1
|
Ferguson L, Bhakta S, Fox KR, Wells G, Brucoli F. Synthesis and Biological Evaluation of a Novel C8-Pyrrolobenzodiazepine (PBD) Adenosine Conjugate. A Study on the Role of the PBD Ring in the Biological Activity of PBD-Conjugates. Molecules 2020; 25:E1243. [PMID: 32164166 PMCID: PMC7179398 DOI: 10.3390/molecules25051243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/16/2022] Open
Abstract
Here we sought to evaluate the contribution of the PBD unit to the biological activity of PBD-conjugates and, to this end, an adenosine nucleoside was attached to the PBD A-ring C8 position. A convergent approach was successfully adopted for the synthesis of a novel C8-linked pyrrolo(2,1-c)(1,4)benzodiazepine(PBD)-adenosine(ADN) hybrid. The PBD and adenosine (ADN) moieties were synthesized separately and then linked through a pentynyl linker. To our knowledge, this is the first report of a PBD connected to a nucleoside. Surprisingly, the compound showed no cytotoxicity against murine cells and was inactive against Mycobacterium aurum and M. bovis strains and did not bind to guanine-containing DNA sequences, as shown by DNase I footprinting experiments. Molecular dynamics simulations revealed that the PBD-ADN conjugate was poorly accommodated in the DNA minor groove of two DNA sequences containing the AGA-PBD binding motif, with the adenosine moiety of the ligand preventing the covalent binding of the PBD unit to the guanine amino group of the DNA duplex. These interesting findings shed further light on the ability of the substituents attached at the C8 position of PBDs to affect and modulate the biological and biophysical properties of PBD hybrids.
Collapse
Affiliation(s)
- Lindsay Ferguson
- School of Science, University of the West of Scotland, Paisley, Scotland PA1 2BE, UK
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Geoff Wells
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, UK
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, UK
| |
Collapse
|
2
|
A Low-Toxicity DNA-Alkylating N-Mustard-Quinoline Conjugate with Preferential Sequence Specificity Exerts Potent Antitumor Activity Against Colorectal Cancer. Neoplasia 2017; 20:119-130. [PMID: 29247884 PMCID: PMC5884014 DOI: 10.1016/j.neo.2017.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/03/2023] Open
Abstract
Efficacy and safety are fundamental prerequisites for anticancer drug development. In the present study, we explored the anti–colorectal cancer (CRC) activity of SL-1, a DNA-directed N-mustard-quinoline conjugate. The N-mustard moiety in SL-1 induced DNA strand breaks, interstrand cross-links (ICLs), G2/M arrest, and apoptosis, whereas its quinoline moiety preferentially directed SL-1 to target the selective guanine sequence 5′-G-G/C-N-G-C/T-3′. Notably, SL-1 was highly cytotoxic to various CRC cell lines. Experiments using xenograft models revealed that SL-1 was more potent than 5-fluorouracil (5-FU) and oxaliplatin for suppressing the growth of RKO and RKO-E6 (oxaliplatin-resistant subline) cells as well as metastatic SW620 cells. In addition, SL-1 combined with 5-FU was more effective than oxaliplatin and 5-FU for suppressing RKO or SW620 cell growth in mice. Significantly, compared with cisplatin, oxaliplatin, or 5-FU, SL-1 alone or in combination with 5-FU did not cause obvious kidney or liver toxicity in ICR mice. In summary, SL-1, a DNA-directed alkylating agent, is established as an anti-CRC agent with high efficacy and low toxicity and thus warrants further development for the treatment of CRC patients.
Collapse
|
3
|
Basher MA, Rahman KM, Jackson PJM, Thurston DE, Fox KR. Sequence-selective binding of C8-conjugated pyrrolobenzodiazepines (PBDs) to DNA. Biophys Chem 2017; 230:53-61. [PMID: 28941814 DOI: 10.1016/j.bpc.2017.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 11/17/2022]
Abstract
DNA footprinting and melting experiments have been used to examine the sequence-specific binding of C8-conjugates of pyrrolobenzodiazepines (PBDs) and benzofused rings including benzothiophene and benzofuran, which are attached using pyrrole- or imidazole-containing linkers. The conjugates modulate the covalent attachment points of the PBDs, so that they bind best to guanines flanked by A/T-rich sequences on either the 5'- or 3'-side. The linker affects the binding, and pyrrole produces larger changes than imidazole. Melting studies with 14-mer oligonucleotide duplexes confirm covalent attachment of the conjugates, which show a different selectivity to anthramycin and reveal that more than one ligand molecule can bind to each duplex.
