1
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Huynh M, Vinck R, Gibert B, Gasser G. Strategies for the Nuclear Delivery of Metal Complexes to Cancer Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311437. [PMID: 38174785 DOI: 10.1002/adma.202311437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/20/2023] [Indexed: 01/05/2024]
Abstract
The nucleus is an essential organelle for the function of cells. It holds most of the genetic material and plays a crucial role in the regulation of cell growth and proliferation. Since many antitumoral therapies target nucleic acids to induce cell death, tumor-specific nuclear drug delivery could potentiate therapeutic effects and prevent potential off-target side effects on healthy tissue. Due to their great structural variety, good biocompatibility, and unique physico-chemical properties, organometallic complexes and other metal-based compounds have sparked great interest as promising anticancer agents. In this review, strategies for specific nuclear delivery of metal complexes are summarized and discussed to highlight crucial parameters to consider for the design of new metal complexes as anticancer drug candidates. Moreover, the existing opportunities and challenges of tumor-specific, nucleus-targeting metal complexes are emphasized to outline some new perspectives and help in the design of new cancer treatments.
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Affiliation(s)
- Marie Huynh
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Robin Vinck
- Orano, 125 avenue de Paris, Châtillon, 92320, France
| | - Benjamin Gibert
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
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2
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Das H, Paul L, Chowdhury S, Goswami R, Das S. New insights into self-structure induction in poly (rA) by Quinacrine through non-classical intercalation: Spectroscopic and theoretical perspectives. Int J Biol Macromol 2023; 251:126189. [PMID: 37586624 DOI: 10.1016/j.ijbiomac.2023.126189] [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: 05/17/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
Self-structure induction in a single stranded polyriboadenylic acid [poly (rA)] is an auspicious physiological phenomenon which switches off protein production in tumor cells. In the present study, the self-structure induction process in poly (rA) moiety was thoroughly investigated using various steady state and time resolved techniques. Optical melting pattern directly evidenced the formation of self-structured assembly in single stranded poly (rA) upon complexation with quinacrine. Further, UV-absorption spectroscopic studies revealed that quinacrine binds to poly (rA) in co-operative fashion and the indication of intercalative mode of binding first came out with the involvement of around two base pairs of poly (rA) in the complexation. Experimental observations established the unconventional or non-classical intercalation of quinacrine molecule inside self-structured duplex poly (rA) moiety. This complexation was accompanied with negative enthalpy change and positive entropy change; suggesting strong van der Waals and the H-bonding interactions as the major governing forces in the complexation. Moreover, ionic strength dependent binding study established that the non-polyelectrolytic forces were the dominating forces. Further, the photo physical behavior of QN was authenticated using time dependent density functional theory (TDDFT) where both the ground and excited states were exploited.
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Affiliation(s)
- Himal Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Lopa Paul
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Rapti Goswami
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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3
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Yuan J, Song JY, Yang HH, Lan HR, Xing AP, Li KH, Zeng D, Zhang ZQ, Feng SY. Synthesis, cytotoxicity and DNA binding of novel Ni(II), Co(II) and Zn(II) complexes bearing pyrimidinyl hydrazone ligand. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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4
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Fudickar W, Roder P, Listek M, Hanack K, Linker T. Pyridinium Alkynylanthracenes as Sensitizers for Photodynamic Therapy. Photochem Photobiol 2021; 98:193-201. [PMID: 34719028 DOI: 10.1111/php.13554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/28/2021] [Indexed: 01/02/2023]
Abstract
Photodynamic therapy (PDT) is a mild but effective method to treat certain types of cancer upon irradiation with visible light. Here, three isomeric methylpyridinium alkynylanthracenes 1o─p were evaluated as sensitizers for PDT. Upon irradiation with blue or green light, all three compounds show the ability to initiate strand breaks of plasmid DNA. The mayor species responsible for cleavage is singlet oxygen (1 O2 ) as confirmed by scavenging reagents. Only isomers 1m and 1p can be incorporated into HeLa cells, whereas isomer 1o cannot permeate through the membrane. While isomer 1m targets the cell nucleus, isomer 1p assembles in the cellular cytoplasm and impacts the cellular integrity. This is in accordance with a moderate toxicity of 1p in the dark, whereas 1m exhibits no dark toxicity. Both isomers are suitable as PDT reagents, with a CC50 of 3 μm and 75 nm, for 1p and 1m, respectively. Thus, derivative 1m, which can be easily synthesized, becomes an interesting candidate for cancer therapy.
