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Tadesse K, Benhamou RI. Targeting MicroRNAs with Small Molecules. Noncoding RNA 2024; 10:17. [PMID: 38525736 PMCID: PMC10961812 DOI: 10.3390/ncrna10020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024] Open
Abstract
MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the identification of small molecules capable of selectively targeting specific disease-associated miRs. This understanding paves the way for developing small molecules that can modulate the activity of disease-associated miRs. Herein, we discuss the progress made in the field of drug discovery processes, transforming the landscape of miR-targeted therapeutics by small molecules. By leveraging various approaches, researchers can systematically identify compounds to modulate miR function, providing a more potent intervention either by inhibiting or degrading miRs. The implementation of these multidisciplinary approaches bears the potential to revolutionize treatments for diverse diseases, signifying a significant stride towards the targeting of miRs by precision medicine.
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Affiliation(s)
| | - Raphael I. Benhamou
- The Institute for Drug Research of the School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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2
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Stokowa-Sołtys K, Kasprowicz A, Wrzesiński J, Ciesiołka J, Gaggelli N, Gaggelli E, Valensin G, Jeżowska-Bojczuk M. Impact of Cu(2+) ions on the structure of colistin and cell-free system nucleic acid degradation. J Inorg Biochem 2015; 151:67-74. [PMID: 26028475 DOI: 10.1016/j.jinorgbio.2015.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 01/06/2023]
Abstract
Colistin and transition metal ions are commonly used as feed additives for livestock animals. This work presents the results of an analysis of combined potentiometric and spectroscopic (UV-vis, EPR, CD, NMR) data which lead to conclude that colistin is able to effectively chelate copper(II) ions. In cell-free system the oxidative activity of the complex manifests itself in the plasmid DNA destruction with simultaneous generation of reactive OH species, when accompanied by hydrogen peroxide or ascorbic acid. The degradation of RNA occurs most likely via a hydrolytic mechanism not only for complexed compound but also colistin alone. Therefore, huge amounts of the used antibiotic for nontherapeutic purposes might have a potential influence on livestock health.
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Affiliation(s)
- Kamila Stokowa-Sołtys
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Aleksandra Kasprowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jan Wrzesiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jerzy Ciesiołka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Nicola Gaggelli
- Department of Biotechnology, Chemistry and Pharmacy Via Aldo Moro, 2-53100 Siena, Italy
| | - Elena Gaggelli
- Department of Biotechnology, Chemistry and Pharmacy Via Aldo Moro, 2-53100 Siena, Italy
| | - Gianni Valensin
- Department of Biotechnology, Chemistry and Pharmacy Via Aldo Moro, 2-53100 Siena, Italy
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3
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Ciesiołka J, Jeżowska-Bojczuk M, Wrzesiński J, Stokowa-Sołtys K, Nagaj J, Kasprowicz A, Błaszczyk L, Szczepanik W. Antibiotic bacitracin induces hydrolytic degradation of nucleic acids. Biochim Biophys Acta Gen Subj 2014; 1840:1782-9. [DOI: 10.1016/j.bbagen.2014.01.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/16/2014] [Accepted: 01/29/2014] [Indexed: 10/25/2022]
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4
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Liu W, Zhang Y, Zhang X, He X, Zhang X, Chen J. Amplified impedimetric DNA sensor based on graphene oxide–phenylboronic acid for sensitive detection of bleomycins. NEW J CHEM 2014. [DOI: 10.1039/c3nj01614e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
This is a review of RNA as a target for small molecules (ribosomes, riboswitches, regulatory RNAs) and RNA-derived oligonucleotides as tools (antisense/small interfering RNA, ribozymes, aptamers/decoy RNA and microRNA). This review highlights the present state of research using RNA as a drug target or as a potential drug candidate and explains at which stage and to what extent rational design could eventually be involved. Special attention has been paid to the recent potential clinical applications of RNA either as drugs or drug targets. The review deals mainly with mechanistic approaches rather than with physicochemical or computational aspects of RNA-based drug design.
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Affiliation(s)
- Irene M Lagoja
- Katholieke Universiteit Leuven, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium +32 16 337396 ; +32 16 337340 ;
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Bozeman TC, Nanjunda R, Tang C, Liu Y, Segerman ZJ, Zaleski PA, Wilson WD, Hecht SM. Dynamics of bleomycin interaction with a strongly bound hairpin DNA substrate, and implications for cleavage of the bound DNA. J Am Chem Soc 2012; 134:17842-5. [PMID: 23072568 PMCID: PMC3840713 DOI: 10.1021/ja306233e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.
