1
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Navazeni M, Zolfigol MA, Ahmadi H, Sepehrmansourie H, Khazaei A, Hosseinifard M. Design, synthesis and application of a magnetic H-bond catalyst in the preparation of new nicotinonitriles via cooperative vinylogous anomeric-based oxidation. RSC Adv 2024; 14:16607-16616. [PMID: 38779389 PMCID: PMC11110150 DOI: 10.1039/d4ra01163e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Herein, we designed and synthesized a new H-bond magnetic catalyst with 2-tosyl-N-(3-(triethoxysilyl)propyl)hydrazine-1-carboxamide as a sensitive H-bond donor/acceptor. We created an organic structure with a urea moiety on the magnetic nanoparticles, which can function as a hydrogen bond catalyst. Hydrogen bond catalysts serve as multi-donor/-acceptor sites. Additionally, we utilized magnetic nanoparticles in the production of the target catalyst, giving it the ability to be recycled and easily separated from the reaction medium with an external magnet. We evaluated the catalytic application of Fe3O4@SiO2@tosyl-carboxamide as a new magnetic H-bond catalyst in the synthesis of new nicotinonitrile compounds through a multicomponent reaction under solvent-free and green conditions with high yields (50-73%). We confirmed the structure of Fe3O4@SiO2@tosyl-carboxamide using various techniques. In addition, the structures of the desired nicotinonitriles were confirmed using melting point, 1H-NMR, 13C-NMR and HR-mass spectrometry analysis. The final step of the reaction mechanism was preceded via cooperative vinylogous anomeric-based oxidation (CVABO).
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Affiliation(s)
- Mahdiyeh Navazeni
- Department of Organic Chemistry, Faculty of Chemistry and Petroleum Sciences, Bu-Ali Sina University Hamedan 6517838683 Iran +98 8138380709 +98 8138282807
| | - Mohammad Ali Zolfigol
- Department of Organic Chemistry, Faculty of Chemistry and Petroleum Sciences, Bu-Ali Sina University Hamedan 6517838683 Iran +98 8138380709 +98 8138282807
| | - Hossein Ahmadi
- Department of Organic Chemistry, Faculty of Chemistry and Petroleum Sciences, Bu-Ali Sina University Hamedan 6517838683 Iran +98 8138380709 +98 8138282807
| | - Hassan Sepehrmansourie
- Department of Organic Chemistry, Faculty of Chemistry and Petroleum Sciences, Bu-Ali Sina University Hamedan 6517838683 Iran +98 8138380709 +98 8138282807
| | - Ardeshir Khazaei
- Department of Organic Chemistry, Faculty of Chemistry and Petroleum Sciences, Bu-Ali Sina University Hamedan 6517838683 Iran +98 8138380709 +98 8138282807
| | - Mojtaba Hosseinifard
- Department of Energy, Materials and Energy Research Center P. O. Box 31787-316 Karaj 401602 Iran
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2
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Gibney A, de Paiva REF, Singh V, Fox R, Thompson D, Hennessy J, Slator C, McKenzie CJ, Johansson P, McKee V, Westerlund F, Kellett A. A Click Chemistry-Based Artificial Metallo-Nuclease. Angew Chem Int Ed Engl 2023; 62:e202305759. [PMID: 37338105 DOI: 10.1002/anie.202305759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023]
Abstract
Artificial metallo-nucleases (AMNs) are promising DNA damaging drug candidates. Here, we demonstrate how the 1,2,3-triazole linker produced by the Cu-catalysed azide-alkyne cycloaddition (CuAAC) reaction can be directed to build Cu-binding AMN scaffolds. We selected biologically inert reaction partners tris(azidomethyl)mesitylene and ethynyl-thiophene to develop TC-Thio, a bioactive C3 -symmetric ligand in which three thiophene-triazole moieties are positioned around a central mesitylene core. The ligand was characterised by X-ray crystallography and forms multinuclear CuII and CuI complexes identified by mass spectrometry and rationalised by density functional theory (DFT). Upon Cu coordination, CuII -TC-Thio becomes a potent DNA binding and cleaving agent. Mechanistic studies reveal DNA recognition occurs exclusively at the minor groove with subsequent oxidative damage promoted through a superoxide- and peroxide-dependent pathway. Single molecule imaging of DNA isolated from peripheral blood mononuclear cells shows that the complex has comparable activity to the clinical drug temozolomide, causing DNA damage that is recognised by a combination of base excision repair (BER) enzymes.
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Affiliation(s)
- Alex Gibney
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Raphael E F de Paiva
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Vandana Singh
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Fox
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Damien Thompson
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, Department of Physics, University of Limerick, Ireland
| | - Joseph Hennessy
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Creina Slator
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Christine J McKenzie
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Pegah Johansson
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Vickie McKee
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew Kellett
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
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3
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Kumar P, Tomar S, Kumar K, Kumar S. Transition metal complexes as self-activating chemical nucleases: proficient DNA cleavage without any exogenous redox agents. Dalton Trans 2023; 52:6961-6977. [PMID: 37128993 DOI: 10.1039/d3dt00368j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Chemical nucleases have found potential applications in the research fields of chemistry, biotechnology and medicine. A variety of metal complexes have been explored as good to outstanding therapeutic agents for DNA cleavage activity most likely via hydrolytic, oxidative or photoinduced cleavage pathways. However, most of these DNA cleaving agents lack their utility in in vivo applications due to their dependence on exogenous oxidants or reductants to achieve successful DNA damage. In view of addressing these issues, the development of metal complexes/organic molecules serving as self-activating chemical nucleases has received growing attention from researchers. In only the last decade, this field has dramatically expanded for the usage of chemical nucleases as therapeutic agents for DNA damage. The present study provides an overview of the opportunities and challenges in the design and development of self-activating chemical nucleases as improved DNA therapeutic candidates in the absence of an external redox agent. The reports on DNA nuclease activity via self-activation, especially with copper, zinc and iron complexes, and their mechanistic investigation have been discussed in this review article.
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Affiliation(s)
- Pramod Kumar
- Department of Chemistry, Mahamana Malviya College Khekra (Baghpat), C.C.S. University Meerut, India.
| | - Sunil Tomar
- Department of Zoology, Mahamana Malviya College Khekra (Baghpat), C.C.S. University Meerut, India
| | - Krishan Kumar
- Department of Chemistry, Motilal Nehru College, South Campus University of Delhi, New Delhi, India
| | - Sushil Kumar
- Department of Chemistry, School of Engineering, University of Petroleum and Energy Studies (UPES), Dehradun-248007, Uttarakhand, India.
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4
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Bhardwaj V, Salunke PS, Puranik AA, Kulkarni ND, Ballabh A. Design and synthesis of novel heterocyclic pivalamide ligands and their copper(II) complexes: Structure, BSA/DNA interactions and SOD synzyme activity. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Shahraki S. Schiff base compounds as artificial metalloenzymes. Colloids Surf B Biointerfaces 2022; 218:112727. [PMID: 35921691 DOI: 10.1016/j.colsurfb.2022.112727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022]
Abstract
Much research has been done on traditional homogeneous metal catalysts and enzymatic catalysts, but recently a new class of hybrid catalysts called synthetic (artificial) metalloenzymes has been considered by researchers. Metalloenzymes as hybrid catalysts (host-guest systems) have been shown that combine the properties of a homogeneous and also enzymatic catalyst. The hybrid catalyst will have added value such as enantioselectivity or chemo-selectivity. This review focuses on Schiff base complexes that either act as homogeneous artificial enzymes or contribute to the structure of a host in the preparation of hybrid metalloenzymes. Because this approach can virtually be applied to any bio- or synthetic host or guest coordination complex, the details of hybrid catalysts seem important for advance in catalysis.
