Dannerfjord
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Christopher J Schofield
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Peter J McHugh
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
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14
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Berney M, Doherty W, Jauslin WT, T Manoj M, Dürr EM, McGouran JF. Synthesis and evaluation of squaramide and thiosquaramide inhibitors of the DNA repair enzyme SNM1A. Bioorg Med Chem 2021; 46:116369. [PMID: 34482229 PMCID: PMC8607331 DOI: 10.1016/j.bmc.2021.116369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 11/24/2022]
Abstract
SNM1A is a zinc-dependent nuclease involved in the removal of interstrand crosslink lesions from DNA. Inhibition of interstrand crosslink repair enzymes such as SNM1A is a promising strategy for improving the efficacy of crosslinking chemotherapy drugs. Initial studies have demonstrated the feasibility of developing SNM1A inhibitors, but the full potential of this enzyme as a drug target has yet to be explored. Herein, the synthesis of a family of squaramide- and thiosquaramide-bearing nucleoside derivatives and their evaluation as SNM1A inhibitors is reported. A gel electrophoresis assay was used to identify nucleoside derivatives bearing an N-hydroxysquaramide or squaric acid moiety at the 3′-position, and a thymidine derivative bearing a 5′-thiosquaramide, as candidate SNM1A inhibitors. Quantitative IC50 determination showed that a thymidine derivative bearing a 5′-thiosquaramide was the most potent inhibitor, followed by a thymidine derivative bearing a 3′-squaric acid. UV–Vis titrations were carried out to evaluate the binding of the (thio)squaramides to zinc ions, allowing the order of inhibitory potency to be rationalised. The membrane permeability of the active inhibitors was investigated, with several compounds showing promise for future in vivo applications.
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Affiliation(s)
- Mark Berney
- School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, Ireland
| | - William Doherty
- School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, Ireland
| | - Werner Theodor Jauslin
- School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, Ireland
| | - Manav T Manoj
- School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, Ireland
| | - Eva-Maria Dürr
- School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, Ireland
| | - Joanna Francelle McGouran
- School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, Ireland.
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15
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Buzon B, Grainger RA, Rzadki C, Huang SYM, Junop M. Identification of Bioactive SNM1A Inhibitors. ACS OMEGA 2021; 6:9352-9361. [PMID: 33869915 PMCID: PMC8047731 DOI: 10.1021/acsomega.0c03528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
SNM1A is a nuclease required to repair DNA interstrand cross-links (ICLs) caused by some anticancer compounds, including cisplatin. Unlike other nucleases involved in ICL repair, SNM1A is not needed to restore other forms of DNA damage. As such, SNM1A is an attractive target for selectively increasing the efficacy of ICL-based chemotherapy. Using a fluorescence-based exonuclease assay, we screened a bioactive library of compounds for inhibition of SNM1A. Of the 52 compounds initially identified as hits, 22 compounds showed dose-response inhibition of SNM1A. An orthogonal gel-based assay further confirmed nine small molecules as SNM1A nuclease activity inhibitors with IC50 values in the mid-nanomolar to low micromolar range. Finally, three compounds showed no toxicity at concentrations able to significantly potentiate the cytotoxicity of cisplatin. These compounds represent potential leads for further optimization to sensitize cells toward chemotherapeutic agents inducing ICL damage.
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Affiliation(s)
- Beverlee Buzon
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department
of Biochemistry, Western University, London, Ontario N6A 5C1, Canada
| | - Ryan A. Grainger
- Department
of Biochemistry, Western University, London, Ontario N6A 5C1, Canada
| | - Cameron Rzadki
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Simon York Ming Huang
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Murray Junop
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department
of Biochemistry, Western University, London, Ontario N6A 5C1, Canada
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16
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Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A. Molecules 2021; 26:molecules26020320. [PMID: 33435514 PMCID: PMC7827217 DOI: 10.3390/molecules26020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5'-position or 3'-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5'-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.
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17
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Baddock HT, Yosaatmadja Y, Newman JA, Schofield CJ, Gileadi O, McHugh PJ. The SNM1A DNA repair nuclease. DNA Repair (Amst) 2020; 95:102941. [PMID: 32866775 PMCID: PMC7607226 DOI: 10.1016/j.dnarep.2020.102941] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 01/17/2023]
Abstract
Unrepaired, or misrepaired, DNA damage can contribute to the pathogenesis of a number of conditions, or disease states; thus, DNA damage repair pathways, and the proteins within them, are required for the safeguarding of the genome. Human SNM1A is a 5'-to-3' exonuclease that plays a role in multiple DNA damage repair processes. To date, most data suggest a role of SNM1A in primarily ICL repair: SNM1A deficient cells exhibit hypersensitivity to ICL-inducing agents (e.g. mitomycin C and cisplatin); and both in vivo and in vitro experiments demonstrate SNM1A and XPF-ERCC1 can function together in the 'unhooking' step of ICL repair. SNM1A further interacts with a number of other proteins that contribute to genome integrity outside canonical ICL repair (e.g. PCNA and CSB), and these may play a role in regulating SNM1As function, subcellular localisation, and post-translational modification state. These data also provide further insight into other DNA repair pathways to which SNM1A may contribute. This review aims to discuss all aspects of the exonuclease, SNM1A, and its contribution to DNA damage tolerance.