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Affiliation(s)
- Trevor C. Bozeman
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Chenhong Tang
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zachary J. Segerman
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul A. Zaleski
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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7
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Giroux RA, Hecht SM. Characterization of Bleomycin Cleavage Sites in Strongly Bound Hairpin DNAs. J Am Chem Soc 2010; 132:16987-96. [DOI: 10.1021/ja107228c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rachel A. Giroux
- Center for BioEnergetics, Biodesign Institute and Department of Chemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute and Department of Chemistry, Arizona State University, Tempe, Arizona 85287, United States
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8
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Yin BC, Wu D, Ye BC. Sensitive DNA-Based Electrochemical Strategy for Trace Bleomycin Detection. Anal Chem 2010; 82:8272-7. [DOI: 10.1021/ac101761q] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin-Cheng Yin
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Di Wu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
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Pavlova AS, Vorob'ev PE, Zarytova VF. [Direct site-specific cleavage of double-stranded DNA by conjugates of bleomycin A5 with triplex-forming oligonucleotide]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:215-25. [PMID: 19537173 DOI: 10.1134/s1068162009020083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Monofunctional conjugates of 15-mer triplex-forming oligonucleotide (TFO) with covalently attached bleomycin A5 residue at the 5'-end (Blm-p15) were synthesized. Bifunctional conjugates of TFO containing, in addition to Blm, the residues of intercalator 6-chloro-2-methoxy-9-aminoacridine (Acr) or (N-(2-hydroxyethyl)phenazinium (Phn) were obtained for the first time. The Acr and Phn residues were attached to the 3'-phosphate group of TFO through L1 and L2 linkers, respectively, resulting in the compounds Blm-p15pL1-Acr and Blm-p15pL2-Phn. The values of dissociation constants of the corresponding triplexes were evaluated using the gel retardation method. The Acr residue in Blm-p15pL1-Acr was shown to enhance the stability of the formed triplex by one order of magnitude. It was demonstrated that all synthesized conjugates are capable of specifically and nonspecifically damaging a target DNA, forming direct breaks and alkaline-labile sites. The extent of the specific cleavage of the target DNA was 15% in the case of a fivefold excess of the conjugates over the DNA duplex. The site-specific triplex-mediated cleavage of a target DNA was shown for the first time to occur predominantly (> 90%) with the formation of the direct breaks of both DNA strands. The results show the availability of bleomycin-containing oligonucleotides as antigene compounds.
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10
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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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11
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Ansari KI, Grant JD, Woldemariam GA, Kasiri S, Mandal SS. Iron(III)-salen complexes with less DNA cleavage activity exhibit more efficient apoptosis in MCF7 cells. Org Biomol Chem 2009; 7:926-32. [PMID: 19225676 DOI: 10.1039/b816858j] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand the relationship between DNA damage potential and biochemical activities, we synthesized nine different Fe(III)-salen derivatives with varying substituents, and analyzed their in vitro DNA cleavage properties and biochemical effects on cultured human cells. Our results demonstrated that Fe(III)-salen complexes affect cell viability, induce nuclear fragmentation, and activate caspases and apoptosis in cultured human cells. The nature and the position of the substituents in the Fe(III)-salen complexes play critical roles in determining their apoptotic efficiencies. Most importantly, our results demonstrated that the in vitro DNA cleavage activities of Fe(III)-salen complexes are not essential for their apoptotic activities in human cells. Instead, the lesser their DNA cleavage activity the greater is their apoptotic efficiency.
