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Mikaelian G, Megariotis G, Theodorou DN. Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment. J Phys Chem B 2024; 128:6291-6307. [PMID: 38899795 PMCID: PMC11228990 DOI: 10.1021/acs.jpcb.4c02213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.
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Affiliation(s)
- Georgios Mikaelian
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
| | - Grigorios Megariotis
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
- School
of Engineering, Department of Mineral Resources Engineering, University of Western Macedonia, 50100 Kozani, Greece
| | - Doros N. Theodorou
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
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2
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Kotynia A, Krzyżak E, Żądło J, Witczak M, Szczukowski Ł, Mucha J, Świątek P, Marciniak A. Anti-Inflammatory and Antioxidant Pyrrolo[3,4- d]pyridazinone Derivatives Interact with DNA and Bind to Plasma Proteins-Spectroscopic and In Silico Studies. Int J Mol Sci 2024; 25:1784. [PMID: 38339061 PMCID: PMC10855066 DOI: 10.3390/ijms25031784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided to continue the research evaluating the activity of pyrrolo[3,4-dpyridazinone derivatives. In this work, we focused on the interactions of five pyridazinone derivatives with the following biomolecules: DNA and two plasma proteins: orosomucoid and gamma globulin. Using several of spectroscopic methods, such as UV-Vis, CD, and fluorescence spectroscopy, we proved that the tested compounds form stable complexes with all biomacromolecules selected for analysis. These findings were also confirmed by the results obtained by molecular modeling. All tested pyridazinone derivatives bind to the ctDNA molecule via groove binding mechanisms. All these molecules can also be bound and transported by the tested plasma proteins; however, the stability of the complexes formed is lower than those formed with serum albumin.
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Affiliation(s)
- Aleksandra Kotynia
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Edward Krzyżak
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Julia Żądło
- “Biomolecule” Student Science Club, Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland; (J.Ż.); (M.W.)
| | - Maja Witczak
- “Biomolecule” Student Science Club, Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland; (J.Ż.); (M.W.)
| | - Łukasz Szczukowski
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland; (Ł.S.); (P.Ś.)
| | - Jakub Mucha
- Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland;
| | - Piotr Świątek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland; (Ł.S.); (P.Ś.)
| | - Aleksandra Marciniak
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
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3
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Mattioli R, Ilari A, Colotti B, Mosca L, Fazi F, Colotti G. Doxorubicin and other anthracyclines in cancers: Activity, chemoresistance and its overcoming. Mol Aspects Med 2023; 93:101205. [PMID: 37515939 DOI: 10.1016/j.mam.2023.101205] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
Anthracyclines have been important and effective treatments against a number of cancers since their discovery. However, their use in therapy has been complicated by severe side effects and toxicity that occur during or after treatment, including cardiotoxicity. The mode of action of anthracyclines is complex, with several mechanisms proposed. It is possible that their high toxicity is due to the large set of processes involved in anthracycline action. The development of resistance is a major barrier to successful treatment when using anthracyclines. This resistance is based on a series of mechanisms that have been studied and addressed in recent years. This work provides an overview of the anthracyclines used in cancer therapy. It discusses their mechanisms of activity, toxicity, and chemoresistance, as well as the approaches used to improve their activity, decrease their toxicity, and overcome resistance.
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Affiliation(s)
- Roberto Mattioli
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, Italian National Research Council IBPM-CNR, Rome, Italy
| | - Beatrice Colotti
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Luciana Mosca
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council IBPM-CNR, Rome, Italy.
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4
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Elghobary MEN, Munekane M, Mishiro K, Fuchigami T, Ogawa K. Preparation and Evaluation of Thermosensitive Liposomes Encapsulating I-125-Labeled Doxorubicin Derivatives for Auger Electron Therapy. Molecules 2023; 28:molecules28041864. [PMID: 36838851 PMCID: PMC9962004 DOI: 10.3390/molecules28041864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Auger electrons (AEs) are very low-energy electrons emitted by radionuclides such as I-125 (125I). This energy is deposited across a small distance (<0.5 μm), resulting in high linear energy transfer that is potent for causing lethal damage to cancer cells. Thus, AE-emitting radiotherapeutic agents have great potential for cancer treatment. In this study, thermosensitive liposomes (TSLs) encapsulating 125I-labeled doxorubicin (DOX) derivatives were developed for Auger electron therapy, targeting the DNA of cancer cells. A radioiodinated DOX derivative [125I]5 highly accumulated in the nuclei of cancer cells and showed potent cytotoxicity against Colon 26 cancer cells by AEs. Subsequently, [125I]5 was loaded into the TSLs with high encapsulation efficiency. Potent release of [125I]5 from TSLs was achieved with heating, whereas a decreased release was observed without heating. Furthermore, TSLs encapsulating [125I]5 showed a high uptake in the nuclei at 42 °C for 1 h. We supposed that [125I]5 was released by heating at 42 °C and accumulated in the nuclei in the cells. These results suggest that the combination of TSLs encapsulating [125I]5 and hyperthermia is an effective cancer therapy.
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Affiliation(s)
| | - Masayuki Munekane
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- Correspondence: (M.M.); (K.O.); Tel./Fax: +81-76-234-4461 (M.M.); +81-76-234-4460 (K.O.)
| | - Kenji Mishiro
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takeshi Fuchigami
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Kazuma Ogawa
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
- Correspondence: (M.M.); (K.O.); Tel./Fax: +81-76-234-4461 (M.M.); +81-76-234-4460 (K.O.)