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Affiliation(s)
- Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | | | - Joseph A Newman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, UK
| | | | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK.
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18
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Karim MF, Liu S, Laciak AR, Volk L, Koszelak-Rosenblum M, Lieber MR, Wu M, Curtis R, Huang NN, Carr G, Zhu G. Structural analysis of the catalytic domain of Artemis endonuclease/SNM1C reveals distinct structural features. J Biol Chem 2020; 295:12368-12377. [PMID: 32576658 PMCID: PMC7458816 DOI: 10.1074/jbc.ra120.014136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
The endonuclease Artemis is responsible for opening DNA hairpins during V(D)J recombination and for processing a subset of pathological DNA double-strand breaks. Artemis is an attractive target for the development of therapeutics to manage various B cell and T cell tumors, because failure to open DNA hairpins and accumulation of chromosomal breaks may reduce the proliferation and viability of pre-T and pre-B cell derivatives. However, structure-based drug discovery of specific Artemis inhibitors has been hampered by a lack of crystal structures. Here, we report the structure of the catalytic domain of recombinant human Artemis. The catalytic domain displayed a polypeptide fold similar overall to those of other members in the DNA cross-link repair gene SNM1 family and in mRNA 3'-end-processing endonuclease CPSF-73, containing metallo-β-lactamase and β-CASP domains and a cluster of conserved histidine and aspartate residues capable of binding two metal atoms in the catalytic site. As in SNM1A, only one zinc ion was located in the Artemis active site. However, Artemis displayed several unique features. Unlike in other members of this enzyme class, a second zinc ion was present in the β-CASP domain that leads to structural reorientation of the putative DNA-binding surface and extends the substrate-binding pocket to a new pocket, pocket III. Moreover, the substrate-binding surface exhibited a dominant and extensive positive charge distribution compared with that in the structures of SNM1A and SNM1B, presumably because of the structurally distinct DNA substrate of Artemis. The structural features identified here may provide opportunities for designing selective Artemis inhibitors.
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Affiliation(s)
- Md Fazlul Karim
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Shanshan Liu
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Adrian R Laciak
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Leah Volk
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | | | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and the Molecular and Computational Biology Section of the Department of Biological Sciences, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - Mousheng Wu
- Chemistry Department, Drug Discovery Division, Southern Research, Birmingham, Alabama, USA
| | - Rory Curtis
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Nian N Huang
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Grant Carr
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Guangyu Zhu
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
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19
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Doherty W, Dürr EM, Baddock HT, Lee SY, McHugh PJ, Brown T, Senge MO, Scanlan EM, McGouran JF. A hydroxamic-acid-containing nucleoside inhibits DNA repair nuclease SNM1A. Org Biomol Chem 2019; 17:8094-8105. [PMID: 31380542 PMCID: PMC6984127 DOI: 10.1039/c9ob01133a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/12/2019] [Indexed: 12/29/2022]
Abstract
Nine modified nucleosides, incorporating zinc-binding pharmacophores, have been synthesised and evaluated as inhibitors of the DNA repair nuclease SNM1A. The series included oxyamides, hydroxamic acids, hydroxamates, a hydrazide, a squarate ester and a squaramide. A hydroxamic acid-derived nucleoside inhibited the enzyme, offering a novel approach for potential therapeutic development through the use of rationally designed nucleoside derived inhibitors.
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Affiliation(s)
- William Doherty
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland.
| | - Eva-Maria Dürr
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland.
| | - Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sook Y Lee
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK and Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Mathias O Senge
- Molecular Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, Trinity College Dublin, The University of Dublin, St James's Hospital, Dublin 8, Ireland
| | - Eoin M Scanlan
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland.
| | - Joanna F McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland.
