1
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Procopiou G, Jackson PJM, di Mascio D, Auer JL, Pepper C, Rahman KM, Fox KR, Thurston DE. DNA sequence-selective G-A cross-linking ADC payloads for use in solid tumour therapies. Commun Biol 2022; 5:741. [PMID: 35906376 PMCID: PMC9338023 DOI: 10.1038/s42003-022-03633-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 06/24/2022] [Indexed: 11/11/2022] Open
Abstract
Antibody-Drug Conjugates (ADCs) are growing in importance for the treatment of both solid and haematological malignancies. There is a demand for new payloads with novel mechanisms of action that may offer enhanced therapeutic efficacy, especially in patients who develop resistance. We report here a class of Cyclopropabenzindole-Pyridinobenzodiazepine (CBI-PDD) DNA cross-linking payloads that simultaneously alkylate guanine (G) and adenine (A) bases in the DNA minor groove with a defined sequence selectivity. The lead payload, FGX8-46 (6), produces sequence-selective G-A cross-links and affords cytotoxicity in the low picomolar region across a panel of 11 human tumour cell lines. When conjugated to the antibody cetuximab at an average Drug-Antibody Ratio (DAR) of 2, an ADC is produced with significant antitumour activity at 1 mg/kg in a target-relevant human tumour xenograft mouse model with an unexpectedly high tolerability (i.e., no weight loss observed at doses as high as 45 mg/kg i.v., single dose). A class of Cyclopropabenzindole-Pyridinobenzodiazepine (CBI-PDD) DNA cross-linking payloads, used in Antibody-Drug Conjugates, alkylate guanine and adenine bases in the DNA minor groove with a defined sequence selectivity.
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Affiliation(s)
- George Procopiou
- Femtogenix, Lawes Open Innovation Hub, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Paul J M Jackson
- Femtogenix, Lawes Open Innovation Hub, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Daniella di Mascio
- School of Biological Sciences, Life Sciences Building B85, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
| | - Jennifer L Auer
- Femtogenix, Lawes Open Innovation Hub, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Chris Pepper
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Khondaker Miraz Rahman
- Femtogenix, Lawes Open Innovation Hub, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.,School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Keith R Fox
- School of Biological Sciences, Life Sciences Building B85, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
| | - David E Thurston
- Femtogenix, Lawes Open Innovation Hub, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK. .,School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
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2
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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.
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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.
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3
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Stephenson MJ, Howell LA, O'Connell MA, Fox KR, Adcock C, Kingston J, Sheldrake H, Pors K, Collingwood SP, Searcey M. Solid-Phase Synthesis of Duocarmycin Analogues and the Effect of C-Terminal Substitution on Biological Activity. J Org Chem 2015; 80:9454-67. [PMID: 26356089 DOI: 10.1021/acs.joc.5b01373] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The duocarmycins are potent antitumor agents with potential for use in the development of antibody-drug conjugates (ADCs) as well as being clinical candidates in their own right. In this article, we describe the synthesis of a duocarmycin monomer (DSA) that is suitably protected for utilization in solid-phase synthesis. The synthesis was performed on a large scale, and the resulting racemic protected Fmoc-DSA subunit was separated by supercritical fluid chromatography (SFC) into the single enantiomers; its application to solid-phase synthesis methodology gave a series of monomeric and extended duocarmycin analogues with amino acid substituents. The DNA sequence selectivity was similar to that in previous reports for both the monomeric and extended compounds. Substitution at the C-terminus of duocarmycin caused a decrease in antiproliferative activity for all of the compounds studied. An extended compound containing an alanine at the C-terminus was converted to the primary amide or to an extended structure containing a terminal tertiary amine, but this had no beneficial effects on biological activity.
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Affiliation(s)
| | | | | | - Keith R Fox
- Centre for Biological Sciences, University of Southampton , Life Sciences Building 85, Southampton SO17 1BJ, United Kingdom
| | - Claire Adcock
- Novartis Institutes for Biomedical Research, Novartis Pharmaceuticals UK Limited , Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex RH12 5AB, United Kingdom
| | - Jenny Kingston
- Novartis Institutes for Biomedical Research, Novartis Pharmaceuticals UK Limited , Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex RH12 5AB, United Kingdom
| | - Helen Sheldrake
- Institute for Cancer Therapeutics, University of Bradford , Bradford, West Yorkshire BD7 1DP, United Kingdom
| | - Klaus Pors
- Institute for Cancer Therapeutics, University of Bradford , Bradford, West Yorkshire BD7 1DP, United Kingdom
| | - Stephen P Collingwood
- Novartis Institutes for Biomedical Research, Novartis Pharmaceuticals UK Limited , Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex RH12 5AB, United Kingdom
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4
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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.