Collapse
Affiliation(s)
- Mohammad A Basher
- Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - Paul J M Jackson
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - David E Thurston
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - Keith R Fox
- Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK.
| |
Collapse
|
4
|
Brucoli F, Guzman JD, Basher MA, Evangelopoulos D, McMahon E, Munshi T, McHugh TD, Fox KR, Bhakta S. DNA sequence-selective C8-linked pyrrolobenzodiazepine–heterocyclic polyamide conjugates show anti-tubercular-specific activities. J Antibiot (Tokyo) 2016; 69:843-849. [DOI: 10.1038/ja.2016.43] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/29/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023]
|
5
|
Brucoli F, Guzman JD, Maitra A, James CH, Fox KR, Bhakta S. Synthesis, anti-mycobacterial activity and DNA sequence-selectivity of a library of biaryl-motifs containing polyamides. Bioorg Med Chem 2015; 23:3705-11. [PMID: 25921267 DOI: 10.1016/j.bmc.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/27/2015] [Accepted: 04/02/2015] [Indexed: 02/07/2023]
Abstract
The alarming rise of extensively drug-resistant tuberculosis (XDR-TB) strains, compel the development of new molecules with novel modes of action to control this world health emergency. Distamycin analogues containing N-terminal biaryl-motifs 2(1-5)(1-7) were synthesised using a solution-phase approach and evaluated for their anti-mycobacterial activity and DNA-sequence selectivity. Thiophene dimer motif-containing polyamide 2(2,6) exhibited 10-fold higher inhibitory activity against Mycobacterium tuberculosis compared to distamycin and library member 2(5,7) showed high binding affinity for the 5'-ACATAT-3' sequence.
Collapse
Affiliation(s)
- Federico Brucoli
- School of Science and Sport, Institute of Biomedical and Environmental Health Research (IBEHR), University of the West of Scotland, Paisley PA1 2BE, UK.
| | - Juan D Guzman
- Mycobacteria Research Laboratory, Department of Biological Sciences, The Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| | - Arundhati Maitra
- Mycobacteria Research Laboratory, Department of Biological Sciences, The Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| | - Colin H James
- UCL School of Pharmacy, London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Keith R Fox
- Centre for Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, The Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| |
Collapse
|
6
|
Zamudio-Vázquez R, Albericio F, Tulla-Puche J, Fox KR. Thioester Bonds of Thiocoraline Can Be Replaced with NMe-Amide Bridges without Affecting Its DNA-Binding Properties. ACS Med Chem Lett 2014; 5:45-50. [PMID: 24900772 DOI: 10.1021/ml400323x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/04/2013] [Indexed: 11/30/2022] Open
Abstract
In the search for new drug candidates for DNA recognition, affinity and sequence selectivity are two of the most important features. NMe-azathiocoraline, a synthetic antitumor bisintercalator derived from the natural marine product thiocoraline, shows similar potency to the parent compound, as well as possessing enhanced stability. Analysis of the DNA-binding selectivity of NMe-azathiocoraline by DNase I footprinting using universal substrates with all 136 tetranucleotides and all possible symmetrical hexanucleotide sequences revealed that, although this ligand binds to all CpG steps with lower affinities than thiocoraline, it displays additional binding to AT-rich sites. Moreover, fluorescence melting studies showed a strong interaction of the synthetic molecule with CACGTG and weaker binding to ACATGT and AGATCT. These findings demonstrate that NMe-azathiocoraline has the same mode of action as thiocoraline, mimicking its DNA-binding selectivity despite the substitution of its thioester bonds by NMe-amide bridges.