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20
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Buzon B, Grainger R, Huang S, Rzadki C, Junop MS. Structure-specific endonuclease activity of SNM1A enables processing of a DNA interstrand crosslink. Nucleic Acids Res 2019; 46:9057-9066. [PMID: 30165656 PMCID: PMC6158701 DOI: 10.1093/nar/gky759] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/20/2018] [Indexed: 01/09/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) covalently join opposing strands, blocking both replication and transcription, therefore making ICL-inducing compounds highly toxic and ideal anti-cancer agents. While incisions surrounding the ICL are required to remove damaged DNA, it is currently unclear which endonucleases are needed for this key event. SNM1A has been shown to play an important function in human ICL repair, however its suggested role has been limited to exonuclease activity and not strand incision. Here we show that SNM1A has endonuclease activity, having the ability to cleave DNA structures that arise during the initiation of ICL repair. In particular, this endonuclease activity cleaves single-stranded DNA. Given that unpaired DNA regions occur 5′ to an ICL, these findings suggest SNM1A may act as either an endonuclease and/or exonuclease during ICL repair. This finding is significant as it expands the potential role of SNM1A in ICL repair.
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Affiliation(s)
- Beverlee Buzon
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada.,Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Ryan Grainger
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Simon Huang
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada
| | - Cameron Rzadki
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada
| | - Murray S Junop
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada.,Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
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21
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Dürr E, Doherty W, Lee SY, El‐Sagheer AH, Shivalingam A, McHugh PJ, Brown T, McGouran JF. Squaramide-Based 5'-Phosphate Replacements Bind to the DNA Repair Exonuclease SNM1A. ChemistrySelect 2018; 3:12824-12829. [PMID: 31414040 PMCID: PMC6685075 DOI: 10.1002/slct.201803375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 12/26/2022]
Abstract
Phosphate groups are often crucial to biological activity and interactions of oligonucleotides, but confer poor membrane permeability. In addition, the group's lability to enzymatic hydrolysis is an obstacle to its use in therapeutics and in biological tools. We present the synthesis of N-oxyamide and squaramide modifications at the 5'-end of oligonucleotides as phosphate replacements and their biological evaluation using the 5'-exonuclease SNM1A. The squaryl diamide modification showed minimal recognition as a 5'-phosphate mimic; however, modest inhibition of SNM1A, postulated to occur through metal coordination at the active site, was observed. Their facile incorporation after solid-phase synthesis and recognition by the exonuclease makes squaryl diamides attractive neutral 5'-phosphate replacements for oligonucleotides. This work is the first example of squaryl diamide modifications at the 5'-terminal position of oligonucleotides and of the potential use of modified oligonucleotides to bind to the metal center of SNM1A.
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Affiliation(s)
- Eva‐Maria Dürr
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - William Doherty
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - Sook Y. Lee
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
- Chemistry Branch, Department of Science and MathematicsFaculty of Petroleum and Mining Engineering, Suez UniversitySuez43721Egypt
| | - Arun Shivalingam
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Peter J. McHugh
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
| | - Tom Brown
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Joanna F. McGouran
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
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22
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Abstract
The SLX4/FANCP tumor suppressor has emerged as a key player in the maintenance of genome stability, making pivotal contributions to the repair of interstrand cross-links, homologous recombination, and in response to replication stress genome-wide as well as at specific loci such as common fragile sites and telomeres. SLX4 does so in part by acting as a scaffold that controls and coordinates the XPF-ERCC1, MUS81-EME1, and SLX1 structure-specific endonucleases in different DNA repair and recombination mechanisms. It also interacts with other important DNA repair and cell cycle control factors including MSH2, PLK1, TRF2, and TOPBP1 as well as with ubiquitin and SUMO. This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts.
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Affiliation(s)
- Jean-Hugues Guervilly
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
| | - Pierre Henri Gaillard
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
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23
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SNM1B/Apollo in the DNA damage response and telomere maintenance. Oncotarget 2018; 8:48398-48409. [PMID: 28430596 PMCID: PMC5564657 DOI: 10.18632/oncotarget.16864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/27/2017] [Indexed: 01/26/2023] Open
Abstract
hSNM1B/Apollo is a member of the highly conserved β-CASP subgroup within the MBL superfamily of proteins. It interacts with several DNA repair proteins and functions within the Fanconi anemia pathway in response to DNA interstrand crosslinks. As a shelterin accessory protein, hSNM1B/Apollo is also vital for the generation and maintenance of telomeric overhangs. In this review, we will summarize studies on hSNM1B/Apollo's function, including its contribution to DNA damage signaling, replication fork maintenance, control of topological stress and telomere protection. Furthermore, we will highlight recent studies illustrating hSNM1B/Apollo's putative role in human disease.