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Affiliation(s)
- Werner Fudickar
- Department of Chemistry, University of Potsdam, Potsdam, Germany
| | - Phillip Roder
- Department of Chemistry, University of Potsdam, Potsdam, Germany
| | - Martin Listek
- Department of Biology, University of Potsdam, Potsdam, Germany
| | - Katja Hanack
- Department of Biology, University of Potsdam, Potsdam, Germany
| | - Torsten Linker
- Department of Chemistry, University of Potsdam, Potsdam, Germany
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5
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Berdnikova DV, Heider J, Ihmels H, Sewald N, Pithan PM. Photoinduced Release of DNA‐Binding Ligands from the [4+4] Dimers of Benzo[ b]quinolizinium and Anthracene Derivatives. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daria V. Berdnikova
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Josef Heider
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Heiko Ihmels
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic ChemistryBielefeld University PO Box 100121 33501 Bielefeld Germany
| | - Phil M. Pithan
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
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6
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Jeon BR, Chitrapriya N, Kwak MI, Jung MJ, Kim SK, Jang YJ. Effect of the bridge structure on the binding mode of the binuclear ruthenium complex to native DNA. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.126954] [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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7
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Phadte AA, Banerjee S, Mate NA, Banerjee A. Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines. Biochem Biophys Rep 2019; 18:100629. [PMID: 30993216 PMCID: PMC6449707 DOI: 10.1016/j.bbrep.2019.100629] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022] Open
Abstract
Push-pull dibenzodioxins and phenazines having ‘anthracene-like’ planar structures and good charge transfer character had been previously synthesised in our laboratory. The dibenzodioxins had earlier proven their anti-proliferative nature against HeLa tumor cell lines. Since phenazines are structural analogues of the former, these molecules were evaluated in course of the current study for their cytotoxic action against HeLa cell lines and they exhibited strong anti-tumor activity. This behavior could be related to their good DNA binding property. The DNA binding modes of molecules 1–4 (Fig. 1) were evaluated using various experimental techniques and they interacted with DNA in a non-covalently by both intercalative as well as groove binding mechanisms. Molecule 1 follows predominantly intercalative binding mode whereas molecules 2 and 3 have nearly equal and opposite preferences for both groove binding and intercalative modes. For molecule 4, groove binding is preferred mode of binding to DNA. A rationale for such differential binding behaviour is provided based on the subtle structural differences in our synthesised dibenzodioxins and phenazines. Elucidation of the mode of a molecule-DNA-binding event is relevant for understanding the mechanism of action of these molecules and will help promote further research into designing better DNA targeting small molecules. DNA binding modes of push-pull planar dibenzodioxins and phenazines were elucidated. DNA binding mechanistic details were obtained by spectroscopic and viscometric techniques. The molecular shape and geometry has a bearing on its choice of binding mode.