Collapse
Affiliation(s)
- Rubí Zamudio-Vázquez
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Organic
Chemistry, Faculty of Chemistry, University of Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
- School of Chemistry, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Keith R. Fox
- Centre for Biological Sciences, Life Sciences Building
85, University of Southampton, Southampton SO17 1BJ, U.K
| |
Collapse
|
7
|
Rackham BD, Howell LA, Round AN, Searcey M. Non-covalent duplex to duplex crosslinking of DNA in solution revealed by single molecule force spectroscopy. Org Biomol Chem 2013; 11:8340-7. [PMID: 24158749 DOI: 10.1039/c3ob42009d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Small molecules that interact with DNA, disrupting the binding of transcription factors or crosslinking DNA into larger structures, have significant potential as cancer therapies and in nanotechnology. Bisintercalators, including natural products such as echinomycin and rationally designed molecules such as the bis-9-aminoacridine-4-carboxamides, are key examples. There is little knowledge of the propensity of these molecules to crosslink duplex DNA. Here we use single molecule force spectroscopy to assay the crosslinking capabilities of bisintercalators. We show that bis-9-aminoacridine-4-carboxamides with both rigid and flexible linkers are able to crosslink duplex strands of DNA, and estimate the equilibrium free energy of a 9-aminoacridine-4-carboxamide bisintercalator from DNA at 5.03 kJ mol(-1). Unexpectedly, we find that echinomycin and its synthetic analogue TANDEM are capable of sequence-specific crosslinking of the terminal base pairs of two duplex DNA strands. In the crowded environment of the nucleosome, small molecules that crosslink neighbouring DNA strands may be expected to have significant effects on transcription, while a small molecule that facilitates sequence-specific blunt-end ligation of DNA may find applications in the developing field of DNA nanotechnology.
Collapse
Affiliation(s)
- Benjamin D Rackham
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | | | | | | |
Collapse
|
8
|
Rahman KM, Jackson PJM, James CH, Basu BP, Hartley JA, de la Fuente M, Schatzlein A, Robson M, Pedley RB, Pepper C, Fox KR, Howard PW, Thurston DE. GC-targeted C8-linked pyrrolobenzodiazepine-biaryl conjugates with femtomolar in vitro cytotoxicity and in vivo antitumor activity in mouse models. J Med Chem 2013; 56:2911-35. [PMID: 23514599 DOI: 10.1021/jm301882a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA binding 4-(1-methyl-1H-pyrrol-3-yl)benzenamine (MPB) building blocks have been developed that span two DNA base pairs with a strong preference for GC-rich DNA. They have been conjugated to a pyrrolo[2,1-c][1,4]benzodiazepine (PBD) molecule to produce C8-linked PBD-MPB hybrids that can stabilize GC-rich DNA by up to 13-fold compared to AT-rich DNA. Some have subpicomolar IC50 values in human tumor cell lines and in primary chronic lymphocytic leukemia cells, while being up to 6 orders less cytotoxic in the non-tumor cell line WI38, suggesting that key DNA sequences may be relevant targets in these ultrasensitive cancer cell lines. One conjugate, 7h (KMR-28-39), which has femtomolar activity in the breast cancer cell line MDA-MB-231, has significant dose-dependent antitumor activity in MDA-MB-231 (breast) and MIA PaCa-2 (pancreatic) human tumor xenograft mouse models with insignificant toxicity at therapeutic doses. Preliminary studies suggest that 7h may sterically inhibit interaction of the transcription factor NF-κB with its cognate DNA binding sequence.
Collapse
Affiliation(s)
- Khondaker M Rahman
- Department of Pharmacy, Institute of Pharmaceutical Sciences, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Khalaf AI, Bourdin C, Breen D, Donoghue G, Scott FJ, Suckling CJ, Macmillan D, Clements C, Fox K, Sekibo DAT. Design, synthesis and antibacterial activity of minor groove binders: the role of non-cationic tail groups. Eur J Med Chem 2012; 56:39-47. [PMID: 22948178 DOI: 10.1016/j.ejmech.2012.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/31/2012] [Accepted: 08/08/2012] [Indexed: 11/18/2022]
Abstract
The design and synthesis of a new class of minor groove binder (MGBs) in which, the cationic tail group has been replaced by a neutral, polar variant including cyanoguanidine, nitroalkene, and trifluoroacetamide groups. Antibacterial activity (against Gram positive bacteria) was found for both the nitroalkene and trifluoroacetamide groups. For the case of the nitroalkene tail group, strong binding of a minor groove binder containing this tail group was demonstrated by both DNA footprinting and melting temperature measurements, showing a correlation between DNA binding and antibacterial activity. The compounds have also been evaluated for binding to the hERG ion channel to determine whether non-cationic but polar substituents might have an advantage compared with conventional cationic tail groups in avoiding hERG binding. In this series of compounds, it was found that whilst non-cationic compounds generally had lower affinity to the hERG ion channel, all of the compounds studied bound weakly to the hERG ion channel, probably associated with the hydrophobic head groups.