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24
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Abdullah UB, McGouran JF, Brolih S, Ptchelkine D, El-Sagheer AH, Brown T, McHugh PJ. RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks. EMBO J 2017; 36:2047-2060. [PMID: 28607004 PMCID: PMC5510000 DOI: 10.15252/embj.201796664] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/13/2017] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF-ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.
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Affiliation(s)
- Ummi B Abdullah
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Sanja Brolih
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Denis Ptchelkine
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, UK
| | | | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, UK.,Department of Oncology, University of Oxford, Oxford, UK
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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25
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Roy U, Schärer OD. Involvement of translesion synthesis DNA polymerases in DNA interstrand crosslink repair. DNA Repair (Amst) 2016; 44:33-41. [PMID: 27311543 DOI: 10.1016/j.dnarep.2016.05.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA interstrand crosslinks (ICLs) covalently join the two strands of a DNA duplex and block essential processes such as DNA replication and transcription. Several important anti-tumor drugs such as cisplatin and nitrogen mustards exert their cytotoxicity by forming ICLs. However, multiple complex pathways repair ICLs and these are thought to contribute to the development of resistance towards ICL-inducing agents. While the understanding of many aspects of ICL repair is still rudimentary, studies in recent years have provided significant insights into the pathways of ICL repair. In this perspective we review the recent advances made in elucidating the mechanisms of ICL repair with a focus on the role of TLS polymerases. We describe the emerging models for how these enzymes contribute to and are regulated in ICL repair, discuss the key open questions and examine the implications for this pathway in anti-cancer therapy.
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Affiliation(s)
- Upasana Roy
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Orlando D Schärer
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-3400, USA.
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26
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Lee SY, Brem J, Pettinati I, Claridge TDW, Gileadi O, Schofield CJ, McHugh PJ. Cephalosporins inhibit human metallo β-lactamase fold DNA repair nucleases SNM1A and SNM1B/apollo. Chem Commun (Camb) 2016; 52:6727-30. [PMID: 27121860 PMCID: PMC5063058 DOI: 10.1039/c6cc00529b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/18/2016] [Indexed: 12/19/2022]
Abstract
Bacterial metallo-β-lactamases (MBLs) are involved in resistance to β-lactam antibiotics including cephalosporins. Human SNM1A and SNM1B are MBL superfamily exonucleases that play a key role in the repair of DNA interstrand cross-links, which are induced by antitumour chemotherapeutics, and are therefore targets for cancer chemosensitization. We report that cephalosporins are competitive inhibitors of SNM1A and SNM1B exonuclease activity; both the intact β-lactam and their hydrolysed products are active. This discovery provides a lead for the development of potent and selective SNM1A and SNM1B inhibitors.
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Affiliation(s)
- Sook Y Lee
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK. and Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Ilaria Pettinati
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Opher Gileadi
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, OX3 7DQ, UK
| | | | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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27
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Huang J, Gali H, Paramasivam M, Muniandy P, Gichimu J, Bellani MA, Seidman MM. Single Molecule Analysis of Laser Localized Interstrand Crosslinks. Front Genet 2016; 7:84. [PMID: 27242893 PMCID: PMC4860505 DOI: 10.3389/fgene.2016.00084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) block unwinding of the double helix, and have always been regarded as major challenges to replication and transcription. Compounds that form these lesions are very toxic and are frequently used in cancer chemotherapy. We have developed two strategies, both based on immunofluorescence (IF), for studying cellular responses to ICLs. The basis of each is psoralen, a photoactive (by long wave ultraviolet light, UVA) DNA crosslinking agent, to which we have linked an antigen tag. In the one approach, we have taken advantage of DNA fiber and immuno-quantum dot technologies for visualizing the encounter of replication forks with ICLs induced by exposure to UVA lamps. In the other, psoralen ICLs are introduced into nuclei in live cells in regions of interest defined by a UVA laser. The antigen tag can be displayed by conventional IF, as can the recruitment and accumulation of DNA damage response proteins to the laser localized ICLs. However, substantial difference between the technologies creates considerable uncertainty as to whether conclusions from one approach are applicable to those of the other. In this report, we have employed the fiber/quantum dot methodology to determine lesion density and spacing on individual DNA molecules carrying laser localized ICLs. We have performed the same measurements on DNA fibers with ICLs induced by exposure of psoralen to UVA lamps. Remarkably, we find little difference in the adduct distribution on fibers prepared from cells exposed to the different treatment protocols. Furthermore, there is considerable similarity in patterns of replication in the vicinity of the ICLs introduced by the two techniques.