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Affiliation(s)
- Apeksha Ashok Phadte
- Department of Chemistry, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
| | - Subhadeep Banerjee
- Department of Chemistry, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
| | - Nayan Anand Mate
- Department of Biological Sciences, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
| | - Arnab Banerjee
- Department of Biological Sciences, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
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8
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Hassan AA, Aly AA, Mohamed NK, El Shaieb KM, Makhlouf MM, Abdelhafez ESMN, Bräse S, Nieger M, Dalby KN, Kaoud TS. Design, synthesis, and DNA interaction studies of furo-imidazo[3.3.3]propellane derivatives: Potential anticancer agents. Bioorg Chem 2019; 85:585-599. [PMID: 30878891 PMCID: PMC6543821 DOI: 10.1016/j.bioorg.2019.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 11/26/2022]
Abstract
A large number of natural products containing the propellane scaffold have been reported to exhibit cytotoxicity against several cancers; however, their mechanism of action is still unknown. Anticancer drugs targeting DNA are mainly composed of small planar molecule/s that can interact with the DNA helix, causing DNA malfunction and cell death. The aim of this study was to design and synthesize propellane derivatives that can act as DNA intercalators and/or groove binders. The unique structure of the propellane derivatives and their ability to display planar ligands with numerous possible geometries, renders them potential starting points to design new drugs targeting DNA in cancer cells. New substituted furo-imidazo[3.3.3]propellanes were synthesized via the reaction of substituted alkenylidene-hydrazinecarbothioamides with 2-(1,3-dioxo-2,3-dihydro-1H-2-ylidene)propanedinitrile in tetrahydrofuran at room temperature. The structures of the products were confirmed by a combination of elemental analysis, NMR, ESI-MS, IR and single crystal X-ray analysis. Interestingly, 5c, 5d and 5f showed an ability to interact with Calf Thymus DNA (CT-DNA). Their DNA-binding mode was investigated using a combination of absorption spectroscopy, DNA melting, viscosity, CD spectroscopy measurements, as well as competitive binding studies with several dyes. Their cytotoxicity was evaluated against the NCI-60 panel of cancer cell lines. 5c, 5d and 5f exhibited similar anti-proliferative activity against the A549 non-small cell lung cancer (NSCLC) cell line. Further mechanistic studies revealed their ability to induce DNA damage in the A549 cell line, as well as apoptosis, evidenced by elevated Annexin V expression, enhanced caspase 3/7 activation and PARP cleavage. In this study, we present the potential for designing novel propellanes to provoke cytotoxic activity, likely through DNA binding-induced DNA damage and apoptosis.
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Affiliation(s)
- Alaa A Hassan
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Ashraf A Aly
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Nasr K Mohamed
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Kamal M El Shaieb
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Maysa M Makhlouf
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | | | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe 76131, Germany; Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Martin Nieger
- Department of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtasen aukio I, Helsinki 00014, Finland
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tamer S Kaoud
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, El-Minia 61519, Egypt; Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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9
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Safiarian MS, Sawoo S, Mapp CT, Williams DE, Gude L, Fernández M, Lorente A, Grant KB. Aminomethylanthracene Dyes as High‐Ionic‐Strength DNA‐Photocleaving Agents: Two Rings are Better than One. ChemistrySelect 2018. [DOI: 10.1002/slct.201703019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Sudeshna Sawoo
- Department of Chemistry Georgia State University, Atlanta GA 30302–3965 USA
| | - Carla T. Mapp
- Department of Chemistry Georgia State University, Atlanta GA 30302–3965 USA
| | | | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805-Alcalá de Henares Madrid Spain
| | - María‐José Fernández
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805-Alcalá de Henares Madrid Spain
| | - Antonio Lorente
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805-Alcalá de Henares Madrid Spain
| | - Kathryn B. Grant
- Department of Chemistry Georgia State University, Atlanta GA 30302–3965 USA
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10
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Inclán M, Guijarro L, Pont I, Frías JC, Rotger C, Orvay F, Costa A, García-España E, Albelda MT. Binding Mode and Selectivity of a Scorpiand-Like Polyamine Ligand to Single- and Double-Stranded DNA and RNA: Metal- and pH-Driven Modulation. Chemistry 2017; 23:15966-15973. [PMID: 28833584 DOI: 10.1002/chem.201702934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/18/2017] [Indexed: 01/07/2023]
Abstract
The interaction of a polyazacyclophane ligand having an ethylamine pendant arm functionalized with an anthryl group (L), with the single-stranded polynucleotides polyA, polyG, polyU, and polyC as well as with the double-stranded polynucleotides polyA-polyU, poly(dAT)2 , and poly(dGC)2 has been followed by UV/Vis titration, steady state fluorescence spectroscopy, and thermal denaturation measurements. In the case of the single-stranded polynucleotides, the UV/Vis and fluorescence titrations permit to distinguish between sequences containing purine and pyrimidine bases. For the double-stranded polynucleotides the UV/Vis measurements show for all of them hypochromicity and bathochromic shifts. However, the fluorescence studies reveal that both polyA-polyU and poly(dAT)2 induce a twofold increase in the fluorescence, whereas interaction of poly(dGC)2 with the ligand L induces a quenching of the fluorescence. Cu2+ modulates the interaction with the double-stranded polynucleotides due to the conformation changes that its coordination induces in compound L. In general, the spectroscopic studies show that intercalation seems to be blocked by the formation of the metal complex. All these features suggest the possibility of using compound L as a sequence-selective fluorescence probe.
