1
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Satange R, Chang CC, Li L, Lin SH, Neidle S, Hou MH. Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects. Nucleic Acids Res 2023; 51:3540-3555. [PMID: 36919604 PMCID: PMC10164580 DOI: 10.1093/nar/gkad156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Combination cancer chemotherapy is one of the most useful treatment methods to achieve a synergistic effect and reduce the toxicity of dosing with a single drug. Here, we use a combination of two well-established anticancer DNA intercalators, actinomycin D (ActD) and echinomycin (Echi), to screen their binding capabilities with DNA duplexes containing different mismatches embedded within Watson-Crick base-pairs. We have found that combining ActD and Echi preferentially stabilised thymine-related T:T mismatches. The enhanced stability of the DNA duplex-drug complexes is mainly due to the cooperative binding of the two drugs to the mismatch duplex, with many stacking interactions between the two different drug molecules. Since the repair of thymine-related mismatches is less efficient in mismatch repair (MMR)-deficient cancer cells, we have also demonstrated that the combination of ActD and Echi exhibits enhanced synergistic effects against MMR-deficient HCT116 cells and synergy is maintained in a MMR-related MLH1 gene knockdown in SW620 cells. We further accessed the clinical potential of the two-drug combination approach with a xenograft mouse model of a colorectal MMR-deficient cancer, which has resulted in a significant synergistic anti-tumour effect. The current study provides a novel approach for the development of combination chemotherapy for the treatment of cancers related to DNA-mismatches.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung402, Taiwan
| | - Chih-Chun Chang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung402, Taiwan
| | - Long‐Yuan Li
- Department of Life Sciences, National Chung Hsing University, Taichung402, Taiwan
| | - Sheng-Hao Lin
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Division of Chest Medicine, Changhua Christian Hospital, Changhua City, Taiwan
- Departement of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung402, Taiwan
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2
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Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH. Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism. Nucleic Acids Res 2022; 50:8867-8881. [PMID: 35871296 PMCID: PMC9410880 DOI: 10.1093/nar/gkac629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/24/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
The use of multiple drugs simultaneously targeting DNA is a promising strategy in cancer therapy for potentially overcoming single drug resistance. In support of this concept, we report that a combination of actinomycin D (ActD) and echinomycin (Echi), can interact in novel ways with native and mismatched DNA sequences, distinct from the structural effects produced by either drug alone. Changes in the former with GpC and CpG steps separated by a A:G or G:A mismatch or in a native DNA with canonical G:C and C:G base pairs, result in significant asymmetric backbone twists through staggered intercalation and base pair modulations. A wobble or Watson–Crick base pair at the two drug-binding interfaces can result in a single-stranded ‘chair-shaped’ DNA duplex with a straight helical axis. However, a novel sugar-edged hydrogen bonding geometry in the G:A mismatch leads to a ‘curved-shaped’ duplex. Two non-canonical G:C Hoogsteen base pairings produce a sharply kinked duplex in different forms and a four-way junction-like superstructure, respectively. Therefore, single base pair modulations on the two drug-binding interfaces could significantly affect global DNA structure. These structures thus provide a rationale for atypical DNA recognition via multiple DNA intercalators and a structural basis for the drugs’ potential synergetic use.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
| | - Shih-Hao Kao
- Institute of Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
| | - Ching-Ming Chien
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University , Taichung 402, Taiwan
| | - Chi-Chien Lin
- Institute of Biomedical Science, National Chung Hsing University , Taichung 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London , London WC1N 1AX, United Kingdom
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
- Institute of Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
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3