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Affiliation(s)
- Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Himabindu Gali
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Manikandan Paramasivam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Parameswary Muniandy
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Julia Gichimu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
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28
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EXD2 promotes homologous recombination by facilitating DNA end resection. Nat Cell Biol 2016; 18:271-280. [PMID: 26807646 PMCID: PMC4829102 DOI: 10.1038/ncb3303] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/17/2015] [Indexed: 01/13/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is critical for survival and genome stability of individual cells and organisms, but also contributes to the genetic diversity of species. A vital step in HR is MRN-CtIP-dependent end resection, which generates the 3' single-stranded DNA overhangs required for the subsequent strand exchange reaction. Here, we identify EXD2 (also known as EXDL2) as an exonuclease essential for DSB resection and efficient HR. EXD2 is recruited to chromatin in a damage-dependent manner and confers resistance to DSB-inducing agents. EXD2 functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks. Finally, we establish that EXD2 stimulates both short- and long-range DSB resection, and thus, together with MRE11, is required for efficient HR. This establishes a key role for EXD2 in controlling the initial steps of chromosomal break repair.
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29
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The Chemical Biology of Human Metallo-β-Lactamase Fold Proteins. Trends Biochem Sci 2016; 41:338-355. [PMID: 26805042 PMCID: PMC4819959 DOI: 10.1016/j.tibs.2015.12.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/19/2015] [Accepted: 12/22/2015] [Indexed: 01/30/2023]
Abstract
The αββα metallo β-lactamase (MBL) fold (MBLf) was first observed in bacterial enzymes that catalyze the hydrolysis of almost all β-lactam antibiotics, but is now known to be widely distributed. The MBL core protein fold is present in human enzymes with diverse biological roles, including cell detoxification pathways and enabling resistance to clinically important anticancer medicines. Human (h)MBLf enzymes can bind metals, including zinc and iron ions, and catalyze a range of chemically interesting reactions, including both redox (e.g., ETHE1) and hydrolytic processes (e.g., Glyoxalase II, SNM1 nucleases, and CPSF73). With a view to promoting basic research on MBLf enzymes and their medicinal targeting, here we summarize current knowledge of the mechanisms and roles of these important molecules. MBLs are mono- or di-zinc ion-dependent hydrolases that enable bacterial resistance to almost all β-lactam antibiotics. The αββα MBL core fold is widely distributed and supports a range of catalytic activities, including redox reactions. hMBL proteins are a small family of approximately 18 zinc- and iron-dependent proteins with roles in metabolism and/or detoxification and nucleic acid modification. In a notable parallel with the role of bacterial MBLs in antibiotic resistance, some hMBLf enzymes enable resistance to chemotherapy drugs, such as cisplatin and mitomycin C.
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30
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Allerston CK, Lee SY, Newman JA, Schofield CJ, McHugh PJ, Gileadi O. The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities. Nucleic Acids Res 2015; 43:11047-60. [PMID: 26582912 PMCID: PMC4678830 DOI: 10.1093/nar/gkv1256] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/30/2015] [Indexed: 11/30/2022] Open
Abstract
The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions.
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Affiliation(s)
- Charles K Allerston
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| | - Sook Y Lee
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Joseph A Newman
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Opher Gileadi
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
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31
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Structural Basis of Metallo-β-Lactamase Inhibition by Captopril Stereoisomers. Antimicrob Agents Chemother 2015; 60:142-50. [PMID: 26482303 PMCID: PMC4704194 DOI: 10.1128/aac.01335-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022] Open
Abstract
β-Lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (MBLs). MBLs are of increasing concern because they catalyze the hydrolysis of almost all β-lactam antibiotics, including recent-generation carbapenems. Clinically useful serine-β-lactamase inhibitors have been developed, but such inhibitors are not available for MBLs. l-Captopril, which is used to treat hypertension via angiotensin-converting enzyme inhibition, has been reported to inhibit MBLs by chelating the active site zinc ions via its thiol(ate). We report systematic studies on B1 MBL inhibition by all four captopril stereoisomers. High-resolution crystal structures of three MBLs (IMP-1, BcII, and VIM-2) in complex with either the l- or d-captopril stereoisomer reveal correlations between the binding mode and inhibition potency. The results will be useful in the design of MBL inhibitors with the breadth of selectivity required for clinical application against carbapenem-resistant Enterobacteriaceae and other organisms causing MBL-mediated resistant infections.
