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Nandy JP, Prakesch M, Khadem S, Reddy PT, Sharma U, Arya P. Advances in Solution- and Solid-Phase Synthesis toward the Generation of Natural Product-like Libraries. Chem Rev 2009; 109:1999-2060. [DOI: 10.1021/cr800188v] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jyoti P. Nandy
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael Prakesch
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Shahriar Khadem
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - P. Thirupathi Reddy
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Utpal Sharma
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Prabhat Arya
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Ma Q, Akiyama Y, Xu Z, Konishi K, Hecht SM. Identification and Cleavage Site Analysis of DNA Sequences Bound Strongly by Bleomycin. J Am Chem Soc 2009; 131:2013-22. [DOI: 10.1021/ja808629s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Yoshitsugu Akiyama
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Zhidong Xu
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Kazuhide Konishi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Sidney M. Hecht
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
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Akiyama Y, Ma Q, Edgar E, Laikhter A, Hecht SM. A Novel DNA Hairpin Substrate for Bleomycin. Org Lett 2008; 10:2127-30. [DOI: 10.1021/ol800445x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yoshitsugu Akiyama
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Erin Edgar
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Andrei Laikhter
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Sidney M. Hecht
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
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Ma Q, Xu Z, Schroeder BR, Sun W, Wei F, Hashimoto S, Konishi K, Leitheiser CJ, Hecht SM. Biochemical evaluation of a 108-member deglycobleomycin library: viability of a selection strategy for identifying bleomycin analogues with altered properties. J Am Chem Soc 2007; 129:12439-52. [PMID: 17887752 DOI: 10.1021/ja0722729] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bleomycins (BLMs) are clinically used glycopeptide antitumor antibiotics that have been shown to mediate the sequence-selective oxidative damage of both DNA and RNA. Previously, we described the solid-phase synthesis of a library of 108 unique analogues of deglycoBLM A6, a congener that cleaves DNA analogously to BLM itself. Each member of the library was assayed for its ability to effect single- and double-strand nicking of duplex DNA, sequence-selective DNA cleavage, and RNA cleavage in the presence and absence of a metal ion cofactor. All of the analogues tested were found to mediate concentration-dependent plasmid DNA relaxation to some extent, and a number exhibited double-strand cleavage with an efficiency comparable to or greater than deglycoBLM A6. Further, some analogues having altered linker and metal-binding domains mediated altered sequence-selective cleavage, and a few were found to cleave a tRNA3Lys transcript both in the presence and in the absence of a metal cofactor. The results provide insights into structural elements within BLM that control DNA and RNA cleavage. The present study also permits inferences to be drawn regarding the practicality of a selection strategy for the solid-phase construction and evaluation of large libraries of BLM analogues having altered properties.
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Affiliation(s)
- Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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Cagir A, Tao ZF, Sucheck SJ, Hecht SM. Solid-phase synthesis and biochemical evaluation of conformationally constrained analogues of deglycobleomycin A5. Bioorg Med Chem 2003; 11:5179-87. [PMID: 14604681 DOI: 10.1016/j.bmc.2003.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Deglycobleomycin binds to and degrades the self-complementary oligonucleotide d(CGCTAGCG)(2) in a sequence selective fashion. A previous modeling study [J. Am. Chem. Soc. 120, (1998), 7450] had shown that, during binding to double stranded DNA, the conformation of the methylvalerate domain of deglycoBLM approximated that of S-proline. In the belief that an analogue of deglycoBLM structurally constrained to mimic the DNA-bound conformation might exhibit facilitated DNA binding and cleavage, an analogue of deglycoBLM was prepared in which the methylvalerate moiety was replaced by S-proline. This deglycoBLM analogue, as well as the related analogue containing R-proline, was synthesized on a TentaGel resin. Both of the analogues were found to be capable of binding Fe(2+) and activating O(2) for transfer to styrene. However, both deglycoBLM analogues exhibited diminished abilities to effect the relaxation of supercoiled plasmid DNA, and neither mediated sequence selective DNA cleavage.