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6
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McGorman B, Fantoni NZ, O'Carroll S, Ziemele A, El-Sagheer AH, Brown T, Kellett A. Enzymatic Synthesis of Chemical Nuclease Triplex-Forming Oligonucleotides with Gene-Silencing Applications. Nucleic Acids Res 2022; 50:5467-5481. [PMID: 35640595 PMCID: PMC9177962 DOI: 10.1093/nar/gkac438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/10/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) are short, single-stranded oligomers that hybridise to a specific sequence of duplex DNA. TFOs can block transcription and thereby inhibit protein production, making them highly appealing in the field of antigene therapeutics. In this work, a primer extension protocol was developed to enzymatically prepare chemical nuclease TFO hybrid constructs, with gene-silencing applications. Click chemistry was employed to generate novel artificial metallo-nuclease (AMN)-dNTPs, which were selectively incorporated into the TFO strand by a DNA polymerase. This purely enzymatic protocol was then extended to facilitate the construction of 5-methylcytosine (5mC) modified TFOs that displayed increased thermal stability. The utility of the enzymatically synthesised di-(2-picolyl)amine (DPA)-TFOs was assessed and compared to a specifically prepared solid-phase synthesis counterpart through gel electrophoresis, quantitative PCR, and Sanger sequencing, which revealed similar recognition and damage properties to target genes. The specificity was then enhanced through coordinated designer intercalators-DPQ and DPPZ-and high-precision DNA cleavage was achieved. To our knowledge, this is the first example of the enzymatic production of an AMN-TFO hybrid and is the largest base modification incorporated using this method. These results indicate how chemical nuclease-TFOs may overcome limitations associated with non-molecularly targeted metallodrugs and open new avenues for artificial gene-editing technology.
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Affiliation(s)
- Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nicolò Zuin Fantoni
- Chemistry Research Laboratory, University of Oxford, South Parks Rd, Oxford, UK
| | - Sinéad O'Carroll
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Anna Ziemele
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, South Parks Rd, Oxford, UK.,Department of Science and Mathematics, Suez University, Faculty of Petroleum and Mining, Engineering, Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, South Parks Rd, Oxford, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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7
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Tang JW, Liu X, Ye W, Li ZR, Qian PY. Biosynthesis and bioactivities of microbial genotoxin colibactins. Nat Prod Rep 2022; 39:991-1014. [PMID: 35288725 DOI: 10.1039/d1np00050k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to 2021Colibactin(s), a group of secondary metabolites produced by the pks island (clb cluster) of Escherichia coli, shows genotoxicity relevant to colorectal cancer and thus significantly affects human health. Over the last 15 years, substantial efforts have been exerted to reveal the molecular structure of colibactin, but progress is slow owing to its instability, low titer, and elusive and complex biosynthesis logic. Fortunately, benefiting from the discovery of the prodrug mechanism, over 40 precursors of colibactin have been reported. Some key biosynthesis genes located on the pks island have also been characterised. Using an integrated bioinformatics, metabolomics, and chemical synthesis approach, researchers have recently characterised the structure and possible biosynthesis processes of colibactin, thereby providing new insights into the unique biosynthesis logic and the underlying mechanism of the biological activity of colibactin. Early developments in the study of colibactin have been summarised in several previous reviews covering various study periods, whereas the two most recent reviews have focused primarily on the chemical synthesis of colibactin. The present review aims to provide an update on the biosynthesis and bioactivities of colibactin.
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Affiliation(s)
- Jian-Wei Tang
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Xin Liu
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Wei Ye
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhong-Rui Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
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8
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Porous N, P co-doped carbon-coated ultrafine Co2P nanoparticles derived from DNA: An electrocatalyst for highly efficient hydrogen evolution reaction. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.139051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Samuel M, Raman N. Comprehensive biological evaluation (DNA-binding, cleavage, and antimicrobial activity) of β-diketimine Schiff base ligands and their Cu(II) and Zn(II) complexes. J COORD CHEM 2021. [DOI: 10.1080/00958972.2021.1931848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- M. Samuel
- Research Department of Chemistry, VHNSN College, Virudhunagar, India
| | - N. Raman
- Research Department of Chemistry, VHNSN College, Virudhunagar, India
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10
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Fantoni NZ, Brown T, Kellett A. DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for, Cellular Biotechnology and Nano Research Facility, Dublin City University, Glasnevin, Dublin, 9, Ireland
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11
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Bell M, Kumar A, Sevilla MD. Electron-Induced Repair of 2'-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study. Int J Mol Sci 2021; 22:ijms22041736. [PMID: 33572317 PMCID: PMC7916153 DOI: 10.3390/ijms22041736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′• > C1′• > C5′• > C3′• > C2′•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier.
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Chatgilialoglu C, Ferreri C, Krokidis MG, Masi A, Terzidis MA. On the relevance of hydroxyl radical to purine DNA damage. Free Radic Res 2021; 55:384-404. [PMID: 33494618 DOI: 10.1080/10715762.2021.1876855] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hydroxyl radical (HO•) is the most reactive toward DNA among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms. HO• is generated also by exogenous sources such as ionizing radiations. In this review we focus on the purine DNA damage by HO• radicals. In particular, emphasis is given on mechanistic aspects for the various lesion formation and their interconnections. Although the majority of the purine DNA lesions like 8-oxo-purine (8-oxo-Pu) are generated by various ROS (including HO•), the formation of 5',8-cyclopurine (cPu) lesions in vitro and in vivo relies exclusively on the HO• attack. Methodologies generally utilized for the purine lesions quantification in biological samples are reported and critically discussed. Recent results on cPu and 8-oxo-Pu lesions quantification in various types of biological specimens associated with the cellular repair efficiency as well as with distinct pathologies are presented, providing some insights on their biological significance.
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Affiliation(s)
- Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy.,Center for Advanced Technologies, Adam Mickiewicz University, Poznan, Poland
| | - Carla Ferreri
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, NCSR "Demokritos", Athens, Greece
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy.,Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Monterotondo, Italy
| | - Michael A Terzidis
- Department of Nutritional Sciences and Dietetics, International Hellenic University, Thessaloniki, Greece
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13
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Galindo-Murillo R, Winkler L, García-Ramos JC, Ruiz-Azuara L, Cortés-Guzmán F, Cheatham TE. Ancillary Ligand in Ternary Cu II Complexes Guides Binding Selectivity toward Minor-Groove DNA. J Phys Chem B 2020; 124:11648-11658. [PMID: 33320672 PMCID: PMC7770820 DOI: 10.1021/acs.jpcb.0c09296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Copper-containing
compounds known as Casiopeínas are
biologically active molecules which show promising antineoplastic
effects against several cancer types. Two possible hypotheses regarding
the mode of action of the Casiopeínas have emerged from
the experimental evidence: the generation of reactive oxygen species
or the ability of the compounds to bind and interact with nucleic
acids. Using robust molecular dynamics simulations, we investigate
the interaction of four different Casiopeínas with the DNA duplex d(GCACGAACGAACGAACGC). The studied copper complexes contain either 4–7- or 5–6-substituted
dimethyl phenanthroline as the primary ligand and either glycinate
or acetylacetonate as the secondary ligand. For statistical significance
and to reduce bias in the simulations, four molecules of each copper
compound were manually placed at a distance of 10 Å away from
the DNA and 20 independent molecular dynamics simulations were performed,
each reaching at least 30 μs. This time scale allows us to reproduce
expected DNA terminal base-pair fraying and also to observe intercalation/base-pair
eversion events generated by the compounds interacting with DNA. The
results reveal that the secondary ligand is the guide toward the mode
of binding between the copper complex and DNA in which glycinate prefers
minor-groove binding and acetylacetonate produces base-pair eversion
and intercalation. The CuII complexes containing glycinate
interact within the DNA minor groove which are stabilized principally
by the hydrogen bonds formed between the amino group of the aminoacidate
moiety, whereas the compounds with the acetylacetonate do not present
a stable network of hydrogen bonds and the ligand interactions enhance
DNA breathing dynamics that result in base-pair eversion.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Lauren Winkler
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Juan Carlos García-Ramos
- Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Blvd. Zertuche y Blvd. Los Lagos, Fraccionamiento Valle Dorado, Ensenada, Baja California 22890, Mexico
| | - Lena Ruiz-Azuara
- Departamento de Química Inorgánica y Nuclear. Facultad de Química. Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Fernando Cortés-Guzmán
- Departamento de Fisicoquímica. Instituto de Química. Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
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Shiju C, Arish D, Kumaresan S. Novel water soluble Schiff base metal complexes: Synthesis, characterization, antimicrobial-, DNA cleavage, and anticancer activity. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128770] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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Fantoni NZ, Molphy Z, O'Carroll S, Menounou G, Mitrikas G, Krokidis MG, Chatgilialoglu C, Colleran J, Banasiak A, Clynes M, Roche S, Kelly S, McKee V, Kellett A. Polypyridyl-Based Copper Phenanthrene Complexes: Combining Stability with Enhanced DNA Recognition. Chemistry 2020; 27:971-983. [PMID: 32519773 DOI: 10.1002/chem.202001996] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/09/2020] [Indexed: 02/06/2023]
Abstract
We report a series of copper(II) artificial metallo-nucleases (AMNs) and demonstrate their DNA damaging properties and in-vitro cytotoxicity against human-derived pancreatic cancer cells. The compounds combine a tris-chelating polypyridyl ligand, di-(2-pycolyl)amine (DPA), and a DNA intercalating phenanthrene unit. Their general formula is Cu-DPA-N,N' (where N,N'=1,10-phenanthroline (Phen), dipyridoquinoxaline (DPQ) or dipyridophenazine (DPPZ)). Characterisation was achieved by X-ray crystallography and continuous-wave EPR (cw-EPR), hyperfine sublevel correlation (HYSCORE) and Davies electron-nuclear double resonance (ENDOR) spectroscopies. The presence of the DPA ligand enhances solution stability and facilitates enhanced DNA recognition with apparent binding constants (Kapp ) rising from 105 to 107 m-1 with increasing extent of planar phenanthrene. Cu-DPA-DPPZ, the complex with greatest DNA binding and intercalation effects, recognises the minor groove of guanine-cytosine (G-C) rich sequences. Oxidative DNA damage also occurs in the minor groove and can be inhibited by superoxide and hydroxyl radical trapping agents. The complexes, particularly Cu-DPA-DPPZ, display promising anticancer activity against human pancreatic tumour cells with in-vitro results surpassing the clinical platinum(II) drug oxaliplatin.