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32
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Iyama T, Lee SY, Berquist BR, Gileadi O, Bohr VA, Seidman MM, McHugh PJ, Wilson DM. CSB interacts with SNM1A and promotes DNA interstrand crosslink processing. Nucleic Acids Res 2014; 43:247-58. [PMID: 25505141 PMCID: PMC4288174 DOI: 10.1093/nar/gku1279] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cockayne syndrome (CS) is a premature aging disorder characterized by photosensitivity, impaired development and multisystem progressive degeneration, and consists of two strict complementation groups, A and B. Using a yeast two-hybrid approach, we identified the 5′-3′ exonuclease SNM1A as one of four strong interacting partners of CSB. This direct interaction was confirmed using purified recombinant proteins—with CSB able to modulate the exonuclease activity of SNM1A on oligonucleotide substrates in vitro—and the two proteins were shown to exist in a common complex in human cell extracts. CSB and SNM1A were also found, using fluorescently tagged proteins in combination with confocal microscopy and laser microirradiation, to be recruited to localized trioxsalen-induced ICL damage in human cells, with accumulation being suppressed by transcription inhibition. Moreover, SNM1A recruitment was significantly reduced in CSB-deficient cells, suggesting coordination between the two proteins in vivo. CSB-deficient neural cells exhibited increased sensitivity to DNA crosslinking agents, particularly, in a non-cycling, differentiated state, as well as delayed ICL processing as revealed by a modified Comet assay and γ-H2AX foci persistence. The results indicate that CSB coordinates the resolution of ICLs, possibly in a transcription-associated repair mechanism involving SNM1A, and that defects in the process could contribute to the post-mitotic degenerative pathologies associated with CS.
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Affiliation(s)
- Teruaki Iyama
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sook Y Lee
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | | | - Opher Gileadi
- The Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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33
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Abstract
A critical step in DNA interstrand cross-link repair is the programmed collapse of replication forks that have stalled at an ICL. This event is regulated by the Fanconi anemia pathway, which suppresses bone marrow failure and cancer. In this perspective, we focus on the structure of forks that have stalled at ICLs, how these structures might be incised by endonucleases, and how incision is regulated by the Fanconi anemia pathway.
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Affiliation(s)
- Jieqiong Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States; Howard Hughes Medical Institute.
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34
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Hodskinson MRG, Silhan J, Crossan GP, Garaycoechea JI, Mukherjee S, Johnson CM, Schärer OD, Patel KJ. Mouse SLX4 is a tumor suppressor that stimulates the activity of the nuclease XPF-ERCC1 in DNA crosslink repair. Mol Cell 2014; 54:472-84. [PMID: 24726326 PMCID: PMC4017094 DOI: 10.1016/j.molcel.2014.03.014] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/21/2014] [Accepted: 02/28/2014] [Indexed: 11/18/2022]
Abstract
SLX4 binds to three nucleases (XPF-ERCC1, MUS81-EME1, and SLX1), and its deficiency leads to genomic instability, sensitivity to DNA crosslinking agents, and Fanconi anemia. However, it is not understood how SLX4 and its associated nucleases act in DNA crosslink repair. Here, we uncover consequences of mouse Slx4 deficiency and reveal its function in DNA crosslink repair. Slx4-deficient mice develop epithelial cancers and have a contracted hematopoietic stem cell pool. The N-terminal domain of SLX4 (mini-SLX4) that only binds to XPF-ERCC1 is sufficient to confer resistance to DNA crosslinking agents. Recombinant mini-SLX4 enhances XPF-ERCC1 nuclease activity up to 100-fold, directing specificity toward DNA forks. Mini-SLX4-XPF-ERCC1 also vigorously stimulates dual incisions around a DNA crosslink embedded in a synthetic replication fork, an essential step in the repair of this lesion. These observations define vertebrate SLX4 as a tumor suppressor, which activates XPF-ERCC1 nuclease specificity in DNA crosslink repair.
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Affiliation(s)
| | - Jan Silhan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Juan I Garaycoechea
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Shivam Mukherjee
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | - Orlando D Schärer
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Department of Medicine, Level 5, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK.