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Affiliation(s)
- Ali Cagir
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22901, USA
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Rishel MJ, Thomas CJ, Tao ZF, Vialas C, Leitheiser CJ, Hecht SM. Conformationally constrained analogues of bleomycin A5. J Am Chem Soc 2003; 125:10194-205. [PMID: 12926941 DOI: 10.1021/ja030057w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bleomycin (BLM) group antitumor antibiotics are glycopeptide-derived natural products shown to cause sequence selective lesions in DNA. Prior studies have indicated that the linker region, composed of the methylvalerate and threonine residues, may be responsible for a conformational bend in the agent required for efficient DNA cleavage. We have synthesized a number of conformationally constrained methylvalerate analogues and incorporated them into deglycobleomycin A(5) congeners using our recently reported procedure for the solid phase construction of (deglyco)bleomycin and its analogues. These analogues were designed to probe the effects of conformational constraint of the native valerate moiety. Initial experiments indicated that the constrained molecules, none of which mimic the conformation proposed for the natural valerate linker, possessed DNA cleavage activity, albeit with potencies less than that of (deglyco)BLM and lacking sequence selectivity. Further experiments demonstrated that these analogues failed to produce alkali-labile lesions in DNA or sequence selective oxidative damage in RNA. However, two of the conformationally constrained deglycoBLM analogues were shown to mediate RNA cleavage in the absence of added Fe(2+). The ability of the analogues to mediate the oxygenation of small molecules was also assayed, and it was shown that they were as competent in the transfer of oxygen to low molecular weight substrates as the parent compound.
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Affiliation(s)
- Michael J Rishel
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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Leitheiser CJ, Smith KL, Rishel MJ, Hashimoto S, Konishi K, Thomas CJ, Li C, McCormick MM, Hecht SM. Solid-phase synthesis of bleomycin group antibiotics. Construction of a 108-member deglycobleomycin library. J Am Chem Soc 2003; 125:8218-27. [PMID: 12837092 DOI: 10.1021/ja021388w] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bleomycins (BLMs) are structurally related glycopeptide antibiotics isolated from Streptomyces verticillus that mediate the sequence-selective oxidative damage of DNA and RNA. Deglycobleomycin, which lacks the carbohydrate moiety, cleaves DNA analogously to bleomycin itself, albeit less potently, and has been used successfully for analyzing the functional domains of bleomycin. Although structural modifications to bleomycin and deglycobleomycin have been reported, no bleomycin or deglycobleomycin analogue having enhanced DNA cleavage activity has yet been described. The successful synthesis of a deglycobleomycin on a solid support has permitted the facile solid-phase synthesis of 108 unique deglycobleomycin analogues through parallel solid-phase synthesis. Each of the deglycobleomycin analogues was synthesized efficiently; the purity of each crude product was greater than 60%, as determined by HPLC integration. The solid-phase synthesis of the deglycobleomycin library provided near-milligram to milligram quantities of each deglycobleomycin, thereby permitting characterization by (1)H NMR and high-resolution mass spectrometry. Each analogue demonstrated supercoiled plasmid DNA relaxation above background cleavage; the library included two analogues that mediated plasmid relaxation to a greater extent than the parent deglycobleomycin molecule.
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Thomas CJ, Chizhov AO, Leitheiser CJ, Rishel MJ, Konishi K, Tao ZF, Hecht SM. Solid-phase synthesis of bleomycin A(5) and three monosaccharide analogues: exploring the role of the carbohydrate moiety in RNA cleavage. J Am Chem Soc 2002; 124:12926-7. [PMID: 12405801 DOI: 10.1021/ja0208916] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solid-phase synthesis of bleomycin A5 (BLM A5) and three monosaccharide analogues is presented. The monosaccharide analogues incorporated alpha-d-mannose, alpha-l-gulose, and alpha-l-rhamnose moieties in lieu of the disaccharide normally present in BLM A5. Also explored were the abilities of each of the monosaccharide congeners to cleave a 53-nt RNA. The elaboration of these carbohydrate-modified bleomycin analogues helps to define the role of the disaccharide moiety during the RNA cleavage event. The relatively facile solid-phase synthesis of bleomycin A5 and each of the carbohydrate analogues constitutes an important advance in the continuing mechanistic studies of bleomycin.
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Affiliation(s)
- Craig J Thomas
- Department of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA
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