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Affiliation(s)
- Nicoló Zuin Fantoni
- School of Chemical Sciences and National Institute for Cellular, Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Nicolò Zuin Fantoni-Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular, Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,SSPC, the SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Dublin, 9, Ireland
| | - Sinéad O'Carroll
- School of Chemical Sciences and National Institute for Cellular, Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Georgia Menounou
- Consiglio Nazionale delle Ricerche, ISOF, Via P. Gobetti 101, 40129, Bologna, Italy
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology Demokritos, NCSR "Demokritos", Agia Paraskevi Attikis, 153, 10, Athens, Greece
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology Demokritos, NCSR "Demokritos", Agia Paraskevi Attikis, 153, 10, Athens, Greece
| | | | - John Colleran
- School of Chemical and Pharmaceutical Sciences, TU Dublin, Kevin Street, Dublin 8, Ireland.,Applied Electrochemistry Group, Focas Research Institute, TU Dublin, Camden Row, Dublin 8, Ireland
| | - Anna Banasiak
- Applied Electrochemistry Group, Focas Research Institute, TU Dublin, Camden Row, Dublin 8, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, 9, Ireland
| | - Sandra Roche
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, 9, Ireland
| | - Suainibhe Kelly
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular, Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular, Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,SSPC, the SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Dublin, 9, Ireland
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17
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Copper bis-Dipyridoquinoxaline Is a Potent DNA Intercalator that Induces Superoxide-Mediated Cleavage via the Minor Groove. Molecules 2019; 24:molecules24234301. [PMID: 31779066 PMCID: PMC6930674 DOI: 10.3390/molecules24234301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/25/2023] Open
Abstract
Herein, we report the synthesis, characterisation, X-ray crystallography, and oxidative DNA binding interactions of the copper artificial metallo-nuclease [Cu(DPQ)2(NO3)](NO3), where DPQ = dipyrido[3,2-f:2',3'-h]quinoxaline. The cation [Cu(DPQ)2]2+ (Cu-DPQ), is a high-affinity binder of duplex DNA and presents an intercalative profile in topoisomerase unwinding and viscosity experiments. Artificial metallo-nuclease activity occurs in the absence of exogenous reductant but is greatly enhanced by the presence of the reductant Na-L-ascorbate. Mechanistically, oxidative DNA damage occurs in the minor groove, is mediated aerobically by the Cu(I) complex and is dependent on both superoxide and hydroxyl radical generation. To corroborate cleavage at the minor groove, DNA oxidation of a cytosine-guanine (5'-CCGG-3')-rich oligomer was examined in tandem with a 5-methylcytosine (5'-C5mCGG-3') derivative where 5mC served to sterically block the major groove and direct damage to the minor groove. Overall, both the DNA binding affinity and cleavage mechanism of Cu-DPQ depart from Sigman's reagent [Cu(1,10-phenanthroline)2]2+; however, both complexes are potent oxidants of the minor groove.
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18
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Zhao YH, Ren FD, Gao L, Tan YX, Wang YY. Theoretical explanation for the DNA cleavage by GO with cation: anti-cooperativity effect among the π⋯π, cation⋯π/σ and H-bonding interactions in cytosine⋯GO⋯Mn+ (Mn+ = Na+, Mg2+, Al3+). Mol Phys 2019. [DOI: 10.1080/00268976.2019.1692149] [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)
- Ying-hu Zhao
- School of Environment and Safety Engineering, North University of China, Taiyuan, People’s Republic of China
| | - Fu-de Ren
- School of Chemical Engineering and Technology, North University of China, Taiyuan, People’s Republic of China
| | - Li Gao
- School of Chemical Engineering and Technology, North University of China, Taiyuan, People’s Republic of China
| | - Ying-xin Tan
- School of Environment and Safety Engineering, North University of China, Taiyuan, People’s Republic of China
| | - Ying-yong Wang
- State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
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19
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Oliveira Pinho J, Matias M, Gaspar MM. Emergent Nanotechnological Strategies for Systemic Chemotherapy against Melanoma. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E1455. [PMID: 31614947 PMCID: PMC6836019 DOI: 10.3390/nano9101455] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022]
Abstract
Melanoma is an aggressive form of skin cancer, being one of the deadliest cancers in the world. The current treatment options involve surgery, radiotherapy, targeted therapy, immunotherapy and the use of chemotherapeutic agents. Although the last approach is the most used, the high toxicity and the lack of efficacy in advanced stages of the disease have demanded the search for novel bioactive molecules and/or efficient drug delivery systems. The current review aims to discuss the most recent advances on the elucidation of potential targets for melanoma treatment, such as aquaporin-3 and tyrosinase. In addition, the role of nanotechnology as a valuable strategy to effectively deliver selective drugs is emphasized, either incorporating/encapsulating synthetic molecules or natural-derived compounds in lipid-based nanosystems such as liposomes. Nanoformulated compounds have been explored for their improved anticancer activity against melanoma and promising results have been obtained. Indeed, they displayed improved physicochemical properties and higher accumulation in tumoral tissues, which potentiated the efficacy of the compounds in pre-clinical experiments. Overall, these experiments opened new doors for the discovery and development of more effective drug formulations for melanoma treatment.
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Affiliation(s)
- Jacinta Oliveira Pinho
- Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
| | - Mariana Matias
- Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
| | - Maria Manuela Gaspar
- Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
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20
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Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage. Nat Chem 2019; 11:880-889. [PMID: 31527851 PMCID: PMC6761029 DOI: 10.1038/s41557-019-0317-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/24/2019] [Indexed: 12/13/2022]
Abstract
Colibactin is an assumed human gut bacterial genotoxin, whose biosynthesis is linked to clb genomic island that distributes widespread in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumor formation and enhance progression of colorectal cancer via DNA double-strand breaks-induced cellular senescence and death; however, the chemical basis contributing to the pathogenesis at the molecular level has not been fully characterized. Here we report the discovery of colibactin-645 a macrocyclic colibactin metabolite that recapitulates the previously assumed genotoxicity and cytotoxicity. Colibactin-645 shows strong DNA DSBs activity in vitro and in human cell cultures via a unique copper-mediated oxidative mechanism. We also delineate a complete biosynthetic model for colibactin-645, highlighting a unique fate of the aminomalonate building monomer in forming the C-terminal 5-hydroxy 4-oxazolecarboxylic acid moiety through the activities of both the polyketide synthase ClbO and the amidase ClbL. This work thus provides a molecular basis for colibactin’s DNA DSBs activity and facilitates further mechanistic study of colibactin-related CRC incidence and prevention.