Collapse
Affiliation(s)
- Abedawn I Khalaf
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Rahman KM, Rosado H, Moreira JB, Feuerbaum EA, Fox KR, Stecher E, Howard PW, Gregson SJ, James CH, de la Fuente M, Waldron DE, Thurston DE, Taylor PW. Antistaphylococcal activity of DNA-interactive pyrrolobenzodiazepine (PBD) dimers and PBD-biaryl conjugates. J Antimicrob Chemother 2012; 67:1683-96. [PMID: 22547662 PMCID: PMC3370821 DOI: 10.1093/jac/dks127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Objectives Pyrrolobenzodiazepine (PBD) dimers, tethered through inert propyldioxy or pentyldioxy linkers, possess potent bactericidal activity against a range of Gram-positive bacteria by virtue of their capacity to cross-link duplex DNA in sequence-selective fashion. Here we attempt to improve the antibacterial activity and cytotoxicity profile of PBD-containing conjugates by extension of dimer linkers and replacement of one PBD unit with phenyl-substituted or benzo-fused heterocycles that facilitate non-covalent interactions with duplex DNA. Methods DNase I footprinting was used to identify high-affinity DNA binding sites. A staphylococcal gene microarray was used to assess epidemic methicillin-resistant Staphylococcus aureus 16 phenotypes induced by PBD conjugates. Molecular dynamics simulations were employed to investigate the accommodation of compounds within the DNA helix. Results Increasing the length of the linker in PBD dimers led to a progressive reduction in antibacterial activity, but not in their cytotoxic capacity. Complex patterns of DNA binding were noted for extended PBD dimers. Modelling of DNA strand cross-linking by PBD dimers indicated distortion of the helix. A majority (26 of 43) of PBD-biaryl conjugates possessed potent antibacterial activity with little or no helical distortion and a more favourable cytotoxicity profile. Bactericidal activity of PBD-biaryl conjugates was determined by inability to excise covalently bound drug molecules from bacterial duplex DNA. Conclusions PBD-biaryl conjugates have a superior antibacterial profile compared with PBD dimers such as ELB-21. We have identified six PBD-biaryl conjugates as potential drug development candidates.
Collapse
|
11
|
Rosado H, Rahman KM, Feuerbaum EA, Hinds J, Thurston DE, Taylor PW. The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother 2011; 66:985-96. [PMID: 21393142 PMCID: PMC3073633 DOI: 10.1093/jac/dkr044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives The antistaphylococcal pyrrolobenzodiazepine dimer ELB-21 forms multiple adducts with duplex DNA through covalent interactions with appropriately spaced guanine residues; it is now known to form interstrand and intrastrand adducts with oligonucleotide sequences of variable length. We determined the DNA sequence preferences of ELB-21 in relation to its capacity to exert a bactericidal effect by damaging DNA. Methods Formation of adducts by ELB-21 and 12- to 14-mer DNA duplexes was investigated using ion-pair reversed phase liquid chromatography and mass spectrometry. Drug-induced changes in gene expression were measured in prophage-free Staphylococcus aureus RN4220 by microarray analysis. Results ELB-21 preferentially formed intrastrand adducts with guanines separated by three nucleotide base pairs. Interstrand and intrastrand adducts were formed with duplexes both longer and shorter than the preferred target sequences. ELB-21 elicited rapid bactericidal effects against prophage-carrying and prophage-free S. aureus strains; cell lysis occurred following activation and release of resident prophages. Killing appeared to be due to irreparable damage to bacterial DNA and susceptibility to ELB-21 was governed by the capacity of staphylococci to repair DNA lesions through induction of the SOS DNA damage response mediated by the RecA-LexA pathway. Conclusions The data support the contention that ELB-21 arrests DNA replication, eliciting formation of ssDNA-RecA filaments that inactivate LexA, the SOS repressor, and phage repressors such as Cl, resulting in activation of the DNA damage response and de-repression of resident prophages. Above the MIC threshold, DNA repair is ineffective.
