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Schuurs ZP, Martyn AP, Soltau CP, Beard S, Shah ET, Adams MN, Croft LV, O’Byrne KJ, Richard DJ, Gandhi NS. An Exploration of Small Molecules That Bind Human Single-Stranded DNA Binding Protein 1. Biology (Basel) 2023; 12:1405. [PMID: 37998004 PMCID: PMC10669474 DOI: 10.3390/biology12111405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Human single-stranded DNA binding protein 1 (hSSB1) is critical to preserving genome stability, interacting with single-stranded DNA (ssDNA) through an oligonucleotide/oligosaccharide binding-fold. The depletion of hSSB1 in cell-line models leads to aberrant DNA repair and increased sensitivity to irradiation. hSSB1 is over-expressed in several types of cancers, suggesting that hSSB1 could be a novel therapeutic target in malignant disease. hSSB1 binding studies have focused on DNA; however, despite the availability of 3D structures, small molecules targeting hSSB1 have not been explored. Quinoline derivatives targeting hSSB1 were designed through a virtual fragment-based screening process, synthesizing them using AlphaLISA and EMSA to determine their affinity for hSSB1. In parallel, we further screened a structurally diverse compound library against hSSB1 using the same biochemical assays. Three compounds with nanomolar affinity for hSSB1 were identified, exhibiting cytotoxicity in an osteosarcoma cell line. To our knowledge, this is the first study to identify small molecules that modulate hSSB1 activity. Molecular dynamics simulations indicated that three of the compounds that were tested bound to the ssDNA-binding site of hSSB1, providing a framework for the further elucidation of inhibition mechanisms. These data suggest that small molecules can disrupt the interaction between hSSB1 and ssDNA, and may also affect the ability of cells to repair DNA damage. This test study of small molecules holds the potential to provide insights into fundamental biochemical questions regarding the OB-fold.
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Affiliation(s)
- Zachariah P. Schuurs
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; (Z.P.S.); (A.P.M.)
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
| | - Alexander P. Martyn
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; (Z.P.S.); (A.P.M.)
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
| | - Carl P. Soltau
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Sam Beard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
| | - Esha T. Shah
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Mark N. Adams
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Laura V. Croft
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- Cancer Services, Princess Alexandra Hospital—Metro South Health, Woolloongabba, QLD 4102, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Neha S. Gandhi
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; (Z.P.S.); (A.P.M.)
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, India
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Schuurs ZP, McDonald JP, Croft LV, Richard DJ, Woodgate R, Gandhi NS. Integration of molecular modelling and in vitro studies to inhibit LexA proteolysis. Front Cell Infect Microbiol 2023; 13:1051602. [PMID: 36936756 PMCID: PMC10020695 DOI: 10.3389/fcimb.2023.1051602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction As antibiotic resistance has become more prevalent, the social and economic impacts are increasingly pressing. Indeed, bacteria have developed the SOS response which facilitates the evolution of resistance under genotoxic stress. The transcriptional repressor, LexA, plays a key role in this response. Mutation of LexA to a non-cleavable form that prevents the induction of the SOS response sensitizes bacteria to antibiotics. Achieving the same inhibition of proteolysis with small molecules also increases antibiotic susceptibility and reduces drug resistance acquisition. The availability of multiple LexA crystal structures, and the unique Ser-119 and Lys-156 catalytic dyad in the protein enables the rational design of inhibitors. Methods We pursued a binary approach to inhibit proteolysis; we first investigated β-turn mimetics, and in the second approach we tested covalent warheads targeting the Ser-119 residue. We found that the cleavage site region (CSR) of the LexA protein is a classical Type II β-turn, and that published 1,2,3-triazole compounds mimic the β-turn. Generic covalent molecule libraries and a β-turn mimetic library were docked to the LexA C-terminal domain using molecular modelling methods in FlexX and CovDock respectively. The 133 highest-scoring molecules were screened for their ability to inhibit LexA cleavage under alkaline conditions. The top molecules were then tested using a RecA-mediated cleavage assay. Results The β-turn library screen did not produce any hit compounds that inhibited RecA-mediated cleavage. The covalent screen discovered an electrophilic serine warhead that can inhibit LexA proteolysis, reacting with Ser-119 via a nitrile moiety. Discussion This research presents a starting point for hit-to-lead optimisation, which could lead to inhibition of the SOS response and prevent the acquisition of antibiotic resistance.
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Affiliation(s)
- Zachariah P. Schuurs
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - John P. McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Laura V. Croft
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Neha S. Gandhi, ; Roger Woodgate,
| | - Neha S. Gandhi
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- *Correspondence: Neha S. Gandhi, ; Roger Woodgate,
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Schuurs ZP, Hammond E, Elli S, Rudd TR, Mycroft-West CJ, Lima MA, Skidmore MA, Karlsson R, Chen YH, Bagdonaite I, Yang Z, Ahmed YA, Richard DJ, Turnbull J, Ferro V, Coombe DR, Gandhi NS. Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Comput Struct Biotechnol J 2021; 19:2806-2818. [PMID: 33968333 PMCID: PMC8093007 DOI: 10.1016/j.csbj.2021.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/01/2021] [Accepted: 05/01/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 has rapidly spread throughout the world's population since its initial discovery in 2019. The virus infects cells via a glycosylated spike protein located on its surface. The protein primarily binds to the angiotensin-converting enzyme-2 (ACE2) receptor, using glycosaminoglycans (GAGs) as co-receptors. Here, we performed bioinformatics and molecular dynamics simulations of the spike protein to investigate the existence of additional GAG binding sites on the receptor-binding domain (RBD), separate from previously reported heparin-binding sites. A putative GAG binding site in the N-terminal domain (NTD) of the protein was identified, encompassing residues 245-246. We hypothesized that GAGs of a sufficient length might bridge the gap between this site and the PRRARS furin cleavage site, including the mutation S247R. Docking studies using GlycoTorch Vina and subsequent MD simulations of the spike trimer in the presence of dodecasaccharides of the GAGs heparin and heparan sulfate supported this possibility. The heparan sulfate chain bridged the gap, binding the furin cleavage site and S247R. In contrast, the heparin chain bound the furin cleavage site and surrounding glycosylation structures, but not S247R. These findings identify a site in the spike protein that favors heparan sulfate binding that may be particularly pertinent for a better understanding of the recent UK and South African strains. This will also assist in future targeted therapy programs that could include repurposing clinical heparan sulfate mimetics.
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Affiliation(s)
- Zachariah P. Schuurs
- QUT, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program, School of Chemistry and Physics, Faculty of Science and Engineering, Institute of Health and Biomedical Innovation, 2 George Street, Brisbane, QLD 4000, Australia
| | - Edward Hammond
- Zucero Therapeutics Ltd, 1 Westlink Court, Brisbane, Queensland, Australia
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche “G.Ronzoni”, via Giuseppe Colombo 81, 20133 Milano, Italy
| | - Timothy R. Rudd
- National Institute for Biological Standards and Control, Analytical and Biological Sciences Division, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Courtney J. Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, UK
| | - Marcelo A. Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, UK
| | - Mark A. Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, UK
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ieva Bagdonaite
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Yassir A. Ahmed
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Derek J. Richard
- QUT, Centre for Genomics and Personalised Health, Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Queensland 4102, Australia
| | - Jeremy Turnbull
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Deirdre R. Coombe
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Neha S. Gandhi
- QUT, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program, School of Chemistry and Physics, Faculty of Science and Engineering, Institute of Health and Biomedical Innovation, 2 George Street, Brisbane, QLD 4000, Australia
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