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21
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Slator C, Molphy Z, McKee V, Long C, Brown T, Kellett A. Di-copper metallodrugs promote NCI-60 chemotherapy via singlet oxygen and superoxide production with tandem TA/TA and AT/AT oligonucleotide discrimination. Nucleic Acids Res 2019; 46:2733-2750. [PMID: 29474633 PMCID: PMC5888725 DOI: 10.1093/nar/gky105] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/08/2018] [Indexed: 12/29/2022] Open
Abstract
In order to expand the current repertoire of cancer treatments and to help circumvent limitations associated with resistance, the identification of new metallodrugs with high potency and novel mechanisms of action is of significant importance. Here we present a class of di-copper(II) complex based on the synthetic chemical nuclease [Cu(Phen)2]+ (where Phen = 1,10-phenanthroline) that is selective against solid epithelial cancer cells from the National Cancer Institute's 60 human cell line panel (NCI-60). Two metallodrug leads are studied and in each case two [Cu(Phen)2]+ units are bridged by a dicarboxylate linker but the length and rigidity of the linkers differ distinctly. Both agents catalyze intracellular superoxide (O2•-) and singlet oxygen (1O2) formation with radical species mediating oxidative damage within nuclear DNA in the form of double strand breaks and to the mitochondria in terms of membrane depolarization. The complexes are effective DNA binders and can discriminate AT/AT from TA/TA steps of duplex DNA through induction of distinctive Z-like DNA or by intercalative interactions.
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Affiliation(s)
- Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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22
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Bytesnikova Z, Richtera L, Smerkova K, Adam V. Graphene oxide as a tool for antibiotic-resistant gene removal: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:20148-20163. [PMID: 31115815 DOI: 10.1007/s11356-019-05283-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Environmental pollutants, including antibiotics (ATBs), have become an increasingly common health hazard in the last several decades. Overdose and abuse of ATBs led to the emergence of antibiotic-resistant genes (ARGs), which represent a serious health threat. Moreover, water bodies and reservoirs are places where a wide range of bacterial species with ARGs originate, owing to the strong selective pressure from presence of ATB residues. In this regard, graphene oxide (GO) has been utilised in several fields including remediation of the environment. In this review, we present a brief overview of resistant genes of frequently used ATBs, their occurrence in the environment and their behaviour. Further, we discussed the factors influencing the binding of nucleic acids and the response of ARGs to GO, including the presence of salts in the water environment or water pH, because of intrinsic properties of GO of not only binding to nucleic acids but also catalysing their decomposition. This would be helpful in designing new types of water treatment facilities.
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Affiliation(s)
- Zuzana Bytesnikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic.
| | - Kristyna Smerkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic
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23
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Flexible vs. rigid bis(2-benzimidazolyl) ligands in Cu(II) complexes: Impact on redox chemistry and oxidative DNA cleavage activity. J Inorg Biochem 2019; 194:223-232. [DOI: 10.1016/j.jinorgbio.2019.01.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/27/2019] [Accepted: 01/27/2019] [Indexed: 11/21/2022]
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24
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Kellett A, Molphy Z, Slator C, McKee V, Farrell NP. Molecular methods for assessment of non-covalent metallodrug-DNA interactions. Chem Soc Rev 2019; 48:971-988. [PMID: 30714595 PMCID: PMC6657641 DOI: 10.1039/c8cs00157j] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Herein we provide an accessible account of molecular methods to probe inorganic–nucleic acid interactions. Techniques are described using copper(ii) and platinum(ii) complexes prepared in our laboratories.
The binding of small molecule metallodrugs to discrete regions of nucleic acids is an important branch of medicinal chemistry and the nature of these interactions, allied with sequence selectivity, forms part of the backbone of modern medicinal inorganic chemistry research. In this tutorial review we describe a range of molecular methods currently employed within our laboratories to explore novel metallodrug–DNA interactions. At the outset, an introduction to DNA from a structural perspective is provided along with descriptions of non-covalent DNA recognition focusing on intercalation, insertion, and phosphate binding. Molecular methods, described from a non-expert perspective, to identify non-covalent and pre-associative nucleic acid recognition are then demonstrated using a variety of techniques including direct (non-optical) and indirect (optical) methods. Direct methods include: X-ray crystallography; NMR spectroscopy; mass spectrometry; and viscosity while indirect approaches detail: competitive inhibition experiments; fluorescence and absorbance spectroscopy; circular dichroism; and electrophoresis-based techniques. For each method described we provide an overview of the technique, a detailed examination of results obtained and relevant follow-on of advanced biophysical/analytical techniques. To achieve this, a selection of relevant copper(ii) and platinum(ii) complexes developed within our laboratories are discussed and are compared, where possible, to classical DNA binding agents. Applying these molecular methods enables us to determine structure–activity factors important to rational metallodrug design. In many cases, combinations of molecular methods are required to comprehensively elucidate new metallodrug–DNA interactions and, from a drug discovery perspective, coupling this data with cellular responses helps to inform understanding of how metallodrug–DNA binding interactions manifest cytotoxic action.
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Affiliation(s)
- Andrew Kellett
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Zara Molphy
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Creina Slator
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Vickie McKee
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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25
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Pinho JO, Amaral JD, Castro RE, Rodrigues CMP, Casini A, Soveral G, Gaspar MM. Copper complex nanoformulations featuring highly promising therapeutic potential in murine melanoma models. Nanomedicine (Lond) 2019; 14:835-850. [DOI: 10.2217/nnm-2018-0388] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: Preclinical evaluation of a cytotoxic copper (II) complex formulated in long circulating nanoliposomes for melanoma treatment. Materials & methods: Liposomal nanoformulations of the copper complex were characterized in terms of thermodynamic behavior (differential scanning calorimeter), pH-sensitivity (spectrophotometry) and antiproliferative effects against murine melanoma B16F10 cells in vitro. Preclinical studies were performed in a C57BL/6 syngeneic melanoma model. Results: Nanoformulations were thermodynamically stable, and CHEMS-containing nanoliposomes were pH-sensitive and preserved the antiproliferative properties of the copper compound. These nanoformulations significantly impaired tumor progression in vivo, devoid of toxic side effects, compared with control mice or mice treated with the free metallodrug. Conclusion: Copper complex-containing nanoliposomes demonstrate high anticancer efficacy and safety, constituting a step forward to the development of more effective therapeutic strategies against melanoma.
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Affiliation(s)
- Jacinta O Pinho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Joana D Amaral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Cecília MP Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Angela Casini
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Maria Manuela Gaspar
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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26
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Yang K, Prasse C, Greenberg MM. Effect of Histone Lysine Methylation on DNA Lesion Reactivity in Nucleosome Core Particles. Chem Res Toxicol 2019; 32:910-916. [PMID: 30916939 DOI: 10.1021/acs.chemrestox.9b00049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lysine methylation is a common post-translational histone modification that regulates transcription and gene expression. The lysine residues in the histone tail also react with damaged nucleotides in chromatin, including abasic sites and N7-methyl-2'-deoxyguanosine, the major product of DNA methylating agents. Lysine monomethylation transforms the ε-amine into a secondary amine, which could be more nucleophilic and/or basic than the ε-amine in lysine, and therefore more reactive with damaged DNA. The effect of lysine methylation on the reactivity with abasic sites and N7-methyl-2'-deoxyguanosine was examined in nucleosome core particles using a methylated lysine analogue derived from cysteine. ε-Amine methylation increases the rate constant for abasic site reaction within nucleosome core particles. Reactivity at the two positions examined increased less than twofold. Mechanistic experiments indicate that faster β-elimination from an intermediate iminium ion accounts for accelerated abasic reactivity. The rate constants for nucleophilic attack (Schiff base/iminium ion formation) by the lysine and methylated lysine analogues are indistinguishable. Similarly, the rate constants describing nucleophilic attack by the lysine and methylated lysine analogues on β-2'-fluoro-N7-methyl-2'-deoxyguanosine to form DNA-protein cross-links are also within experimental error of one another. These data indicate that abasic site containing DNA will be destabilized by lysine methylation. However, these experiments do not indicate that DNA-protein cross-link formation, a recently discovered form of damage resulting from N7-guanine methylation, will be affected by this post-translational modification.