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Affiliation(s)
- Mario Inclán
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980, Paterna, Spain
| | - Lluis Guijarro
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980, Paterna, Spain
| | - Isabel Pont
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980, Paterna, Spain
| | - Juan C Frías
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980, Paterna, Spain.,Departamento de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Ramón y Cajal s/n, 46115, Alfara del Patriarca, Spain
| | - Carmen Rotger
- Department of Chemistry, University of Balearic Islands, E-07122, Palma de Mallorca, Baleares, Spain
| | - Francisca Orvay
- Department of Chemistry, University of Balearic Islands, E-07122, Palma de Mallorca, Baleares, Spain
| | - Antoni Costa
- Department of Chemistry, University of Balearic Islands, E-07122, Palma de Mallorca, Baleares, Spain
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980, Paterna, Spain
| | - M Teresa Albelda
- Department of Inorganic Chemistry, Institute for Molecular Science, University of Valencia, Catedratico Jose Beltran 2, 46980, Paterna, Spain.,GIBI230, Grupo de Investigación Biomédica en Imagen IIS La Fe, Valencia, Spain
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11
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Vittala SK, Saraswathi SK, Joseph J. Fullerene Cluster Assisted Self-Assembly of Short DNA Strands into Semiconducting Nanowires. Chemistry 2017; 23:15759-15765. [PMID: 28858402 DOI: 10.1002/chem.201703333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 01/02/2023]
Abstract
Programmable, hierarchical assembly of DNA nanostructures with precise organisation of functional components have been demonstrated previously with tiled assembly and DNA origami. However, building organised nanostructures with random oligonucleotide strands remains as an elusive problem. Herein, a simple and general strategy, in which nanoclusters of a fullerene derivative act as stapler motifs in bringing ordered nanoscale assembly of short oligonucleotide duplexes into micrometre-sized nanowires, is described. In this approach, the fullerene derivative, by virtue of its amphiphilic structure and unique hydrophobic-hydrophilic balance, pre-assembles to form 3-5 nm sized clusters in a mixture of DMSO-phosphate buffer, which further assists the assembly of DNA strands. The optimum cluster size, availability of DNA anchoring motifs and the nature of the DNA strands controls the structure of these nanomaterials. Furthermore, horizontal conductivity measurements through conductive AFM confirmed the charge transport properties of these nanowires. The current strategy could be employed to organise random DNA duplexes and tiles into functional nanostructures, and hence, open up new avenues in DNA nanotechnology.
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Affiliation(s)
- Sandeepa Kulala Vittala
- Photosciences and Photonics Section, CSIR, National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST Campus, Thiruvananthapuram, Kerala, 695019, India
| | - Sajena Kanangat Saraswathi
- Photosciences and Photonics Section, CSIR, National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST Campus, Thiruvananthapuram, Kerala, 695019, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR, National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST Campus, Thiruvananthapuram, Kerala, 695019, India
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12
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Kataev EA, Shumilova TA, Fiedler B, Anacker T, Friedrich J. Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study. J Org Chem 2016; 81:6505-14. [PMID: 27314892 DOI: 10.1021/acs.joc.6b01130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations.
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Affiliation(s)
- Evgeny A Kataev
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Tatiana A Shumilova
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Benjamin Fiedler
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Tony Anacker
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Joachim Friedrich
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
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13
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Bullen GA, Tucker JHR, Peacock AFA. Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding. Chem Commun (Camb) 2015; 51:8130-3. [DOI: 10.1039/c5cc01618e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we detail the first example of anthracene photodimerisation in peptides, and use it to trigger a selective biomolecular recognition event.