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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
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5
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Munde M, Kumar A, Nhili R, Depauw S, David-Cordonnier MH, Ismail MA, Stephens CE, Farahat AA, Batista-Parra A, Boykin DW, Wilson WD. DNA minor groove induced dimerization of heterocyclic cations: compound structure, binding affinity, and specificity for a TTAA site. J Mol Biol 2010; 402:847-64. [PMID: 20713062 DOI: 10.1016/j.jmb.2010.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 08/05/2010] [Accepted: 08/09/2010] [Indexed: 12/24/2022]
Abstract
With the increasing number and variations of genome sequences available, control of gene expression with synthetic, cell-permeable molecules is within reach. The variety of sequence-specific binding agents is, however, still quite limited. Many minor groove binding agents selectivity recognize AT over GC sequences but have less ability to distinguish among different AT sequences. The goal with this article is to develop compounds that can bind selectively to different AT sequences. A number of studies indicate that AATT and TTAA sequences have significantly different physical and interaction properties and different requirements for minor groove recognition. Although it has been difficult to get minor groove binding at TTAA, DB293, a phenyl-furan-benzimidazole diamidine, was found to bind as a strong, cooperative dimer at TTAA but with no selectivity over AATT. In order to improve selectivity, we made modifications to each unit of DB293. Binding affinities and stoichiometries obtained from biosensor-surface plasmon resonance experiments show that DB1003, a furan-furan-benzimidazole diamidine, binds strongly to TTAA as a dimer and has selectivity (K(TTAA)/K(AATT)=6). CD and DNase I footprinting studies confirmed the preference of this compound for TTAA. In summary, (i) a favorable stacking surface provided by the pi system, (ii) H-bond donors to interact with TA base pairs at the floor of the groove provided by a benzimidazole (or indole) -NH and amidines, and (iii) appropriate curvature of the dimer complex to match the curvature of the minor groove play important roles in differentiating the TTAA and AATT minor grooves.
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Affiliation(s)
- Manoj Munde
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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6
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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.
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Affiliation(s)
- Antonia S Cardew
- School of Biological Sciences, University of Southampton, Southampton, UK
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7
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Koketsu K, Oguri H, Watanabe K, Oikawa H. Enzymatic Macrolactonization in the Presence of DNA Leading to Triostin A Analogs. ACTA ACUST UNITED AC 2008; 15:818-28. [DOI: 10.1016/j.chembiol.2008.05.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 05/02/2008] [Accepted: 05/30/2008] [Indexed: 11/29/2022]
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8
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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
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9
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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]
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10
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Hampshire AJ, Fox KR. Preferred binding sites for the bifunctional intercalator TANDEM determined using DNA fragments that contain every symmetrical hexanucleotide sequence. Anal Biochem 2007; 374:298-303. [PMID: 17980140 DOI: 10.1016/j.ab.2007.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 10/04/2007] [Accepted: 10/07/2007] [Indexed: 11/19/2022]
Abstract
We have prepared novel DNA footprinting substrates that contain all 64 symmetrical hexanucleotide sequences. These were contained in two restriction fragments that were cloned into the pUC19 polylinker site; each fragment was also obtained in both orientations. These fragments were used to assess the sequence binding preferences of the synthetic quinoxaline antibiotic TANDEM. We found that, although the ligand binds to most TpA steps, the affinity is affected by the flanking sequences. The best binding sites contain the tetranucleotide sequence ATAT, although YATATR is a better site than RATATY. TTAA always is a poor binding site, especially TTTAAA. The binding to GTAC is strongly dependent on the flanking bases, with good binding to GGTACC but none at all to CGTACG.