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Affiliation(s)
- Kun Yang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Carsten Prasse
- Department of Environmental Health and Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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27
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Toniolo G, Louka M, Menounou G, Fantoni NZ, Mitrikas G, Efthimiadou EK, Masi A, Bortolotti M, Polito L, Bolognesi A, Kellett A, Ferreri C, Chatgilialoglu C. [Cu(TPMA)(Phen)](ClO 4) 2: Metallodrug Nanocontainer Delivery and Membrane Lipidomics of a Neuroblastoma Cell Line Coupled with a Liposome Biomimetic Model Focusing on Fatty Acid Reactivity. ACS OMEGA 2018; 3:15952-15965. [PMID: 30556020 PMCID: PMC6288809 DOI: 10.1021/acsomega.8b02526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The use of copper complexes for redox and oxidative-based mechanisms in therapeutic strategies is an important field of multidisciplinary research. Here, a novel Cu(II) complex [Cu(TPMA)(Phen)](ClO4)2 (Cu-TPMA-Phen, where TPMA = tris-(2-pyridylmethyl)amine and Phen = 1,10-phenanthroline) was studied using both the free and encapsulated forms. A hollow pH-sensitive drug-delivery system was synthesized, characterized, and used to encapsulate and release the copper complex, thus allowing for the comparison with the free drug. The human neuroblastoma-derived cell line NB100 was treated with 5 μM Cu-PMA-Phen for 24 h, pointing to the consequences on mono- and polyunsaturated fatty acids (MUFA and PUFA) present in the membrane lipidome, coupled with cell viability and death pathways (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium viability assay, flow cytometry, microscopy, caspase activation). In parallel, the Cu-TPMA-Phen reactivity with the fatty acid moieties of phospholipids was studied using the liposome model to work in a biomimetic environment. The main results concerned: (i) the membrane lipidome in treated cells, involving remodeling with a specific increase of saturated fatty acids (SFAs) and a decrease of MUFA, but not PUFA; (ii) cytotoxic events and lipidome changes did not occur for the encapsulated Cu-TPMA-Phen, showing the influence of such nanocarriers on drug activity; and (iii) the liposome behavior confirmed that MUFA and PUFA fatty acid moieties in membranes are not affected by oxidative and isomerization reactions, proving the different reactivities of thiyl radicals generated from amphiphilic and hydrophilic thiols and Cu-TPMA-Phen. This study gives preliminary but important elements of copper(II) complex reactivity in cellular and biomimetic models, pointing mainly to the effects on membrane reactivity and remodeling based on the balance between SFA and MUFA in cell membranes that are subjects of strong interest for chemotherapeutic activities as well as connected to nutritional strategies.
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Affiliation(s)
- Gianluca Toniolo
- ISOF,
Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
- Institute
of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos”, 15310 Agia Paraskevi
Attikis, Greece
| | - Maria Louka
- ISOF,
Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
- Laboratory
of Lipidomics, Lipinutragen Srl, Via Piero Gobetti 101, 40129 Bologna, Italy
- Department
of Experimental, Diagnostic and Specialty Medicine-DIMES, Alma Mater
Studiorum, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Georgia Menounou
- ISOF,
Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
| | - Nicolò Zuin Fantoni
- School
of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - George Mitrikas
- Institute
of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos”, 15310 Agia Paraskevi
Attikis, Greece
| | - Eleni K. Efthimiadou
- Institute
of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos”, 15310 Agia Paraskevi
Attikis, Greece
| | - Annalisa Masi
- ISOF,
Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
| | - Massimo Bortolotti
- Department
of Experimental, Diagnostic and Specialty Medicine-DIMES, Alma Mater
Studiorum, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Letizia Polito
- Department
of Experimental, Diagnostic and Specialty Medicine-DIMES, Alma Mater
Studiorum, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Andrea Bolognesi
- Department
of Experimental, Diagnostic and Specialty Medicine-DIMES, Alma Mater
Studiorum, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Andrew Kellett
- School
of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Carla Ferreri
- ISOF,
Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
- Laboratory
of Lipidomics, Lipinutragen Srl, Via Piero Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF,
Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
- Institute
of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos”, 15310 Agia Paraskevi
Attikis, Greece
- Laboratory
of Lipidomics, Lipinutragen Srl, Via Piero Gobetti 101, 40129 Bologna, Italy
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28
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Zuin Fantoni N, Molphy Z, Slator C, Menounou G, Toniolo G, Mitrikas G, McKee V, Chatgilialoglu C, Kellett A. Polypyridyl‐Based Copper Phenanthrene Complexes: A New Type of Stabilized Artificial Chemical Nuclease. Chemistry 2018; 25:221-237. [DOI: 10.1002/chem.201804084] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Nicoló Zuin Fantoni
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
| | - Georgia Menounou
- ISOF-CNR Area della Ricerca di Bologna Via P. Gobetti 101 40129 Bologna Italy
| | - Gianluca Toniolo
- Institute of Nanoscience and Nanotechnology, N.C.S.R. Demokritos Agia Paraskevi Attikis P.O. Box 60037, 15341 Athens Greece
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, N.C.S.R. Demokritos Agia Paraskevi Attikis P.O. Box 60037, 15341 Athens Greece
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Chryssostomos Chatgilialoglu
- ISOF-CNR Area della Ricerca di Bologna Via P. Gobetti 101 40129 Bologna Italy
- Institute of Nanoscience and Nanotechnology, N.C.S.R. Demokritos Agia Paraskevi Attikis P.O. Box 60037, 15341 Athens Greece
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular, BiotechnologyDublin City University 9 Glasnevin, Dublin Ireland
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29
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Molphy Z, Montagner D, Bhat SS, Slator C, Long C, Erxleben A, Kellett A. A phosphate-targeted dinuclear Cu(II) complex combining major groove binding and oxidative DNA cleavage. Nucleic Acids Res 2018; 46:9918-9931. [PMID: 30239938 PMCID: PMC6212767 DOI: 10.1093/nar/gky806] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/05/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022] Open
Abstract
Free radical generation is an inevitable consequence of aerobic existence and is implicated in a wide variety of pathological conditions including cancer, cardiovascular disease, ageing and neurodegenerative disorder. Free radicals can, however, be used to our advantage since their production is catalysed by synthetic inorganic molecules-termed artificial metallonucleases-that cut DNA strands by oxidative cleavage reactions. Here, we report the rational design and DNA binding interactions of a novel di-Cu2+ artificial metallonuclease [Cu2(tetra-(2-pyridyl)-NMe-naphthalene)Cl4] (Cu2TPNap). Cu2TPNap is a high-affinity binder of duplex DNA with an apparent binding constant (Kapp) of 107 M(bp)-1. The agent binds non-intercalatively in the major groove causing condensation and G-C specific destabilization. Artificial metallonuclease activity occurs in the absence of exogenous reductant, is dependent on superoxide and hydrogen peroxide, and gives rise to single strand DNA breaks. Pre-associative molecular docking studies with the 8-mer d(GGGGCCCC)2, a model for poly[d(G-C)2], identified selective major groove incorporation of the complex with ancillary Cu2+-phosphate backbone binding. Molecular mechanics methods then showed the d(GGGGCCCC)2 adduct to relax about the complex and this interaction is supported by UV melting experiments where poly[d(G-C)2] is selectively destabilized.