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Sagar S, Singh S, Mallareddy JR, Sonawane YA, Napoleon JV, Rana S, Contreras JI, Rajesh C, Ezell EL, Kizhake S, Garrison JC, Radhakrishnan P, Natarajan A. Structure activity relationship (SAR) study identifies a quinoxaline urea analog that modulates IKKβ phosphorylation for pancreatic cancer therapy. Eur J Med Chem 2021; 222:113579. [PMID: 34098465 PMCID: PMC8373685 DOI: 10.1016/j.ejmech.2021.113579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/19/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023]
Abstract
Genetic models validated Inhibitor of nuclear factor (NF) kappa B kinase beta (IKKβ) as a therapeutic target for KRAS mutation associated pancreatic cancer. Phosphorylation of the activation loop serine residues (S177, S181) in IKKβ is a key event that drives tumor necrosis factor (TNF) α induced NF-κB mediated gene expression. Here we conducted structure activity relationship (SAR) study to improve potency and oral bioavailability of a quinoxaline analog 13-197 that was previously reported as a NFκB inhibitor for pancreatic cancer therapy. The SAR led to the identification of a novel quinoxaline urea analog 84 that reduced the levels of p-IKKβ in dose- and time-dependent studies. When compared to 13-197, analog 84 was ∼2.5-fold more potent in TNFα-induced NFκB inhibition and ∼4-fold more potent in inhibiting pancreatic cancer cell growth. Analog 84 exhibited ∼4.3-fold greater exposure (AUC0-∞) resulting in ∼5.7-fold increase in oral bioavailability (%F) when compared to 13-197. Importantly, oral administration of 84 by itself and in combination of gemcitabine reduced p-IKKβ levels and inhibited pancreatic tumor growth in a xenograft model.
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Affiliation(s)
- Satish Sagar
- Eppley Institute for Cancer Research, Omaha, NE, USA
| | - Sarbjit Singh
- Eppley Institute for Cancer Research, Omaha, NE, USA
| | | | | | | | - Sandeep Rana
- Eppley Institute for Cancer Research, Omaha, NE, USA
| | | | | | | | | | | | - Prakash Radhakrishnan
- Eppley Institute for Cancer Research, Omaha, NE, USA; Department of Biochemistry and Molecular Biology, Omaha, NE, USA; Department of Genetics Cell Biology and Anatomy, Omaha, NE, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Amarnath Natarajan
- Eppley Institute for Cancer Research, Omaha, NE, USA; Department of Pharmaceutical Sciences, Omaha, NE, USA; Department of Genetics Cell Biology and Anatomy, Omaha, NE, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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4
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Laskowski T, Andrałojć W, Grynda J, Gwarda P, Mazerski J, Gdaniec Z. A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies. Sci Rep 2020; 10:11697. [PMID: 32678133 PMCID: PMC7366671 DOI: 10.1038/s41598-020-68609-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/29/2020] [Indexed: 11/09/2022] Open
Abstract
Triazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures of the d(CGATATCG)2:C-1305 and d(CCCTAGGG)2:C-1305 non-covalent adducts. In both cases, the ligand intercalates at the TA/TA site, forming well-defined dsDNA:drug 1:1 mol/mol complexes. Orientation of the ligand within the binding site was unambiguously established by the DNA/ligand proton-proton NOE contacts. A subsequent, NMR-driven study of the sequence-specificity of C-1305 using a series of DNA duplexes, allowed us to confirm a strong preference towards TA/TA dinucleotide steps, followed by the TG/CA steps. Interestingly, no interaction at all was observed with duplexes containing exclusively the AT/AT, GG/CC and GA/TC steps.
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Affiliation(s)
- Tomasz Laskowski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza Str. 11/12, 80-233, Gdańsk, Poland.
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego Str. 12/14, 61-704, Poznań, Poland.
| | - Jakub Grynda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza Str. 11/12, 80-233, Gdańsk, Poland
| | - Paulina Gwarda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza Str. 11/12, 80-233, Gdańsk, Poland
| | - Jan Mazerski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza Str. 11/12, 80-233, Gdańsk, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego Str. 12/14, 61-704, Poznań, Poland
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5
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Zarrouk A, Zarrok H, Ramli Y, Bouachrine M, Hammouti B, Sahibed-dine A, Bentiss F. Inhibitive properties, adsorption and theoretical study of 3,7-dimethyl-1-(prop-2-yn-1-yl)quinoxalin-2(1H)-one as efficient corrosion inhibitor for carbon steel in hydrochloric acid solution. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.07.046] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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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.