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Affiliation(s)
- Andrew J Hampshire
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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11
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Negri A, Marco E, García-Hernández V, Domingo A, Llamas-Saiz AL, Porto-Sandá S, Riguera R, Laine W, David-Cordonnier MH, Bailly C, García-Fernández LF, Vaquero JJ, Gago F. Antitumor Activity, X-ray Crystal Structure, and DNA Binding Properties of Thiocoraline A, a Natural Bisintercalating Thiodepsipeptide. J Med Chem 2007; 50:3322-33. [PMID: 17571868 DOI: 10.1021/jm070381s] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine natural product thiocoraline A displayed approximately equal cytotoxic activity at nanomolar concentrations in a panel of 12 human cancer cell lines. X-ray diffraction analyses of orthorhombic crystals of this DNA-binding drug revealed arrays of docked pairs of staple-shaped molecules in which one pendent hydroxyquinoline chromophore from each cysteine-rich molecule appears intercalated between the two chromophores of a facing molecule. This arrangement is in contrast to the proposed mode of binding to DNA that shows the two drug chromophores clamping two stacked base pairs, in agreement with the nearest-neighbor exclusion principle. Proof of DNA sequence recognition was obtained from both classical DNase I footprinting experiments and determination of the melting temperatures of several custom-designed fluorescently labeled oligonucleotides. A rationale for the DNA-binding behavior was gained when models of thiocoraline clamping a central step embedded in several octanucleotides were built and studied by means of unrestrained molecular dynamics simulations in aqueous solution.
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Affiliation(s)
- Ana Negri
- Departamento de Farmacología, Universidad de AlcalA, E-28871 Madrid, Spain
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12
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Dawson S, Malkinson JP, Paumier D, Searcey M. Bisintercalator natural products with potential therapeutic applications: isolation, structure determination, synthetic and biological studies. Nat Prod Rep 2007; 24:109-26. [PMID: 17268609 DOI: 10.1039/b516347c] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Echinomycin is the prototypical bisintercalator, a molecule that binds to DNA by inserting two planar chromophores between the base-pairs of duplex DNA, placing its cyclic depsipeptide backbone in the minor groove. As such, it has been the focus of an extensive number of investigations into its biological activity, nucleic acid binding and, to some extent, its structure-activity relationships. However, echinomycin is also the parent member of an extended family of natural products that interact with DNA by a similar mechanism of bisintercalation. The structural variety in these compounds leads to changes in sequence selectivity and and biological activity, particularly as anti-tumour and anti-viral agents. One of the more recently identified marine natural products that is moving close to clinical development is thiocoraline, and it therefore seems timely to review the various bisintercalator natural products.
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Affiliation(s)
- Simon Dawson
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29-39 Brunswick Square, London, WC1N 1AX, UK
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13
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Hampshire AJ, Khairallah H, Khalaf AI, Ebrahimabadi AH, Waigh RD, Suckling CJ, Brown T, Fox KR. DNA sequence recognition by an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B). Bioorg Med Chem Lett 2006; 16:3469-74. [PMID: 16644214 DOI: 10.1016/j.bmcl.2006.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Accepted: 04/02/2006] [Indexed: 11/24/2022]
Abstract
We have used DNA footprinting and fluorescence melting experiments to study the sequence specific binding of an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B) to DNA. While the parent compound (thiazotropsin A) binds to the hexanucleotide sequence ACTAGT, changing one of the N-methylpyrrole groups to N-methylimidazole changes the preferred binding sequence to (A/T)CGCG(T/A). Experiments with DNA fragments that contain variants of this sequence suggest that the ligand can also bind, with lower affinity, to sequences which differ from this by 1bp in any position.
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Affiliation(s)
- Andrew J Hampshire
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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14
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Anderson JW, Fox KR, Niblo GA. A fast algorithm for the construction of universal footprinting templates in DNA. J Math Biol 2005; 52:307-42. [PMID: 16328479 DOI: 10.1007/s00285-005-0357-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 07/17/2005] [Indexed: 12/01/2022]
Abstract
We introduce and give a complete description of a new graph to be used for DNA sequencing questions. This graph has the advantage over the classical de Bruijn graph that it fully accounts for the double stranded nature of DNA, rather than dealing with single strands. Technically, our graph may be thought of as the quotient of the de Bruijn graph under the natural involution of sending a DNA strand to its complementary strand. However, this involution has fixed points, and this complicates the structure of the quotient graph which we have therefore modified herein. As an application and motivating example, we give an efficient algorithm for constructing universal footprinting templates for n-mers. This problem may be formulated as the task of finding a shortest possible segment of DNA which contains every possible sequence of base pairs of some fixed length n. Previous work by Kwan et al has attacked this problem from a numerical point of view and generated minimal length universal footprinting templates for n = 2, 3, 5, 7, together with unsubstantiated candidates for the case n = 4. We show that their candidates for n = 4 are indeed minimal length universal footprinting templates.