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14
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Jaividhya P, Ganeshpandian M, Dhivya R, Akbarsha MA, Palaniandavar M. Fluorescent mixed ligand copper(ii) complexes of anthracene-appended Schiff bases: studies on DNA binding, nuclease activity and cytotoxicity. Dalton Trans 2015; 44:11997-2010. [DOI: 10.1039/c5dt00899a] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
While the phen of [Cu(L1–L5)(phen)(ACN)]2+ partially inserts into DNA base pairs the anthracenyl moiety of L1–L5 interacts with DNA hydrophobically.
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Affiliation(s)
| | | | - Rajkumar Dhivya
- Department of Animal Science
- Bharathidasan University
- Tiruchirappalli 620 024
- India
| | - Mohammad Abdulkadher Akbarsha
- Mahatma Gandhi-Doerenkamp Center for Alternatives to use of Animals in Life Science Education
- Bharathidasan University
- Tiruchirappalli
- India
- Department of Food Sciences and Nutrition
| | - Mallayan Palaniandavar
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli 620 024
- India
- Department of Chemistry
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15
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Pujari SS, Ingale SA, Seela F. High-density functionalization and cross-linking of DNA: "click" and "bis-click" cycloadditions performed on alkynylated oligonucleotides with fluorogenic anthracene azides. Bioconjug Chem 2014; 25:1855-70. [PMID: 25154019 DOI: 10.1021/bc5003532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High density functionalization of DNA with ethynyl and octadiynyl side chains followed by CuAAC "click labeling" with 9-azidomethylanthracene was performed. Alkynyl DNA was also cross-linked with fluorogenic 9,10-bis-azidomethylanthracene employing the "bis-click" reaction. By this means the fluorescence of the anthracene moiety was imparted to the virtually nonfluorescent DNA. Phosphoramidites of 8-aza-7-deaza-2'-deoxyadenosine with short and long linker arms in a steric nondemanding 7-position were utilized in solid phase oligodeoxynucleotide synthesis. High density alkynylated DNA-without anthracene residues-was found to be of comparable stability with both long and short linker arms. High density anthracene functionalized DNA became less stable with the short linker compared to that with the long linker connectivity. Interstrand cross-linked homodimers constructed from alkynylated oligonucleotides with fluorogenic 9,10-bis-azidomethylanthracene were hybridized with complementary strands to form double helices. They are more stable when the linker was located at a terminus than in a central position. Short linker anthracene adducts were destabilizing compared to long linker adducts. The fluorogenic anthracene residues not only have a significant effect on the duplex stability, but also impart fluorescence to the species. Fluorescence of cross-linked double helices with long linker connectivity was quenched when the cross-link was in a terminal position and was dequenched when the linker was connecting the two double helices at the center of the molecule. The fluorescence of the anthracene cross-linked double helices was strongly increased (dequenched) when the correct base pair was formed, while no change occurred upon mismatch formation.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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16
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Paul P, Suresh Kumar G. Self-structure formation in polyadenylic acid by small molecules: new insights from the binding of planar dyes thionine and toluidine blue O. RSC Adv 2014. [DOI: 10.1039/c4ra02671c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Thionine and toluidine blue targeting poly(A).