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Affiliation(s)
- Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Diego Montagner
- Department of Chemistry, Maynooth University, Maynooth, Kildare, Ireland
| | - Satish S Bhat
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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30
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Santoro A, Walke G, Vileno B, Kulkarni PP, Raibaut L, Faller P. Low catalytic activity of the Cu(ii)-binding motif (Xxx-Zzz-His; ATCUN) in reactive oxygen species production and inhibition by the Cu(i)-chelator BCS. Chem Commun (Camb) 2018; 54:11945-11948. [PMID: 30288543 DOI: 10.1039/c8cc06040a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The catalytic redox activity of Cu(ii) bound to the motif NH2-Xxx-Zzz-His (ATCUN) with ascorbate and H2O2/O2 is very low and can be stopped via Cu(i)-chelation. This impacts its application as an artificial Cu-enzyme to degrade biomolecules via production of reactive oxygen species in a Cu(i)-chelator rich environment like the cytosol.
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Affiliation(s)
- Alice Santoro
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000, Strasbourg, France.
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31
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Belostotskii AM. Nanosecond-Scale Isomerization of the 4'-Carboxonium Cation Oxidatively Produced in Pyrimidine Units of DNA. J Org Chem 2018; 83:11604-11613. [PMID: 30153025 DOI: 10.1021/acs.joc.8b01580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The long-standing puzzle of the chemistry producing the Stubbe-Kozarich abasic site, which is the minor product in the oxidation of 2'-deoxycytidine units of DNA by Fe(II)-bleomycin, has been computationally solved in this study. Scrupulous DFT-based calculations that included extensive screening of the potential energy surface of model-solvated nucleotides and the elucidation of the chemical structure of the located nucleotide cations via natural bond orbital analysis demonstrated that the 2'-deoxycytidine unit bearing the 2'-deoxyribose ring 2e-oxidized at the 4'-position undergoes carboxonium ion- iminium ion (C═O+-C → C═N+) isomerization. This 1,2-elimination of the carbonyl group 4'-C═O from the carboxonium cation fragment is associated with minimal spatial reorganization of the molecule and appears to be an ultrafast reaction. The calculated barrier Δ G0# of 2.7 kcal mol-1 for this isomerization is lower than that reported for the addition of water to oxocarbenium ions. Thus, this unusual nucleotide transformation is the key chemical reaction that yields the Stubbe-Kozarich product. Such a product cannot be formed for purine nucleotide units in DNA. The isomerization of 4'-dehydro-2'-deoxyribose-4'-carboxonium cations formed in these DNA units is slower because it destroys the purine aromaticity, and the cations are intercepted by water molecules before they isomerize.
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32
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Silva MA, Romo AI, Abreu DS, Carepo MS, Lemus L, Jafelicci M, Paulo TF, Nascimento OR, Vargas E, Denardin JC, Diógenes IC. Magnetic nanoparticles as a support for a copper (II) complex with nuclease activity. J Inorg Biochem 2018; 186:294-300. [DOI: 10.1016/j.jinorgbio.2018.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/17/2018] [Accepted: 06/24/2018] [Indexed: 11/16/2022]
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33
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Murray V, Chen JK, Chung LH. The Interaction of the Metallo-Glycopeptide Anti-Tumour Drug Bleomycin with DNA. Int J Mol Sci 2018; 19:E1372. [PMID: 29734689 PMCID: PMC5983701 DOI: 10.3390/ijms19051372] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/17/2022] Open
Abstract
The cancer chemotherapeutic drug, bleomycin, is clinically used to treat several neoplasms including testicular and ovarian cancers. Bleomycin is a metallo-glycopeptide antibiotic that requires a transition metal ion, usually Fe(II), for activity. In this review, the properties of bleomycin are examined, especially the interaction of bleomycin with DNA. A Fe(II)-bleomycin complex is capable of DNA cleavage and this process is thought to be the major determinant for the cytotoxicity of bleomycin. The DNA sequence specificity of bleomycin cleavage is found to at 5′-GT* and 5′-GC* dinucleotides (where * indicates the cleaved nucleotide). Using next-generation DNA sequencing, over 200 million double-strand breaks were analysed, and an expanded bleomycin sequence specificity was found to be 5′-RTGT*AY (where R is G or A and Y is T or C) in cellular DNA and 5′-TGT*AT in purified DNA. The different environment of cellular DNA compared to purified DNA was proposed to be responsible for the difference. A number of bleomycin analogues have been examined and their interaction with DNA is also discussed. In particular, the production of bleomycin analogues via genetic manipulation of the modular non-ribosomal peptide synthetases and polyketide synthases in the bleomycin gene cluster is reviewed. The prospects for the synthesis of bleomycin analogues with increased effectiveness as cancer chemotherapeutic agents is also explored.
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Affiliation(s)
- Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Jon K Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Long H Chung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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34
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McGivern T, Afsharpour S, Marmion C. Copper complexes as artificial DNA metallonucleases: From Sigman’s reagent to next generation anti-cancer agent? Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.08.043] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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An oxidized abasic lesion inhibits base excision repair leading to DNA strand breaks in a trinucleotide repeat tract. PLoS One 2018; 13:e0192148. [PMID: 29389977 PMCID: PMC5794147 DOI: 10.1371/journal.pone.0192148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/17/2018] [Indexed: 01/13/2023] Open
Abstract
Oxidative DNA damage and base excision repair (BER) play important roles in modulating trinucleotide repeat (TNR) instability that is associated with human neurodegenerative diseases and cancer. We have reported that BER of base lesions can lead to TNR instability. However, it is unknown if modifications of the sugar in an abasic lesion modulate TNR instability. In this study, we characterized the effects of the oxidized sugar, 5’-(2-phosphoryl-1,4-dioxobutane)(DOB) in CAG repeat tracts on the activities of key BER enzymes, as well as on repeat instability. We found that DOB crosslinked with DNA polymerase β and inhibited its synthesis activity in CAG repeat tracts. Surprisingly, we found that DOB also formed crosslinks with DNA ligase I and inhibited its ligation activity, thereby reducing the efficiency of BER. This subsequently resulted in the accumulation of DNA strand breaks in a CAG repeat tract. Our study provides important new insights into the adverse effects of an oxidized abasic lesion on BER and suggests a potential alternate repair pathway through which an oxidized abasic lesion may modulate TNR instability.
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36
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Lu HF, Chen HF, Kao CL, Chao I, Chen HY. A computational study of the Fenton reaction in different pH ranges. Phys Chem Chem Phys 2018; 20:22890-22901. [DOI: 10.1039/c8cp04381g] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mechanism of the Fenton reaction is pH dependent and four distinct reactive species have been identified and found to display quite different oxidation reactivities.
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Affiliation(s)
- Hsiu-Feng Lu
- Institute of Chemistry
- Academia Sinica
- Taipei 11529
- Taiwan
| | - Hui-Fen Chen
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung 80708
- Taiwan
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung 80708
- Taiwan
| | - Ito Chao
- Institute of Chemistry
- Academia Sinica
- Taipei 11529
- Taiwan
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung 80708
- Taiwan
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37
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Zheng L, Lin L, Qu K, Adhikary A, Sevilla MD, Greenberg MM. Independent Photochemical Generation and Reactivity of Nitrogen-Centered Purine Nucleoside Radicals from Hydrazines. Org Lett 2017; 19:6444-6447. [PMID: 29125775 DOI: 10.1021/acs.orglett.7b03368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Photochemical precursors that produce dA• and dG(N2-H)• are needed to investigate their reactivity. The synthesis of two 1,1-diphenylhydrazines (1, 2) and their use as photochemical sources of dA• and dG(N2-H)• is presented. Trapping studies indicate production of these radicals with good fidelity, and 1 was incorporated into an oligonucleotide via solid-phase synthesis. Cyclic voltammetric studies show that reduction potentials of 1 and 2 are lower than those of widely used "hole sinks", e.g., 8-oxodGuo and 7-deazadGuo, to investigate DNA-hole transfer processes. These molecules could be useful (a) as sources of dA• and dG(N2-H)• at specific sites in oligonucleotides and (b) as "hole sinks" for the study of DNA-hole transfer processes.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lu Lin
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ke Qu
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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38
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Bhat SS, Revankar VK, Shivalingegowda N, Lokanath NK. A fluorophore-labelled copper complex: crystal structure, hybrid cyclic water-perchlorate cluster and biological properties. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:710-717. [PMID: 28872069 DOI: 10.1107/s2053229617011639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/08/2017] [Indexed: 03/06/2023]
Abstract
A fluorophore-labelled copper(II) complex, aquabis(dimethylformamide-κO)(perchlorato-κO)[2-(quinolin-2-yl)-1,3-oxazolo[4,5-f][1,10]phenanthroline]copper(II) perchlorate monohydrate, [Cu(ClO4)(C22H12N4O)(C3H7NO)2(H2O)]ClO4·H2O, has been synthesized and characterized. A cyclic hydrogen-bonded water-perchlorate anionic cluster, i.e. [(ClO4)2(H2O)2]2-, has been identified within the structure. Each cyclic anionic cluster unit is interconnected by hydrogen bonding to the cation. The cations join into an infinite hydrogen-bonded chain running in the [010] direction. Furthermore, interaction of the complex with calf-thymus DNA (CT-DNA) and cellular localization within the cells was explored. Spectroscopic studies indicate that the compound has a good affinity for DNA and stains the nucleus of the cells.