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Affiliation(s)
- James W Anderson
- School of Mathematics, University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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15
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Marco E, Negri A, Luque FJ, Gago F. Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations. Nucleic Acids Res 2005; 33:6214-24. [PMID: 16282585 PMCID: PMC1283521 DOI: 10.1093/nar/gki916] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The major structural determinant of the preference to bind to CpG binding sites on DNA exhibited by the natural quinoxaline bis-intercalators echinomycin and triostin A, or the quinoline echinomycin derivative, 2QN, is the 2-amino group of guanine (G). However, relocation of this group by means of introduction into the DNA molecule of the 2-aminoadenine (=2,6-diaminopurine, D) base in place of adenine (A) has been shown to lead to a drastic redistribution of binding sites, together with ultratight binding of 2QN to the sequence DTDT. Also, the demethylated triostin analogs, TANDEM and CysMeTANDEM, which bind with high affinity to TpA steps in natural DNA, bind much less tightly to CpI steps, despite the fact that both adenosine and the hypoxanthine-containing nucleoside, inosine (I), provide the same hydrogen bonding possibilities in the minor groove. To study both the increased binding affinity of 2QN for DTDT relative to GCGC sites and the remarkable loss of binding energy between CysMeTANDEM and ICIC compared with ATAT, a series of thermodynamic integration free energy simulations involving conversions between DNA base pairs have been performed. Our results demonstrate that the electrostatic component of the stacking interactions between the heteroaromatic rings of these compounds and the bases that make up the intercalation sites plays a very important role in the modulation of their binding affinities.
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Affiliation(s)
| | | | - F. Javier Luque
- Departamento de Fisicoquímica, Facultad de Farmacia, Universidad de BarcelonaE-08028 Barcelona, Spain
| | - Federico Gago
- To whom correspondence should be addressed. Tel: +34 918 854 514; Fax: +34 918 854 591;
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16
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Malkinson JP, Anim MK, Zloh M, Searcey M, Hampshire AJ, Fox KR. Efficient Solid-Phase-Based Total Synthesis of the Bisintercalator TANDEM. J Org Chem 2005; 70:7654-61. [PMID: 16149796 DOI: 10.1021/jo050959a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] In this article, the first solid-phase-based total synthesis of TANDEM, a synthetic analogue of triostin A, is described. In initial studies, the synthesis incorporated depsipeptide formation, introduction of chromophores, and disulfide bond formation on the solid phase, prior to a final solution-phase macrolactamization, to give the target molecule. Although pure TANDEM was obtained in an overall yield comparable to those for all syntheses to date, the yield of the final cyclization was low (11%). A more efficient approach involved removal from the solid phase prior to disulfide bond formation. The resulting linear peptide underwent macrolactamization under mild conditions and high dilution. Final disulfide bond formation was essentially quantitative and gave the target molecule, TANDEM, in an overall yield of 18%. The final compound was assessed for its ability to bind to 5'-TpA sequences on DNA by DNase I footprinting. This efficient synthesis sets the stage for a study of the structure-activity relationship of TANDEM and the natural product triostin A, with analogues containing "point mutations" at every site within the cyclic compounds.
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Affiliation(s)
- John P Malkinson
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, UK.
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17
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Urbach AR, Waring MJ. Visualising DNA: Footprinting and 1-2D Gels. MOLECULAR BIOSYSTEMS 2005; 1:287-93. [PMID: 16880993 DOI: 10.1039/b509471m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular recognition of DNA by natural and synthetic ligands has made enormous progress due in large part to the discovery and development of methods for separating DNA fragments by gel electrophoresis in one and two dimensions, and for characterizing DNA-ligand complexes by footprinting techniques.
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Affiliation(s)
- Adam R Urbach
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, TX 78212, USA.