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Affiliation(s)
- Puja Paul
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032, India
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17
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Ganeshpandian M, Loganathan R, Suresh E, Riyasdeen A, Akbarsha MA, Palaniandavar M. New ruthenium(ii) arene complexes of anthracenyl-appended diazacycloalkanes: effect of ligand intercalation and hydrophobicity on DNA and protein binding and cleavage and cytotoxicity. Dalton Trans 2014; 43:1203-19. [DOI: 10.1039/c3dt51641e] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Chitrapriya N, Kim R, Jang YJ, Cho DW, Han SW, Kim SK. Sequence Dependent Binding Modes of the ΔΔ- and ΛΛ-binuclear Ru(II) Complexes to poly[d(G-C) 2] and poly[d(A-T) 2]. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Karunakaran SC, Ramaiah D, Schulz I, Epe B. Study of the Mode and Efficiency of DNA Binding in the Damage Induced by Photoactivated Water Soluble Porphyrins. Photochem Photobiol 2013; 89:1100-5. [DOI: 10.1111/php.12088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/28/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Suneesh C. Karunakaran
- Chemical Sciences and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Trivandrum; India
| | - Danaboyina Ramaiah
- Chemical Sciences and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Trivandrum; India
| | - Ina Schulz
- Institute of Pharmacy and Biochemistry; University of Mainz; Mainz; Germany
| | - Bernd Epe
- Institute of Pharmacy and Biochemistry; University of Mainz; Mainz; Germany
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20
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Avirah RR, Schuster GB. Fluorescence Quenching by Intercalation of a Pyrene Group Tethered to anN4-modified Cytosine in Duplex DNA. Photochem Photobiol 2012; 89:332-5. [DOI: 10.1111/j.1751-1097.2012.01243.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/11/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Rekha R. Avirah
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta; GA; USA
| | - Gary B. Schuster
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta; GA; USA
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21
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Kim HN, Lee EH, Xu Z, Kim HE, Lee HS, Lee JH, Yoon J. A pyrene-imidazolium derivative that selectively Recognizes G-Quadruplex DNA. Biomaterials 2012; 33:2282-8. [DOI: 10.1016/j.biomaterials.2011.11.073] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/25/2011] [Indexed: 01/06/2023]
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22
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Basu A, Jaisankar P, Kumar GS. 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogues induce self-structure in polyadenylic acid. RSC Adv 2012. [DOI: 10.1039/c2ra20841e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Terry CA, Fernández MJ, Gude L, Lorente A, Grant KB. Physiologically relevant concentrations of NaCl and KCl increase DNA photocleavage by an N-substituted 9-aminomethylanthracene dye. Biochemistry 2011; 50:10375-89. [PMID: 22014335 DOI: 10.1021/bi200972c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This paper describes the synthesis of a new 9-aminomethylanthracene dye N-substituted with a pyridinylpolyamine side chain (4). The effects of NaCl and KCl on anthracene/DNA interactions were then studied, with the goal of simulating the conditions of high ionic strength that a DNA photosensitizer might encounter in the cell nucleus (~150 mM of NaCl and 260 mM of KCl). As exemplified by methylene blue (5), the expected effect of increasing ionic strength is to decrease DNA binding and photocleavage yields. In contrast, the addition of 150 mM of NaCl in combination with 260 mM of KCl to photocleavage reactions containing micromolar concentrations of 4 triggers the conversion of supercoiled, nicked, and linear forms of pUC19 plasmid into a highly degraded band of DNA fragments (350 nm hν, pH 7.0). Circular dichroism spectra point to a correlation between salt-induced unwinding of the DNA helix and the increase in DNA photocleavage yields. The results of circular dichroism, UV-vis absorption, fluorescence emission, thermal denaturation, and photocleavage inhibition experiments suggest that the combination of salts causes a change in the DNA binding mode of 4 from intercalation to an external interaction. This in turn leads to an increase in the anthracene-sensitized production of DNA-damaging reactive oxygen species.