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Affiliation(s)
- Khairul I Ansari
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA
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12
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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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13
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Rakić B, Brûlotte M, Rouleau Y, Bélanger S, Pezacki JP. Bleomycin is a potent small-molecule inhibitor of hepatitis C virus replication. Chembiochem 2006; 7:1330-3. [PMID: 16888741 DOI: 10.1002/cbic.200600180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bojana Rakić
- The Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, K1A 0R6, Canada
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14
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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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15
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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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16
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Ramotar D, Wang H. Protective mechanisms against the antitumor agent bleomycin: lessons from Saccharomyces cerevisiae. Curr Genet 2003; 43:213-24. [PMID: 12698269 DOI: 10.1007/s00294-003-0396-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2003] [Revised: 03/17/2003] [Accepted: 03/18/2003] [Indexed: 10/26/2022]
Abstract
Bleomycin is a small glycopeptide antibiotic used in combination therapy for the treatment of a few types of human cancer. The antitumor effect of bleomycin is most likely caused by its ability to bind to DNA and induce the formation of toxic DNA lesions via a free radical reactive (Fe.bleomycin) complex. However, the chemotherapeutic potential of bleomycin is limited, as it causes pulmonary fibrosis and tumor resistance at high doses. The chemical structure and modes of action of bleomycin have been extensively studied and these provide a foundation towards improving the therapeutic value of the drug. This review provides a first account of the current state of knowledge of the cellular processes that can allow the yeast Saccharomyces cerevisiae to evade the lethal effects of bleomycin. This model organism is likely to provide rapid clues in our understanding of bleomycin resistance in tumor cells.
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Affiliation(s)
- Dindial Ramotar
- Maisonneuve-Rosemont Hospital, Guy-Bernier Research Center, 5415 Boulevard de l'Assomption, H1T 2M4, Montreal, Quebec, Canada.
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Zou Y, Fahmi NE, Vialas C, Miller GM, Hecht SM. Total synthesis of deamido bleomycin a(2), the major catabolite of the antitumor agent bleomycin. J Am Chem Soc 2002; 124:9476-88. [PMID: 12167044 DOI: 10.1021/ja012741l] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic inactivation of the antitumor antibiotic bleomycin is believed to be mediated exclusively via the action of bleomycin hydrolase, a cysteine proteinase that is widely distributed in nature. While the spectrum of antitumor activity exhibited by the bleomycins is believed to reflect the anatomical distribution of bleomycin hydrolase within the host, little has been done to characterize the product of the putative inactivation at a chemical or biochemical level. The present report describes the synthesis of deamidobleomycin demethyl A(2) (3) and deamido bleomycin A(2) (4), as well as the respective aglycones. These compounds were all accessible via the key intermediate N(alpha)-Boc-N(beta)-[1-amino-3(S)-(4-amino-6-carboxy-5-methylpyrimidin-2-yl)propion-3-yl]-(S)-beta-aminoalanine tert-butyl ester (16). Synthetic deamido bleomycin A(2) was shown to be identical to the product formed by treatment of bleomycin A(2) with human bleomycin hydrolase, as judged by reversed-phase HPLC analysis and (1)H NMR spectroscopy. Deamido bleomycin A(2) was found to retain significant DNA cleavage activity in DNA plasmid relaxation assays and had the same sequence selectivity of DNA cleavage as bleomycin A(2). The most significant alteration of function noted in this study was a reduction in the ability of deamido bleomycin A(2) to mediate double-strand DNA cleavage, relative to that produced by BLM A(2).
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Affiliation(s)
- Ying Zou
- Contribution from the Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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18
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Thomas CJ, McCormick MM, Vialas C, Tao ZF, Leitheiser CJ, Rishel MJ, Wu X, Hecht SM. Alteration of the selectivity of DNA cleavage by a deglycobleomycin analogue containing a trithiazole moiety. J Am Chem Soc 2002; 124:3875-84. [PMID: 11942824 DOI: 10.1021/ja011820u] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bleomycin (BLM) group of antitumor antibiotics effects DNA cleavage in a sequence-selective manner. Previous studies have indicated that the metal-binding and bithiazole moieties of BLM are both involved in the binding of BLM to DNA. The metal-binding domain is normally the predominant structural element in determining the sequence selectivity of DNA binding, but it has been shown that replacement of the bithiazole moiety with a strong DNA binder can alter the sequence selectivity of DNA binding and cleavage. To further explore the mechanism by which BLM and DNA interact, a trithiazole-containing deglycoBLM analogue was synthesized and tested for its ability to relax supercoiled DNA and cleave linear duplex DNA in a sequence-selective fashion. Also studied was cleavage of a novel RNA substrate. Solid-phase synthesis of the trithiazole deglycoBLM A(5) analogue was achieved using a TentaGel resin containing a Dde linker and elaborated from five key intermediates. The ability of the resulting BLM analogue to relax supercoiled DNA was largely unaffected by introduction of the additional thiazole moiety. Remarkably, while no new sites of DNA cleavage were observed for this analogue, there was a strong preference for cleavage at two 5'-GT-3' sites when a 5'-(32)P end-labeled DNA duplex was used as a substrate. The alteration of sequence selectivity of cleavage was accompanied by some decrease in the potency of DNA cleavage, albeit without a dramatic diminution. In common with BLM, the trithiazole analogue of deglycoBLM A(5) effected both hydrolytic cleavage of RNA in the absence of added metal ion and oxidative cleavage in the presence of Fe(2+) and O(2). In comparison with BLM A(5), the relative efficiencies of hydrolytic cleavage at individual sites were altered.