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35
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Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer JA. Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst) 2014; 17:110-20. [PMID: 24656613 PMCID: PMC4102006 DOI: 10.1016/j.dnarep.2014.02.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/27/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for repair of DNA double-strand breaks (DSBs) in human cells. NHEJ is also needed for V(D)J recombination and the development of T and B cells in vertebrate immune systems, and acts in both the generation and prevention of non-homologous chromosomal translocations, a hallmark of genomic instability and many human cancers. X-ray crystal structures, cryo-electron microscopy envelopes, and small angle X-ray scattering (SAXS) solution conformations and assemblies are defining most of the core protein components for NHEJ: Ku70/Ku80 heterodimer; the DNA dependent protein kinase catalytic subunit (DNA-PKcs); the structure-specific endonuclease Artemis along with polynucleotide kinase/phosphatase (PNKP), aprataxin and PNKP related protein (APLF); the scaffolding proteins XRCC4 and XLF (XRCC4-like factor); DNA polymerases, and DNA ligase IV (Lig IV). The dynamic assembly of multi-protein NHEJ complexes at DSBs is regulated in part by protein phosphorylation. The basic steps of NHEJ have been biochemically defined to require: (1) DSB detection by the Ku heterodimer with subsequent DNA-PKcs tethering to form the DNA-PKcs-Ku-DNA complex (termed DNA-PK), (2) lesion processing, and (3) DNA end ligation by Lig IV, which functions in complex with XRCC4 and XLF. The current integration of structures by combined methods is resolving puzzles regarding the mechanisms, coordination and regulation of these three basic steps. Overall, structural results suggest the NHEJ system forms a flexing scaffold with the DNA-PKcs HEAT repeats acting as compressible macromolecular springs suitable to store and release conformational energy to apply forces to regulate NHEJ complexes and the DNA substrate for DNA end protection, processing, and ligation.
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Affiliation(s)
- Gareth J Williams
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Sarvan Kumar Radhakrishnan
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, T2 N 4N1 Canada
| | - Dale Ramsden
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 2759, United States
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, T2 N 4N1 Canada; Department of Oncology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, T2 N 4N1 Canada.
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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36
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Li S, Chang HH, Niewolik D, Hedrick MP, Pinkerton AB, Hassig CA, Schwarz K, Lieber MR. Evidence that the DNA endonuclease ARTEMIS also has intrinsic 5'-exonuclease activity. J Biol Chem 2014; 289:7825-34. [PMID: 24500713 DOI: 10.1074/jbc.m113.544874] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
ARTEMIS is a member of the metallo-β-lactamase protein family. ARTEMIS has endonuclease activity at DNA hairpins and at 5'- and 3'-DNA overhangs of duplex DNA, and this endonucleolytic activity is dependent upon DNA-PKcs. There has been uncertainty about whether ARTEMIS also has 5'-exonuclease activity on single-stranded DNA and 5'-overhangs, because this 5'-exonuclease is not dependent upon DNA-PKcs. Here, we show that the 5'-exonuclease and the endonuclease activities co-purify. Second, we show that a point mutant of ARTEMIS at a putative active site residue (H115A) markedly reduces both the endonuclease activity and the 5'-exonuclease activity. Third, divalent cation effects on the 5'-exonuclease and the endonuclease parallel one another. Fourth, both the endonuclease activity and 5'-exonuclease activity of ARTEMIS can be blocked in parallel by small molecule inhibitors, which do not block unrelated nucleases. We conclude that the 5'-exonuclease is intrinsic to ARTEMIS, making it relevant to the role of ARTEMIS in nonhomologous DNA end joining.
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Affiliation(s)
- Sicong Li
- From the Departments of Pathology, Biochemistry and Molecular Biology, Biological Sciences, and Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California 90089-9176
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37
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Huang J, Liu S, Bellani MA, Thazhathveetil AK, Ling C, de Winter JP, Wang Y, Wang W, Seidman MM. The DNA translocase FANCM/MHF promotes replication traverse of DNA interstrand crosslinks. Mol Cell 2013; 52:434-46. [PMID: 24207054 DOI: 10.1016/j.molcel.2013.09.021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/09/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The replicative machinery encounters many impediments, some of which can be overcome by lesion bypass or replication restart pathways, leaving repair for a later time. However, interstrand crosslinks (ICLs), which preclude DNA unwinding, are considered absolute blocks to replication. Current models suggest that fork collisions, either from one or both sides of an ICL, initiate repair processes required for resumption of replication. To test these proposals, we developed a single-molecule technique for visualizing encounters of replication forks with ICLs as they occur in living cells. Surprisingly, the most frequent patterns were consistent with replication traverse of an ICL, without lesion repair. The traverse frequency was strongly reduced by inactivation of the translocase and DNA binding activities of the FANCM/MHF complex. The results indicate that translocase-based mechanisms enable DNA synthesis to continue past ICLs and that these lesions are not always absolute blocks to replication.