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Affiliation(s)
- Satish S Bhat
- Department of Chemistry, Karnatak University, Pavate Nagar, Dharwad, Karnataka 580 003, India
| | - Vidyanand K Revankar
- Department of Chemistry, Karnatak University, Pavate Nagar, Dharwad, Karnataka 580 003, India
| | | | - N K Lokanath
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka 570 006, India
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39
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Paul R, Banerjee S, Greenberg MM. Synergistic Effects of an Irreversible DNA Polymerase Inhibitor and DNA Damaging Agents on HeLa Cells. ACS Chem Biol 2017; 12:1576-1583. [PMID: 28459532 DOI: 10.1021/acschembio.7b00259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA repair is vital to maintaining genome integrity but thwarts the effects of cytotoxic agents that target nucleic acids. Consequently, repair enzymes are potential targets for molecules that modulate cell function and anticancer therapeutics. DNA polymerase β (Pol β) is an attractive target because it plays a key role in base excision repair (BER), a primary pathway that repairs the effects of many DNA damaging agents. We previously identified an irreversible inhibitor of Pol β whose design was based upon a DNA lesion that inactivates Pol β and its back up BER enzyme, DNA polymerase λ (Pol λ). Using this molecule as a starting point, we characterized an irreversible inhibitor (13) of Pol β (IC50 = 0.4 μM) and Pol λ (IC50 = 0.25 μM) from a 130-member library of candidates that is ∼50-fold more effective against Pol β. Pro-13 (5 μM) is only slightly cytotoxic to human cervical cancer cells (HeLa) but potentiates the cytotoxicity of methyl methanesulfonate (MMS). DNA isolated from HeLa cells treated with MMS contains a ∼3-fold greater amount of abasic sites when pro-13 is present, consistent with inhibition of DNA repair. Proinhibitor pro-13 continues to induce cytotoxicity in DNA damaged cells following MMS removal. HeLa cell cytotoxicity is increased ∼100-fold following an 8 h incubation with pro-13 after cells were originally subjected to conditions under which 20% of the cells survive and reproduce. The potentiation of MMS cytotoxicity by pro-13 is greater than any previously reported BER enzyme repair inhibitor.
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Affiliation(s)
- Rakesh Paul
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Samya Banerjee
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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40
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Laverty DJ, Averill AM, Doublié S, Greenberg MM. The A-Rule and Deletion Formation During Abasic and Oxidized Abasic Site Bypass by DNA Polymerase θ. ACS Chem Biol 2017; 12:1584-1592. [PMID: 28459528 DOI: 10.1021/acschembio.7b00211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
DNA polymerase θ (Pol θ) is implicated in various cellular processes including double-strand break repair and apurinic/apyrimidinic site bypass. Because Pol θ expression correlates with poor cancer prognosis, the ability of Pol θ to bypass the C4'-oxidized abasic site (C4-AP) and 2-deoxyribonolactone (L), which are generated by cytotoxic agents, is of interest. Translesion synthesis and subsequent extension by Pol θ past C4-AP or L and an abasic site (AP) or its tetrahydrofuran analogue (F) was examined. Pol θ conducts translesion synthesis on templates containing AP and F with similar efficiencies and follows the "A-rule," inserting nucleotides in the order A > G > T. Translesion synthesis on templates containing C4-AP and L is less efficient than AP and F, and the preference for A insertion is reduced for L and absent for C4-AP. Extension past all abasic lesions (AP, F, C4-AP, and L) was significantly less efficient than translesion synthesis and yielded deletions caused by the base one or two nucleotides downstream from the lesion being used as a template, with the latter being favored. These results suggest that bypass of abasic lesions by Pol θ is highly mutagenic.
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Affiliation(s)
- Daniel J. Laverty
- Department
of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - April M. Averill
- Department
of Microbiology and Molecular Genetics, The Markey Center for Molecular
Genetics, The University of Vermont, 95 Carrigan Drive, Burlington, Vermont 05405, United States
| | - Sylvie Doublié
- Department
of Microbiology and Molecular Genetics, The Markey Center for Molecular
Genetics, The University of Vermont, 95 Carrigan Drive, Burlington, Vermont 05405, United States
| | - Marc M. Greenberg
- Department
of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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41
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Schäfer K, Ihmels H, Porcù E, Viola G. Control of the DNA-Binding and Antiproliferative Properties of Hydroxybenzo[b]quinolizinium Derivatives with pH and Light. Chemistry 2016; 23:370-379. [PMID: 27758047 DOI: 10.1002/chem.201603807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Indexed: 11/06/2022]
Abstract
The interactions of 8-hydroxybenzo[b]quinolizinium and 9-hydroxybenzo[b]quinolizinium with DNA are investigated in detail. Specifically, spectrophotometric and spectrofluorimetric titrations, thermal DNA-denaturation experiments as well as CD- and LD-spectroscopic analysis show that a pH shift by just one or two orders of magnitude has a significant impact on the interactions of the acidic ligands with the nucleic acid. Both ligands bind with high affinity to DNA at pH 6 (Kb ≈105 m-1 ). At pH 7 or 8, however, the binding interactions are much weaker because of the formation of the corresponding charge-neutral conjugate bases, the affinity to DNA of which is reduced because of the resulting lack of a positive charge. Notably, the variation of DNA affinity occurs in a range that corresponds to the fluctuations of pH values under physiological conditions, so that these ligands may be employed to target DNA in tissue with particular pH values, especially, cancer cells. The antiproliferative activity of the title compounds under different conditions is also investigated. In the absence of irradiation, both compounds show only a modest cytotoxicity toward cancer cells. However, upon irradiation, even at low UV-A doses, a significant reduction of cell viability of tumor cell lines is induced by the ligands.
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Affiliation(s)
- Katy Schäfer
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Heiko Ihmels
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Elena Porcù
- Dipartimento di Salute della Donna e del Bambino, Laboratorio di Oncoematologia, University of Padova, via Giustiniani 3, 35128, Padova, Italy
| | - Giampietro Viola
- Dipartimento di Salute della Donna e del Bambino, Laboratorio di Oncoematologia, University of Padova, via Giustiniani 3, 35128, Padova, Italy
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42
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Huang Z, Zhou L. A theoretical study on electrons attachment to the trans-[Pt(P)NH3Cl2] (P=3-picoline or pyridine) and the subsequent interacting with ribose moiety or thymine(T). COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Synthesis, characterization and biological studies on some metal complexes with Schiff base ligand containing pyrazolone moiety. JOURNAL OF SAUDI CHEMICAL SOCIETY 2016. [DOI: 10.1016/j.jscs.2013.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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45
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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46
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Liu C, Zhu Y, Tang M. Theoretical studies on binding modes of copper-based nucleases with DNA. J Mol Graph Model 2015; 64:11-29. [PMID: 26766349 DOI: 10.1016/j.jmgm.2015.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/06/2023]
Abstract
In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.