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Affiliation(s)
- Benjamin D Rackham
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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7
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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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8
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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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9
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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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10
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Mustaphi NEH, Ferfra S, Essassi EM, Garrigues B. Synthese Des 2,3-Di(Pyrazolyl, Isoxazolyl et 1,2,3-Triazolyl) Methylsulfanylquinoxalines. PHOSPHORUS SULFUR 2005. [DOI: 10.1080/104265090917727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- N. E. H. Mustaphi
- a Laboratoire de Chimie Organique Hétérocyclique, Université Mohamed V, Rabat , Maroc
| | - S. Ferfra
- a Laboratoire de Chimie Organique Hétérocyclique, Université Mohamed V, Rabat , Maroc
| | - E. M. Essassi
- a Laboratoire de Chimie Organique Hétérocyclique, Université Mohamed V, Rabat , Maroc
| | - B. Garrigues
- b Laboratoire d'Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier , France
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11
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2,3-Bifunctionalized Quinoxalines: Synthesis, DNA Interactions and Evaluation of Anticancer, Anti-tuberculosis and Antifungal Activity. Molecules 2002. [PMCID: PMC6146788 DOI: 10.3390/70800641] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A variety of 2,3-bifunctionalized quinoxalines (6-14) have been prepared by the condensation of 1,6-disubstituted-hexan-1,3,4,6-tetraones (1-4) with o-phenylenediamine, (R,R)-1,2-diaminocyclohexane and p-nitro-o-phenylenediamine. It is concluded that strong intramolecular N-H----O bonds in the favoured keto-enamine form may be responsible for the minimal biological activities observed in DNA footprinting, anti-tubercular, anti-fungal and anticancer tests with these hyper π-conjugated quinoxaline derivatives. However, subtle alteration by addition of a nitro group affecting the charge distribution confers significant improvements in biological effects and binding to DNA.
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12
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Castellano RK, Gramlich V, Diederich F. Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution. Chemistry 2002; 8:118-29. [PMID: 11822445 DOI: 10.1002/1521-3765(20020104)8:1<118::aid-chem118>3.0.co;2-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rebek imides (3), formed from Kemp's triacid, were developed in the mid-1980's as model receptors for adenine derivatives. We report here the first account of their hydrogen-bonding preferences upon binding 9-ethyladenine (1a) in the solid state. Structural analysis begins with simple imides 3a-e that form discrete dimers, while bis-imide 4 forms ribbon-like structures in the crystalline phase. The hydrogen-bonding interface within each of the representative assemblies features short intermolecular N(3)imide...O(8*)imide* distances (ca. 2.95 A), indicative of two-point hydrogen bonding. Imides 3f-h could be co-crystallized with 1a; single-crystal X-ray analysis of the resulting complexes reveals hydrogen-bonding geometries nearly identical to those observed in nucleobase complexes of adenine and pyrimidine derivatives. Imides 3f and 3g form 2:1 ternary assemblies with 1a; the complex of the former, (3f)2 x 1a, displays both Watson-Crick- and Hoogsteen-type hydrogen bonding, whereas the complex of the latter, (3g)2 x 1a, shows the Hoogsteen motif and imide hydrogen bonding to N(3) of the purine base (N(3)adenine...N(3'')imide = 3.07(1) A). Imide 3h forms a 1:1 complex with 1a (3h x 1a x CHCl3) and displays Hoogsteen binding exclusively. All of the 3 x 1a assemblies show C(adenine)...O(imide) distances (3.38-3.75 A) that are consistent with C-H...O hydrogen bonding. Base-pairing preferences for the Rebek imides are further explored in solution by 1H NMR one-dimensional NOE experiments and by computational means; in all cases the Hoogsteen motif is modestly favored relative to its Watson-Crick counterpart.