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Affiliation(s)
- Craig J Thomas
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
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Smith KL, Tao ZF, Hashimoto S, Leitheiser CJ, Wu X, Hecht SM. Deglycobleomycin: solid-phase synthesis and DNA cleavage by the resin-bound ligand. Org Lett 2002; 4:1079-82. [PMID: 11922787 DOI: 10.1021/ol010293g] [Citation(s) in RCA: 17] [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
[structure: see text] A greatly improved solid-phase synthesis of deglycobleomycin using a Dde-based linker is reported. The resin-bound deglycobleomycin could be completely deblocked and assayed for DNA plasmid relaxation, sequence-selective DNA cleavage, and light production from a molecular beacon.
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Affiliation(s)
- Kenneth L Smith
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA
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Davis TM, Wilson WD. Surface plasmon resonance biosensor analysis of RNA-small molecule interactions. Methods Enzymol 2001; 340:22-51. [PMID: 11494851 DOI: 10.1016/s0076-6879(01)40416-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- T M Davis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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21
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Affiliation(s)
- S Hashimoto
- Departments of Chemistry and Biology University of Virginia, Charlottesville, Virginia 22901, USA
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Choudhury AK, Tao ZF, Hecht SM. Synthesis and DNA cleavage activity of a novel bleomycin A(5) glycoconjugate. Org Lett 2001; 3:1291-4. [PMID: 11348217 DOI: 10.1021/ol010015h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure in text] To explore the possibility of modifying bleomycin in a fashion that could alter its physiological distribution in a therapeutic setting, a new analogue of bleomycin has been prepared. This analogue is intended to target the asialoglycoprotein receptor on liver cells. Critically, despite the large C-substituent, the bleomycin conjugate was found to degrade DNA in the same fashion as bleomycin A(5) itself, and with only modestly decreased efficiency.
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Affiliation(s)
- A K Choudhury
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
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Abraham AT, Zhou X, Hecht SM. Metallobleomycin-mediated cleavage of DNA not involving a threading-intercalation mechanism. J Am Chem Soc 2001; 123:5167-75. [PMID: 11457377 DOI: 10.1021/ja002460y] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA cleavage properties of metallobleomycins conjugated to three solid supports were investigated using plasmid DNA, relaxed covalently closed circular DNA, and linear duplex DNA as substrates. Cleavage of pBR322 and pSP64 plasmid DNAs by Fe(II).BLM A(5)-CPG-C(2) was observed with efficiencies not dissimilar to that obtained using free Fe(II).BLM A(5). Similar results were observed following Fe(II).BLM A(5)-CPG-C(2)-mediated cleavage of a relaxed plasmid, a substrate that lacks ends or negative supercoiling capable of facilitating strand separation. BLMs covalently tethered to solid supports, including Fe(II).BLM A(5)-Sepharose 4B, Fe(II).BLM A(5)-CPG-C(6), and Fe(II).BLM A(5)-CPG-C(2), cleaved a 5'-(32)P end labeled linear DNA duplex with a sequence selectivity identical to that of free Fe(II).BLM A(5); cleavage predominated at 5'-G(82)T(83)-3' and 5'-G(84)T(85)-3'. To verify that these results could also be obtained using other metallobleomycins, supercoiled plasmid DNA and a linear DNA duplex were employed as substrates for Co(III).BLM A(5)-CPG-C(2). Free green Co(III).BLM A(5) was only about 2-fold more efficient than green Co(III).BLM A(5)-CPG-C(2) in effecting DNA cleavage. A similar result was obtained using Cu(II).BLM A(5)-CPG-C(2) + dithiothreitol. In addition, the conjugated Co.BLM A(5) and Cu.BLM A(5) cleaved the linear duplex DNA with a sequence selectivity identical to that of the respective free metalloBLMs. Interestingly, when supercoiled plasmid DNA was used as a substrate, conjugated Fe.BLM A(5) and Co.BLM A(5) were both found to produce Form III DNA in addition to Form II DNA. The formation of Form III DNA by conjugated Fe.BLM A(5) was assessed quantitatively. When corrected for differences in the intrinsic efficiencies of DNA cleavage by conjugated vs free BLMs, conjugated Fe.BLM A(5) was found to produce Form III DNA to about the same extent as the respective free Fe.BLM A(5), arguing that this conjugated BLM can also effect double-strand cleavage of DNA. Although previous evidence supporting DNA intercalation by some metallobleomycins is convincing, the present evidence indicates that threading intercalation is not a requirement for DNA cleavage by Fe(II).BLM A(5), Co(III).BLM A(5), or Cu(I).BLM A(5).
