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Jarrad AM, Ang CW, Debnath A, Hahn HJ, Woods K, Tan L, Sykes ML, Jones AJ, Pelingon R, Butler MS, Avery VM, West NP, Karoli T, Blaskovich MAT, Cooper MA. Design, Synthesis, and Biological Evaluation of 2-Nitroimidazopyrazin-one/-es with Antitubercular and Antiparasitic Activity. J Med Chem 2018; 61:11349-11371. [PMID: 30468386 PMCID: PMC6311682 DOI: 10.1021/acs.jmedchem.8b01578] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tuberculosis and parasitic diseases, such as giardiasis, amebiasis, leishmaniasis, and trypanosomiasis, all urgently require improved treatment options. Recently, it has been shown that antitubercular bicyclic nitroimidazoles such as pretomanid and delamanid have potential as repurposed therapeutics for the treatment of visceral leishmaniasis. Here, we show that pretomanid also possesses potent activity against Giardia lamblia and Entamoeba histolytica, thus expanding the therapeutic potential of nitroimidazooxazines. Synthetic analogues with a novel nitroimidazopyrazin-one/-e bicyclic nitroimidazole chemotype were designed and synthesized, and structure-activity relationships were generated. Selected derivatives had potent antiparasitic and antitubercular activity while maintaining drug-like properties such as low cytotoxicity, good metabolic stability in liver microsomes and high apparent permeability across Caco-2 cells. The kinetic solubility of the new bicyclic derivatives varied and was found to be a key parameter for future optimization. Taken together, these results suggest that promising subclasses of bicyclic nitroimidazoles containing different core architectures have potential for further development.
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Affiliation(s)
| | | | - Anjan Debnath
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Hye Jee Hahn
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Kyra Woods
- Australian Infectious Diseases Research Centre , St. Lucia , Queensland 4067 Australia
| | - Lendl Tan
- Australian Infectious Diseases Research Centre , St. Lucia , Queensland 4067 Australia
| | - Melissa L Sykes
- Discovery Biology, Griffith Institute for Drug Discovery , Griffith University , Nathan , Queensland 4111 , Australia
| | - Amy J Jones
- Discovery Biology, Griffith Institute for Drug Discovery , Griffith University , Nathan , Queensland 4111 , Australia
| | | | - Mark S Butler
- Australian Infectious Diseases Research Centre , St. Lucia , Queensland 4067 Australia
| | - Vicky M Avery
- Discovery Biology, Griffith Institute for Drug Discovery , Griffith University , Nathan , Queensland 4111 , Australia
| | - Nicholas P West
- Australian Infectious Diseases Research Centre , St. Lucia , Queensland 4067 Australia
| | | | - Mark A T Blaskovich
- Australian Infectious Diseases Research Centre , St. Lucia , Queensland 4067 Australia
| | - Matthew A Cooper
- Australian Infectious Diseases Research Centre , St. Lucia , Queensland 4067 Australia
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Kolganova NA, Shchyolkina AK, Chudinov AV, Zasedatelev AS, Florentiev VL, Timofeev EN. Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides. Nucleic Acids Res 2012; 40:8175-85. [PMID: 22641847 PMCID: PMC3439883 DOI: 10.1093/nar/gks410] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/14/2022] Open
Abstract
Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.
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Affiliation(s)
| | | | | | | | | | - E. N. Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991, Russia
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Hari Y, Obika S, Imanishi T. Towards the Sequence-Selective Recognition of Double-Stranded DNA Containing Pyrimidine-Purine Interruptions by Triplex-Forming Oligonucleotides. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101821] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Malnuit V, Duca M, Benhida R. Targeting DNA base pair mismatch with artificial nucleobases. Advances and perspectives in triple helix strategy. Org Biomol Chem 2010; 9:326-36. [PMID: 21046036 DOI: 10.1039/c0ob00418a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review, divided into three sections, describes the contribution of the chemists' community to the development and application of triple helix strategy by using artificial nucleic acids, particularly for the recognition of DNA sequences incorporating base pair inversions. Firstly, the development of nucleobases that recognise CG inversion is surveyed followed secondly by specific recognition of TA inverted base pair. Finally, we point out in the last section recent perspectives and applications, driven from knowledge in nucleic acids interactions, in the growing field of nanotechnology and supramolecular chemistry at the border area of physics, chemistry and molecular biology.
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Affiliation(s)
- Vincent Malnuit
- Laboratoire de Chimie des Molécules Bioactives et des Arômes, LCMBA, UMR 6001, Institut de Chimie de Nice, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
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Ben Gaied N, Zhao Z, Gerrard SR, Fox KR, Brown T. Potent triple helix stabilization by 5',3'-modified triplex-forming oligonucleotides. Chembiochem 2009; 10:1839-51. [PMID: 19554592 DOI: 10.1002/cbic.200900232] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Anthraquinone and pyrene analogues attached to the 3' and/or 5' termini of triplex-forming oligonucleotides (TFOs) by various linkers increased the stability of parallel triple helices. The modifications are simple to synthesize and can be introduced during standard solid-phase oligonucleotide synthesis. Potent triplex stability was achieved by using doubly modified TFOs, which in the most favourable cases gave an increase in melting temperature of 30 degrees C over the unmodified counterparts and maintained their selectivity for the correct target duplex. Such TFOs can produce triplexes with melting temperatures of 40 degrees C at pH 7 even though they do not contain any triplex-stabilizing base analogues. These studies have implications for the design of triplex-forming oligonucleotides for use in biology and nanotechnology.
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Affiliation(s)
- Nouha Ben Gaied
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
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Rusling DA, Rachwal PA, Brown T, Fox KR. The stability of triplex DNA is affected by the stability of the underlying duplex. Biophys Chem 2009; 145:105-10. [PMID: 19819611 DOI: 10.1016/j.bpc.2009.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/16/2009] [Accepted: 09/16/2009] [Indexed: 11/16/2022]
Abstract
We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C(+).GC and T.AT triplets) at pH 5.0 the T(m) is more than 10 degrees C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the T(m) is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogues.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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Bergstrom DE. Unnatural nucleosides with unusual base pairing properties. ACTA ACUST UNITED AC 2009; Chapter 1:1.4.1-1.4.32. [PMID: 19488968 DOI: 10.1002/0471142700.nc0104s37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.
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Selective recognition of CG interruption by 2′,4′-BNA having 1-isoquinolone as a nucleobase in a pyrimidine motif triplex formation. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00728-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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