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13
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Lavesa M, Fox KR. Preferred binding sites for [N-MeCYs(3), N-MeCys(7)]TANDEM determined using a universal footprinting substrate. Anal Biochem 2001; 293:246-50. [PMID: 11399039 DOI: 10.1006/abio.2001.5124] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have prepared a novel footprinting substrate which contains all 136 tetranucleotide sequences and have used this to determine the preferred binding sites for the synthetic quinoxaline antibiotic [N-MeCys(3),N-MeCys(7)]TANDEM. We find that, although the ligand binds to all TpA steps, it binds best to the tetranucleotide sequence ATAT and shows only weak interaction with TTAA and GTAC. The best binding sites contain the sequences ATAX and XTAT.
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Affiliation(s)
- M Lavesa
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, United Kingdom
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14
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Boger DL, Lee JK. Development of a solution-phase synthesis of minor groove binding bis-intercalators based on triostin A suitable for combinatorial synthesis. J Org Chem 2000; 65:5996-6000. [PMID: 10987932 DOI: 10.1021/jo000382r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a solution phase synthesis of azatriostin A (2) suitable for the preparation of combinatorial libraries enlisting only liquid-liquid acid/base extractions for the isolation and purification of all intermediates and the final product is disclosed.
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Affiliation(s)
- D L Boger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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15
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Abstract
The DNA-binding properties of many ligands can be rationalized on the basis of their structural and electronic complementarity with the functional groups present in the minor and major grooves of particular DNA sequences. Specific hydrogen bonding patterns are particularly useful for the purpose of sequence recognition. Less obvious, however, is the influence of base composition on the conformational preferences of individual base steps and on the binding of intercalating moieties which become sandwiched between contiguous base pairs. Improved knowledge of stacking interactions may lead to a better understanding of the architecture and inherent flexibility of particular DNA sequences and may provide insight into the principles that dictate the structural changes and specificity patterns observed in the binding of some intercalating ligands to DNA.
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Affiliation(s)
- F Gago
- Departamento de Farmacología, Universidad de Alcalá, Madrid, Spain
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16
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Jennewein S, Waring MJ. Footprinting of echinomycin and actinomycin D on DNA molecules asymmetrically substituted with inosine and/or 2,6-diaminopurine. Nucleic Acids Res 1997; 25:1502-10. [PMID: 9092655 PMCID: PMC146638 DOI: 10.1093/nar/25.8.1502] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In order to clarify the role of the purine 2-amino group in the recognition of DNA by small molecules we have examined the binding of actinomycin D and echinomycin to artificial DNA molecules asymmetrically substituted with inosine and/or 2,6-diaminopurine (DAP) in one of the complementary strands. These DNAs, prepared by a method based upon PCR, present various potential sites for antibiotic binding, including several containing only a single purine 2-amino group in different configurations. The results show unambiguously that the presence of two 2-amino groups is mandatory for binding of actinomycin D to double-stranded DNA. In the case of echinomycin only one purine 2-amino group is required for remarkably strong binding to the asymmetric TpDAP.TpA dinucleotide step, but the CpDAP.TpI step (which also contains only a single purine-2 amino group) does not afford a binding site. Evidently, removing a 2-amino group (G-->I substitution) is dominant over adding one (A-->DAP substitution). No sequences containing just a single guanine residue are acceptable. The possibility is raised that replacing guanosine with inosine may do more than remove a group endowed with hydrogen bonding capability and interfere with ligand binding in other ways. The new methodology developed to construct asymmetrically substituted DNA substrates for this work provides a novel strategy that should be generally applicable for studying ligand-DNA interactions, beyond the specific interest in drug binding to DNA, and may help to elucidate how proteins and oligonucleotides recognize their target sites.
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Affiliation(s)
- S Jennewein
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
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