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Affiliation(s)
- A T Abraham
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA
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Leitheiser CJ, Rishel MJ, Wu X, Hecht SM. Solid-phase synthesis of bleomycin group antibiotics. Elaboration of deglycobleomycin A(5). Org Lett 2000; 2:3397-9. [PMID: 11029220 DOI: 10.1021/ol0002469] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solid-phase syntheses of two deglycobleomycin A(5) analogues were achieved using a commercially available polystyrene resin containing triphenylmethyl-linked spermidine. The final products were deblocked and released from the resin, analyzed, and purified by C(18) reversed phase HPLC and characterized by high-field (1)H NMR spectroscopy and mass spectrometry. The purified products relaxed supercoiled plasmid DNA in a concentration-dependent fashion and to the same extent as authentic material derived from natural BLM A(5).
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Affiliation(s)
- C J Leitheiser
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA
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Hecht SM. Bleomycin: new perspectives on the mechanism of action. JOURNAL OF NATURAL PRODUCTS 2000; 63:158-168. [PMID: 10650103 DOI: 10.1021/np990549f] [Citation(s) in RCA: 411] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The bleomycin group antitumor antibiotics have long been of interest as a consequence of their efficacy in the treatment of certain tumors, not to mention their unique structures and properties in mediating dioxygen activation and sequence selective degradation of DNA. At a chemical level, the structure originally assigned to bleomycin was subsequently reassigned and the new structure has been confirmed by total synthesis. Through the elaboration of structurally modified bleomycin congeners and fragments, synthetic efforts have also facilitated an understanding of the contribution of individual structural domains in bleomycin to sequence selective DNA binding and cleavage, and have also provided insights into the nature of the chemical processes by which DNA degradation takes place. Within the last several years, it has also become apparent that bleomycin can mediate the oxidative degradation of all major classes of cellular RNAs; it seems entirely plausible that RNA may also represent an important locus of action for this class of antitumor agent. In parallel with ongoing synthetic and mechanistic efforts using classical methods, the study of bleomycins attached to solid supports has been shown to provide important mechanistic insights, and the actual elaboration of modified bleomycins by solid phase synthesis constitutes a logical extension of such efforts.
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Affiliation(s)
- S M Hecht
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA.
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Aso M, Kondo M, Suemune H, Hecht SM. Chemistry of the Bleomycin-Induced Alkali-Labile DNA Lesion. J Am Chem Soc 1999. [DOI: 10.1021/ja991574a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Affiliation(s)
- Richard M. Burger
- Public Health Research Institute, 455 First Avenue, New York, New York 10016
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28
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Abstract
Dramatic technical progress in RNA synthesis and structure determination has allowed several difficulties inherent to the preparation, handling and structural analysis of RNA to be overcome, and this has led to a wealth of information about RNA structure and its relationship with biological function. It is now fully recognized that RNA molecules intervene at all stages of cell life, not only because of key sequence motifs but also because of intricate three-dimensional folds. This realization has promoted RNA to a potential therapeutic target. As in protein motifs recognizing nucleic acids, groups of the molecule interacting with RNA contribute to specific binding through defined hydrogen bonds and van der Waals docking, while other parts contribute to the driving force of binding via less specific electrostatic interactions accompanied by water and ion displacement.
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Affiliation(s)
- T Hermann
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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