Collapse
Affiliation(s)
- Helena Rosado
- School of Pharmacy, University of London, London, UK
| | | | | | | | | | | |
Collapse
|
12
|
Abstract
Footprinting is a method for determining the sequence selectivity of DNA-binding compounds in which ligands protect DNA from cleavage at their binding sites. Footprinting templates are typically 50-200 base pairs long, and DNase I is the most commonly used nuclease for these experiments. This chapter describes the preparation and labelling of suitable DNA footprinting substrates, the footprinting experiment itself, and the way in which these data can be used to estimate the dissociation constant of the interaction.
Collapse
Affiliation(s)
- Antonia S Cardew
- School of Biological Sciences, University of Southampton, Southampton, UK
| | | |
Collapse
|
13
|
Doyle M, Feuerbaum EA, Fox KR, Hinds J, Thurston DE, Taylor PW. Response of Staphylococcus aureus to subinhibitory concentrations of a sequence-selective, DNA minor groove cross-linking pyrrolobenzodiazepine dimer. J Antimicrob Chemother 2009; 64:949-59. [PMID: 19744983 PMCID: PMC2764867 DOI: 10.1093/jac/dkp325] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES ELB-21 is a pyrrolo[2,1-c][1,4]benzodiazepine dimer with potent antistaphylococcal activity; it binds covalently to guanine residues on opposing strands of duplex DNA, interfering with regulatory proteins and transcription elongation in a sequence-selective manner. Transcriptional and proteomic alterations induced by exposure of Staphylococcus aureus clinical isolate EMRSA-16 to ELB-21 were determined in order to define more precisely the bactericidal mechanism of the drug. METHODS DNase I footprinting was used to identify high-affinity DNA binding sites. Microarrays and gel electrophoresis were used to assess the ELB-21-induced phenotype. RESULTS High-affinity interstrand binding sites in which guanine residues were separated by 4 bp, and also some intrastrand cross-linking sites of variable length were identified. Exposure of EMRSA-16 to 0.015 mg/L ELB-21 elicited a 2-fold or greater up-regulation of 168 genes in logarithmic phase and 181 genes in stationary phase; the majority of genes affected were associated with resident prophages Sa2 and Sa3, pathogenicity island SaPI4 and DNA damage repair. ELB-21 induced a marked increase in the number of viable phage particles in culture supernatants. The expression of only a limited number of genes showed a >50% reduction. Sixteen extracellular and four intracellular proteins were differentially expressed during logarithmic and stationary phases, including RecA, proteins associated with staphylococcal pathogenesis (IsaA, CspA), cell division and wall synthesis. CONCLUSIONS ELB-21 kills S. aureus by forming multiple interstrand and intrastrand DNA cross-links, resulting in induction of the DNA damage response, derepression of resident prophages and modulation of a limited number of genes involved with cell wall synthesis.
Collapse
Affiliation(s)
- Marie Doyle
- School of Pharmacy, University of London, London WC1N 1AX UK
| | | | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK
| | - Jason Hinds
- Division of Cellular and Molecular Medicine, St. George’s, University of London, London SW17 0RE, UK
| | | | - Peter W. Taylor
- School of Pharmacy, University of London, London WC1N 1AX UK
| |
Collapse
|
14
|
Hampshire AJ, Rusling DA, Bryan S, Paumier D, Dawson SJ, Malkinson JP, Searcey M, Fox KR. DNA Binding by Analogues of the Bifunctional Intercalator TANDEM. Biochemistry 2008; 47:7900-6. [DOI: 10.1021/bi800573p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew J. Hampshire
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - David A. Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - Stephanie Bryan
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - David Paumier
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - Simon J. Dawson
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - John P. Malkinson
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - Mark Searcey
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K., Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29−39 Brunswick Square, London WC1N 1AX, U.K., and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk NR4 7TJ, U.K
| |
Collapse
|
15
|
Hampshire AJ, Fox KR. The effects of local DNA sequence on the interaction of ligands with their preferred binding sites. Biochimie 2008; 90:988-98. [DOI: 10.1016/j.biochi.2008.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022]
|