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Affiliation(s)
- Chunmei Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China
| | - Yanyan Zhu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
| | - Mingsheng Tang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
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Xu W, Ouellette A, Ghosh S, O'Neill TC, Greenberg MM, Zhao L. Mutagenic Bypass of an Oxidized Abasic Lesion-Induced DNA Interstrand Cross-Link Analogue by Human Translesion Synthesis DNA Polymerases. Biochemistry 2015; 54:7409-22. [PMID: 26626537 DOI: 10.1021/acs.biochem.5b01027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5'-(2-Phosphoryl-1,4-dioxobutane) (DOB) is an oxidized abasic site that is produced by several antitumor agents and γ-radiolysis. DOB reacts reversibly with a dA opposite the 3'-adjacent nucleotide to form DNA interstrand cross-links (ICLs), genotoxic DNA lesions that can block DNA replication and transcription. Translesion synthesis (TLS) is an important step in several ICL repair pathways to bypass unhooked intermediates generated by endonucleolytic incision. The instability of DOB-ICLs has made it difficult to learn about their TLS-mediated repair capability and mutagenic potential. We recently developed a method for chemically synthesizing oligonucleotides containing a modified DOB-ICL analogue. Herein, we examined the capabilities of several highly relevant eukaryotic TLS DNA polymerases (pols), including human pol η, pol κ, pol ι, pol ν, REV1, and yeast pol ζ, to bypass this DOB-ICL analogue. The prelesion, translesion, and postlesion replication efficiency and fidelity were examined. Pol η showed moderate bypass activity when encountering the DOB-ICL, giving major products one or two nucleotides beyond the cross-linked template nucleotide. In contrast, DNA synthesis by the other pols was stalled at the position before the cross-linked nucleotide. Steady-state kinetic data and liquid chromatography-mass spectrometry sequencing of primer extension products by pol η unambiguously revealed that pol η-mediated bypass is highly error-prone. Together, our study provides the first set of in vitro evidence that the DOB-ICL is a replication-blocking and highly miscoding lesion. Compared to several other TLS pols examined, pol η is likely to contribute to the TLS-mediated repair of the DOB-ICL in vivo.
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Affiliation(s)
| | | | - Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | | | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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Soler M, Figueras E, Serrano-Plana J, González-Bártulos M, Massaguer A, Company A, Martínez MÁ, Malina J, Brabec V, Feliu L, Planas M, Ribas X, Costas M. Design, Preparation, and Characterization of Zn and Cu Metallopeptides Based On Tetradentate Aminopyridine Ligands Showing Enhanced DNA Cleavage Activity. Inorg Chem 2015; 54:10542-58. [PMID: 26503063 DOI: 10.1021/acs.inorgchem.5b01680] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The conjugation of redox-active complexes that can function as chemical nucleases to cationic tetrapeptides is pursued in this work in order to explore the expected synergistic effect between these two elements in DNA oxidative cleavage. Coordination complexes of biologically relevant first row metal ions, such as Zn(II) or Cu(II), containing the tetradentate ligands 1,4-dimethyl-7-(2-pyridylmethyl)-1,4,7-triazacyclononane ((Me2)PyTACN) and (2S,2S')-1,1'-bis(pyrid-2-ylmethyl)-2,2'-bipyrrolidine ((S,S')-BPBP) have been linked to a cationic LKKL tetrapeptide sequence. Solid-phase synthesis of the peptide-tetradentate ligand conjugates has been developed, and the preparation and characterization of the corresponding metallotetrapeptides is described. The DNA cleavage activity of Cu and Zn metallopeptides has been evaluated and compared to their metal binding conjugates as well as to the parent complexes and ligands. Very interestingly, the oxidative Cu metallopeptides 1Cu and 2Cu show an enhanced activity compared to the parent complexes, [Cu(PyTACN)](2+) and [Cu(BPBP)](2+), respectively. Under optimized conditions, 1Cu displays an apparent pseudo first-order rate constant (kobs) of ∼0.16 min(-1) with a supercoiled DNA half-life time (t1/2) of ∼4.3 min. On the other hand, kobs for 2Cu has been found to be ∼0.11 min(-1) with t1/2 ≈ 6.4 min. Hence, these results point out that the DNA cleavage activities promoted by the metallopeptides 1Cu and 2Cu render ∼4-fold and ∼23 rate accelerations in comparison with their parent Cu complexes. Additional binding assays and mechanistic studies demonstrate that the enhanced cleavage activities are explained by the presence of the cationic LKKL tetrapeptide sequence, which induces an improved binding affinity to the DNA, thus bringing the metal ion, which is responsible for cleavage, in close proximity.
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Affiliation(s)
- Marta Soler
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain.,LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Eduard Figueras
- LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Joan Serrano-Plana
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Marta González-Bártulos
- Biochemistry of Cancer Group, Biochemistry and Molecular Biology Unit, Department de Química and Department of Biology, Universitat de Girona , Campus Montilivi, 17071 Girona, Catalunya, Spain
| | - Anna Massaguer
- Biochemistry of Cancer Group, Biochemistry and Molecular Biology Unit, Department de Química and Department of Biology, Universitat de Girona , Campus Montilivi, 17071 Girona, Catalunya, Spain
| | - Anna Company
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Ma Ángeles Martínez
- Biochemistry of Cancer Group, Biochemistry and Molecular Biology Unit, Department de Química and Department of Biology, Universitat de Girona , Campus Montilivi, 17071 Girona, Catalunya, Spain
| | - Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Lidia Feliu
- LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Marta Planas
- LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Xavi Ribas
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Miquel Costas
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
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49
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Weng L, Greenberg MM. Rapid Histone-Catalyzed DNA Lesion Excision and Accompanying Protein Modification in Nucleosomes and Nucleosome Core Particles. J Am Chem Soc 2015; 137:11022-31. [PMID: 26290445 DOI: 10.1021/jacs.5b05478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
C5'-Hydrogen atoms are frequently abstracted during DNA oxidation. The oxidized abasic lesion 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) is an electrophilic product of the C5'-radical. DOB is a potent irreversible inhibitor of DNA polymerase β, and forms interstrand cross-links in free DNA. We examined the reactivity of DOB within nucleosomes and nucleosome core particles (NCPs), the monomeric component of chromatin. Depending upon the position at which DOB is generated within a NCP, it is excised from nucleosomal DNA at a rate 275-1500-fold faster than that in free DNA. The half-life of DOB (7.0-16.8 min) in NCPs is shorter than any other abasic lesion. DOB's lifetime in NCPs is also significantly shorter than the estimated lifetime of an abasic site within a cell, suggesting that the observed chemistry would occur intracellularly. Histones also catalyze DOB excision when the lesion is present in the DNA linker region of a nucleosome. Schiff-base formation between DOB and histone proteins is detected in nucleosomes and NCPs, resulting in pyrrolone formation at the lysine residues. The lysines modified by DOB are often post-translationally modified. Consequently, the histone modifications described herein could affect the regulation of gene expression and may provide a chemical basis for the cytotoxicity of the DNA damaging agents that produce this lesion.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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50
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Lartia R, Constant JF. Synthetic access to the chemical diversity of DNA and RNA 5′-aldehyde lesions. J Org Chem 2015; 80:705-10. [PMID: 25372153 DOI: 10.1021/jo502170e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen atom abstraction from the C5′-position of nucleotides in DNA results in direct strand scission by generating alkali-labile fragments from the oxidized nucleotide. The major damage consists in a terminus containing a 5′-aldehyde as part of an otherwise undamaged nucleotide. Moreover it is considered as a polymorphic DNA strand break lesion since it can be borne by any of the four nucleosides encountered in DNA. Here we propose an expeditious synthesis of oligonucleotides (ON) ending with this 5′-aldehyde group (5′-AODN). This straightforward and cheap strategy relies on Pfitzner–Moffatt oxidation performed on solid support followed by a transient protection of the resulting aldehyde function. This method is irrespective of the 5′-terminal nucleobase and most interestingly can be directly extended to RNA to produce the corresponding 5′-AORN. We also report preliminary results on recognition of 5′-AODN by base excision repair (BER) enzymes.
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