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Affiliation(s)
- Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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Clauson C, Schärer OD, Niedernhofer L. Advances in understanding the complex mechanisms of DNA interstrand cross-link repair. Cold Spring Harb Perspect Biol 2013; 5:a012732. [PMID: 24086043 DOI: 10.1101/cshperspect.a012732] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA interstrand cross-links (ICLs) are lesions caused by a variety of endogenous metabolites, environmental exposures, and cancer chemotherapeutic agents that have two reactive groups. The common feature of these diverse lesions is that two nucleotides on opposite strands are covalently joined. ICLs prevent the separation of two DNA strands and therefore essential cellular processes including DNA replication and transcription. ICLs are mainly detected in S phase when a replication fork stalls at an ICL. Damage signaling and repair of ICLs are promoted by the Fanconi anemia pathway and numerous posttranslational modifications of DNA repair and chromatin structural proteins. ICLs are also detected and repaired in nonreplicating cells, although the mechanism is less clear. A unique feature of ICL repair is that both strands of DNA must be incised to completely remove the lesion. This is accomplished in sequential steps to prevent creating multiple double-strand breaks. Unhooking of an ICL from one strand is followed by translesion synthesis to fill the gap and create an intact duplex DNA, harboring a remnant of the ICL. Removal of the lesion from the second strand is likely accomplished by nucleotide excision repair. Inadequate repair of ICLs is particularly detrimental to rapidly dividing cells, explaining the bone marrow failure characteristic of Fanconi anemia and why cross-linking agents are efficacious in cancer therapy. Herein, recent advances in our understanding of ICLs and the biological responses they trigger are discussed.
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Affiliation(s)
- Cheryl Clauson
- Department of Microbiology and Molecular Genetics, The University of Pittsburgh, Pittsburgh, Pennsylvania 15219
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Mason JM, Das I, Arlt M, Patel N, Kraftson S, Glover TW, Sekiguchi JM. The SNM1B/APOLLO DNA nuclease functions in resolution of replication stress and maintenance of common fragile site stability. Hum Mol Genet 2013; 22:4901-13. [PMID: 23863462 DOI: 10.1093/hmg/ddt340] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SNM1B/Apollo is a DNA nuclease that has important functions in telomere maintenance and repair of DNA interstrand crosslinks (ICLs) within the Fanconi anemia (FA) pathway. SNM1B is required for efficient localization of key repair proteins, such as the FA protein, FANCD2, to sites of ICL damage and functions epistatically to FANCD2 in cellular survival to ICLs and homology-directed repair. The FA pathway is also activated in response to replication fork stalling. Here, we sought to determine the importance of SNM1B in cellular responses to stalled forks in the absence of a blocking lesion, such as ICLs. We found that depletion of SNM1B results in hypersensitivity to aphidicolin, a DNA polymerase inhibitor that causes replication stress. We observed that the SNM1B nuclease is required for efficient localization of the DNA repair proteins, FANCD2 and BRCA1, to subnuclear foci upon aphidicolin treatment, thereby indicating SNM1B facilitates direct repair of stalled forks. Consistent with a role for SNM1B subsequent to recognition of the lesion, we found that SNM1B is dispensable for upstream events, including activation of ATR-dependent signaling and localization of RPA, γH2AX and the MRE11/RAD50/NBS1 complex to aphidicolin-induced foci. We determined that a major consequence of SNM1B depletion is a marked increase in spontaneous and aphidicolin-induced chromosomal gaps and breaks, including breakage at common fragile sites. Thus, this study provides evidence that SNM1B functions in resolving replication stress and preventing accumulation of genomic damage.
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Yang H, Yung M, Li L, Hoch JA, Ryan CM, Kar UK, Souda P, Whitelegge JP, Miller JH. Evidence that YycJ is a novel 5′–3′ double-stranded DNA exonuclease acting in Bacillus anthracis mismatch repair. DNA Repair (Amst) 2013; 12:334-46. [DOI: 10.1016/j.dnarep.2013.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 01/27/2013] [Accepted: 02/05/2013] [Indexed: 11/29/2022]
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Abstract
The protein Snm1B plays a key role in interstrand crosslink (ICL) repair. In a yeast two-hybrid screen we identified the protein PSF2 to bind Snm1B. PSF2 is a member of the GINS complex involved in replication initiation and elongation, and is known to play a role in ICL repair. Snm1B was shown to bind PSF2 in human cells through two regions, strongly to a 144 amino acid N-terminal region and weakly to a second smaller 37 amino acid C-terminal region. Ectopic expression of PSF2 increased the amount of Mus81, a protein component of the endonucleolytic complex involved in ICL repair, co-immunoprecipitating with Snm1B. Moreover, deleting the N-terminal, but not C-terminal region of Snm1B reduced the amount of co-immunoprecipitated Mus81. Conversely, the telomere-binding protein TRF2 competed with PSF2 for binding to the C-terminus of Snm1B, and deletion of this region, but not the N-terminal region, reduced Snm1B chromatin association. We speculate that the N-terminal region of Snm1B forms a complex containing PSF2 and Mus81, while the C-terminal region is important for PSF2-mediated chromatin association.
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Affiliation(s)
- Jay R. Stringer
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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