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18
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Nguyen B, Hamelberg D, Bailly C, Colson P, Stanek J, Brun R, Neidle S, Wilson WD. Characterization of a novel DNA minor-groove complex. Biophys J 2004; 86:1028-41. [PMID: 14747338 PMCID: PMC1303896 DOI: 10.1016/s0006-3495(04)74178-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Many dicationic amidine compounds bind in the DNA minor groove and have excellent biological activity against a range of infectious diseases. Para-substituted aromatic diamidines such as furamidine, which is currently being tested against trypanosomiasis in humans, and berenil, which is used in animals, are typical examples of this class. Recently, a meta-substituted diamidine, CGP 40215A, has been found to have excellent antitrypanosomal activity. The compound has a linear, conjugated linking group that can be protonated under physiological conditions when the compound interacts with DNA. Structural and molecular dynamics analysis of the DNA complex indicated an unusual AT-specific complex that involved water-mediated H-bonds between one amidine of the compound and DNA bases at the floor of the minor groove. To investigate this unique system in more detail DNase I footprinting, surface plasmon resonance biosensor techniques, linear dichroism, circular dichroism, ultraviolet-visible spectroscopy, and additional molecular dynamics simulations have been conducted. Spectrophotometric titrations of CGP 40215A binding to poly(dAT)(2) have characteristics of DNA-binding-induced spectral changes as well as effects due to binding-induced protonation of the compound linker. Both footprinting and surface plasmon resonance results show that this compound has a high affinity for AT-rich sequences of DNA but very weak binding to GC sequences. The dissociation kinetics of the CGP 40215A-DNA complex are much slower than with similar diamidines such as berenil. The linear dichroism results support a minor-groove complex for the compound in AT DNA sequences. Molecular dynamics studies complement the structural analysis and provide a clear picture of the importance of water in mediating the dynamic interactions between the ligand and the DNA bases in the minor groove.
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Affiliation(s)
- Binh Nguyen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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19
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Fox KR, Webster R, Phelps RJ, Fokt I, Priebe W. Sequence selective binding of bis-daunorubicin WP631 to DNA. ACTA ACUST UNITED AC 2004; 271:3556-66. [PMID: 15317591 DOI: 10.1111/j.0014-2956.2004.04292.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have used footprinting techniques on a wide range of natural and synthetic footprinting substrates to examine the sequence-selective interaction of the bis-daunorubicin antibiotic WP631 with DNA. The ligand produces clear DNase I footprints that are very different from those seen with other anthracycline antibiotics such as daunorubicin and nogalamycin. Footprints are found in a diverse range of sequences, many of which are rich in GT (AC) or GA (TC) residues. As expected, the ligand binds well to the sequences CGTACG and CGATCG, but clear footprints are also found at hexanucleotide sequences such GCATGC and GCTAGC. The various footprints do not contain any particular unique di-, tri- or tetranucleotide sequences, but are frequently contain the sequence (G/C)(A/T)(A/T)(G/C). All sequences with this composition are protected by the ligand, though it can also bind to some sites that differ from this consensus by one base pair.
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Affiliation(s)
- Keith R Fox
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, UK.
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20
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James PL, Merkina EE, Khalaf AI, Suckling CJ, Waigh RD, Brown T, Fox KR. DNA sequence recognition by an isopropyl substituted thiazole polyamide. Nucleic Acids Res 2004; 32:3410-7. [PMID: 15247333 PMCID: PMC443542 DOI: 10.1093/nar/gkh666] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted thiazole polyamide, to DNA. In one fragment, which contains every tetranucleotide sequence, sub-micromolar concentrations of the ligand generate a single footprint at the sequence ACTAGT. This sequence preference is confirmed in melting experiments with fluorescently labelled oligonucleotides. Experiments with DNA fragments that contain variants of this sequence suggest that the ligand also binds, with slightly lower affinity, to sequences of the type XCYRGZ, where X is any base except C, and Z is any base except G.
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Affiliation(s)
- Peter L James
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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21
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Anthony NG, Fox KR, Johnston BF, Khalaf AI, Mackay SP, McGroarty IS, Parkinson JA, Skellern GG, Suckling CJ, Waigh RD. DNA binding of a short lexitropsin. Bioorg Med Chem Lett 2004; 14:1353-6. [PMID: 14980697 DOI: 10.1016/j.bmcl.2003.11.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Revised: 11/12/2003] [Accepted: 11/18/2003] [Indexed: 11/24/2022]
Abstract
Footprinting, capillary electrophoresis, molecular modelling and NMR studies have been used to examine the binding of a short polyamide to DNA. This molecule, which contains an isopropyl-substituted thiazole in place of one of the N-methylpyrroles, is selective for the sequence 5'-ACTAGT-3' to which it binds with high affinity. Two molecules bind side-by-side in the minor groove, but their binding is staggered so that the molecule reads six base pairs, unlike the related natural products, which tend to bind to four-base-pair sequences. The result suggests that high affinity and selectivity may be gained without resort to very large molecules, which may be difficult to deliver to the site of action.