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Affiliation(s)
- Carla A Terry
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, United States
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24
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Xu W, Tan JH, Chen SB, Hou JQ, Li D, Huang ZS, Gu LQ. Studies on the binding of 5-N-methylated quindoline derivative to human telomeric G-quadruplex. Biochem Biophys Res Commun 2011; 406:454-8. [DOI: 10.1016/j.bbrc.2011.02.070] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 02/14/2011] [Indexed: 01/17/2023]
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25
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Islam MM, Basu A, Suresh Kumar G. Binding of 9-O-(ω-amino) alkyl ether analogues of the plant alkaloid berberine to poly(A): insights into self-structure induction. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00209g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Seela F, Pujari SS. Azide-alkyne "click" conjugation of 8-aza-7-deazaadenine-DNA: synthesis, duplex stability, and fluorogenic dye labeling. Bioconjug Chem 2010; 21:1629-41. [PMID: 20681566 DOI: 10.1021/bc100090y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The internal dye labeling of DNA by the Huisgen-Meldal-Sharpless "click" reaction is described. Fluorogenic 9-azidomethyl anthracene 2 and 3-azido-7-hydroxycoumarin 3 were employed in the postsynthetic functionalization of oligonucleotides incorporating octa-(1,7)-diynyl-8-aza-7-deaza-2'-deoxyadenosine 1. Nucleoside 1 was prepared by Sonogashira cross coupling from the corresponding 7-iodo compound, converted into the corresponding phosphoramidite, and oligonucleotides were synthesized. To evaluate the influence of ligands on the oligonucleotide duplex stability, benzyl azide 4 (nonpolar), and 2',3'-dideoxy azidothymidine 5 (AZT) (polar) were introduced along with the fluorogenic dyes 2 and 3. DNA duplexes with octa-1,7-diynyl side chains (i.e., containing 1) are more stable than oligonucleotides containing 8-aza-7-deaza-2'-deoxyadenosine, unveiling that this side chain has steric freedom. A single conjugation by an anthracene residue led to a 9 °C T(m) increase of duplex melting. Contrary to 7-deazaadenine dye conjugates, the 8-aza-7-deazaadenine conjugates show virtually no fluorescence quenching, thereby developing almost as strong fluorescence as side chain click derivatives (32 and 33) in the absence of 8-aza-7-deazaadenine moiety. Duplexes containing the 8-aza-7-deazaadenine dye conjugate show increased fluorescence over single-stranded DNA. Mismatches with dA, dG, and dC develop reduced fluorescence compared to the fully matched base pair. Molecular dynamics simulations revealed that the bulky dye molecules are accommodated well in duplex DNA.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, Münster, Germany.
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27
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Interaction of a copper(II)-Schiff base complexes with calf thymus DNA and their antimicrobial activity. Int J Biol Macromol 2010; 48:319-25. [PMID: 21145345 DOI: 10.1016/j.ijbiomac.2010.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 11/25/2010] [Accepted: 12/01/2010] [Indexed: 11/22/2022]
Abstract
The interaction of a copper complexes containing Schiff bases with calf thymus (CT) DNA was investigated by spectroscopic methods. UV-vis, fluorescence and CD spectroscopies were conducted to assess their binding ability with CT DNA. The binding constants K have been estimated from 0.8 to 9.1×10(4) M(-1). The percentage of hypochromism is found to be over 70% (from spectral titrations). The results showed that the copper(II) complexes could bind to DNA with an intercalative mode. Synergic action of Cu(II) complexes with ascorbic acid against Candida albicans induced the generation of free radicals and increased (more than 60 times) antimicrobial effect of these complexes.
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28
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Saha I, Hossain M, Suresh Kumar G. Sequence-selective binding of phenazinium dyes phenosafranin and safranin O to guanine-cytosine deoxyribopolynucleotides: spectroscopic and thermodynamic studies. J Phys Chem B 2010; 114:15278-87. [PMID: 20979425 DOI: 10.1021/jp1064598] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequence selectivity of the DNA binding of the phenazinium dyes phenosafranin and safranin O have been investigated with four sequence-specific deoxyribopolynucleotides from spectroscopic and calorimetric studies. The alternating guanine-cytosine sequence selectivity of the dyes has been revealed from binding affinity values, circular dichroism, thermal melting, competition dialysis, and calorimetric results. The binding affinities of both the dyes to the polynucleotides were of the order of 10(5) M(-1), but the values were higher for the guanine-cytosine polynucleotides over adenine-thymine ones. Phenosafranin had a higher binding affinity compared to safranin O. Isothermal titration calorimetric studies revealed that the binding reactions were exothermic and favored by negative enthalpy and predominantly large positive entropy contributions in all cases except poly(dA)·poly(dT) where the profile was anomalous. Although charged, nonpolyelectrolytic contribution was revealed to be dominant to the free energy of binding. The negative heat capacity values obtained from the temperature dependence of enthalpy changes, which were higher for phenosafranin compared to safranin O, suggested significant hydrophobic contribution to the binding process. In aggregate, the data presents evidence for the alternating guanine-cytosine base pair selectivity of these phenazinium dyes and a stronger binding of phenosafranin over safranin O.
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Affiliation(s)
- Ishita Saha
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), Kolkata 700 032, India
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