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Affiliation(s)
- Nahoum G Anthony
- Department of Physiology and Pharmacology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO9 3TU, UK
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22
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Kwan AHY, Czolij R, Mackay JP, Crossley M. Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities. Nucleic Acids Res 2004; 31:e124. [PMID: 14530457 PMCID: PMC219492 DOI: 10.1093/nar/gng124] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rapid increase in the number of novel proteins identified in genome projects necessitates simple and rapid methods for assigning function. We describe a strategy for determining whether novel proteins possess typical sequence-specific DNA-binding activity. Many proteins bind recognition sequences of 5 bp or less. Given that there are 4(5) possible 5 bp sites, one might expect the length of sequence required to cover all possibilities would be 4(5) x 5 or 5120 nt. But by allowing overlaps, utilising both strands and using a computer algorithm to generate the minimum sequence, we find the length required is only 516 base pairs. We generated this sequence as six overlapping double-stranded oligonucleotides, termed pentaprobe, and used it in gel retardation experiments to assess DNA binding by both known and putative DNA-binding proteins from several protein families. We have confirmed binding by the zinc finger proteins BKLF, Eos and Pegasus, the Ets domain protein PU.1 and the treble clef N- and C-terminal fingers of GATA-1. We also showed that the N-terminal zinc finger domain of FOG-1 does not behave as a typical DNA-binding domain. Our results suggest that pentaprobe, and related sequences such as hexaprobe, represent useful tools for probing protein function.
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Affiliation(s)
- Ann H Y Kwan
- School of Molecular and Microbial Biosciences, G08, University of Sydney, NSW 2006, Australia
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23
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Tanious FA, Hamelberg D, Bailly C, Czarny A, Boykin DW, Wilson WD. DNA Sequence Dependent Monomer−Dimer Binding Modulation of Asymmetric Benzimidazole Derivatives. J Am Chem Soc 2004; 126:143-53. [PMID: 14709078 DOI: 10.1021/ja030403+] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A number of studies indicate that DNA sequences such as AATT and TTAA have significantly different physical and interaction properties. To probe these interaction differences in detail and determine the influence of charge, we have synthesized three bisbenzimidazole derivatives, a diamidine, DB185, and monoamidines, DB183 and DB210, that are related to the well-known minor groove agent, Hoechst 33258. Footprinting studies with several natural and designed DNA fragments indicate that the synthetic compounds bind at AT sequences in the minor groove and interact more weakly at sites with TpA steps relative to sites without such steps. Circular dichroism spectroscopy also indicates that the compounds bind in the DNA minor groove. Surprisingly, Tm studies as a function of ratio indicate that the monoamidines bind to TTAA sequences as dimers, whereas the diamidine binds as a monomer. Biosensor-surface plasmon resonance (SPR) studies allowed us to quantitate the interaction differences in more detail. SPR results clearly show that the monoamidine compounds bind to the TTAA sequence in a cooperative 2:1 complex but bind as monomers to AATT. The dication binds to both sequences in monomer complexes but the binding to AATT is significantly stronger than binding to TTAA. Molecular dynamics simulations indicate that the AATT sequence has a narrow time-average minor groove width that is a very good receptor site for the bisbenzimidazole compounds. The groove in TTAA sequences is wider and the width must be reduced to form a favorable monomer complex. The monocations thus form cooperative dimers that stack in an antiparallel orientation and closely fit the structure of the TTAA minor groove. The amidine groups in the dimer are oriented in the 5' direction of the strand to which they are closest. Charge repulsion in the dication apparently keeps it from forming the dimer. It instead reduces the TTAA groove width, in an induced fit process, sufficiently to form a minor groove complex. The dimer-binding mode of DB183 and DB210 is a new DNA recognition motif and offers novel design concepts for selective targeting of DNA sequences with a wider minor groove, including those with TpA steps.
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Affiliation(s)
- Farial A Tanious
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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Fox KR, Waring MJ. High-resolution footprinting studies of drug-DNA complexes using chemical and enzymatic probes. Methods Enzymol 2001; 340:412-30. [PMID: 11529207 DOI: 10.1016/s0076-6879(01)40434-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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