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5
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Jawad B, Poudel L, Podgornik R, Ching WY. Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects. J Phys Chem B 2020; 124:7803-7818. [PMID: 32786213 DOI: 10.1021/acs.jpcb.0c05840] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Doxorubicin (DOX) is a cancer drug that binds to dsDNA through intercalation. A comprehensive microsecond timescale molecular dynamics study is performed for DOX with 16 tetradecamer dsDNA sequences in explicit aqueous solvent, in order to investigate the intercalation process at both binding stages (conformational change and insertion binding stages). The molecular mechanics generalized Born surface area (MM-GBSA) method is adapted to quantify and break down the binding free energy (BFE) into its thermodynamic components, for a variety of different solution conditions as well as different DNA sequences. Our results show that the van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)2 or (TA)2 driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings also indicate that the aqueous bathing solution (i.e., water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that the complexation process preferably occurs at low ionic strength and is crucially dependent on solvent effects.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City 64110, Missouri, United States.,Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Lokendra Poudel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City 64110, Missouri, United States
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6
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Harding DP, Kingsley LJ, Spraggon G, Wheeler SE. Importance of model size in quantum mechanical studies of DNA intercalation. J Comput Chem 2020; 41:1175-1184. [PMID: 32011009 DOI: 10.1002/jcc.26164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 01/19/2020] [Indexed: 01/11/2023]
Abstract
The convergence of DFT-computed interaction energies with increasing binding site model size was assessed. The data show that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in noncovalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.
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Affiliation(s)
- Drew P Harding
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia.,Department of Chemistry, Texas A&M University, College Station, Texas
| | - Laura J Kingsley
- Genomics Institute of the Novartis Research Foundation, San Diego, California
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, San Diego, California
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia
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7
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Ionescu A, Caligiuri R, Godbert N, Ricciardi L, La Deda M, Ghedini M, Ferri N, Lupo MG, Facchetti G, Rimoldi I, Aiello I. Cytotoxic performances of new anionic cyclometalated Pt(II) complexes bearing chelated O^O ligands. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andreea Ionescu
- MAT‐InLAB, LASCAMM CR‐INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria Ponte Pietro Bucci Cubo 14C 87036 Arcavacata di Rende (CS) Italy
- CNR NANOTEC‐Istituto di Nanotecnologia UOS Cosenza 87036 Arcavacata di Rende (CS) Italy
| | - Rossella Caligiuri
- MAT‐InLAB, LASCAMM CR‐INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria Ponte Pietro Bucci Cubo 14C 87036 Arcavacata di Rende (CS) Italy
| | - Nicolas Godbert
- MAT‐InLAB, LASCAMM CR‐INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria Ponte Pietro Bucci Cubo 14C 87036 Arcavacata di Rende (CS) Italy
- CNR NANOTEC‐Istituto di Nanotecnologia UOS Cosenza 87036 Arcavacata di Rende (CS) Italy
| | - Loredana Ricciardi
- CNR NANOTEC‐Istituto di Nanotecnologia UOS Cosenza 87036 Arcavacata di Rende (CS) Italy
| | - Massimo La Deda
- MAT‐InLAB, LASCAMM CR‐INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria Ponte Pietro Bucci Cubo 14C 87036 Arcavacata di Rende (CS) Italy
- CNR NANOTEC‐Istituto di Nanotecnologia UOS Cosenza 87036 Arcavacata di Rende (CS) Italy
| | - Mauro Ghedini
- MAT‐InLAB, LASCAMM CR‐INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria Ponte Pietro Bucci Cubo 14C 87036 Arcavacata di Rende (CS) Italy
- CNR NANOTEC‐Istituto di Nanotecnologia UOS Cosenza 87036 Arcavacata di Rende (CS) Italy
| | - Nicola Ferri
- Dipartimento di Scienze del FarmacoUniversità degli Studi di Padova Via Marzolo 5 35131 Padua Italy
| | - Maria Giovanna Lupo
- Dipartimento di Scienze del FarmacoUniversità degli Studi di Padova Via Marzolo 5 35131 Padua Italy
| | - Giorgio Facchetti
- Dipartimento di Scienze FarmaceuticheUniversità degli Studi di Milano Via Venezian 21 20133 Milan Italy
| | - Isabella Rimoldi
- Dipartimento di Scienze FarmaceuticheUniversità degli Studi di Milano Via Venezian 21 20133 Milan Italy
| | - Iolinda Aiello
- MAT‐InLAB, LASCAMM CR‐INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria Ponte Pietro Bucci Cubo 14C 87036 Arcavacata di Rende (CS) Italy
- CNR NANOTEC‐Istituto di Nanotecnologia UOS Cosenza 87036 Arcavacata di Rende (CS) Italy
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8
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Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation. Anal Bioanal Chem 2019; 411:6723-6732. [PMID: 31396648 DOI: 10.1007/s00216-019-02045-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 12/26/2022]
Abstract
Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule's electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids. Graphical abstract.
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9
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Avagliano D, Sánchez-Murcia PA, González L. DNA-binding mechanism of spiropyran photoswitches: the role of electrostatics. Phys Chem Chem Phys 2019; 21:8614-8618. [PMID: 30801589 PMCID: PMC6484825 DOI: 10.1039/c8cp07508e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods.
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods. It is found that the electrostatic term in the probe:DNA binding energy, modulates the binding mode, providing new guidelines for the design of spiropyran photoswitches with specific binding modes to DNA.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria.
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10
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Jawad B, Poudel L, Podgornik R, Steinmetz NF, Ching WY. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA. Phys Chem Chem Phys 2019; 21:3877-3893. [PMID: 30702122 DOI: 10.1039/c8cp06776g] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
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11
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Deo KM, Ang DL, McGhie B, Rajamanickam A, Dhiman A, Khoury A, Holland J, Bjelosevic A, Pages B, Gordon C, Aldrich-Wright JR. Platinum coordination compounds with potent anticancer activity. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2017.11.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Shi JH, Lou YY, Zhou KL, Pan DQ. Probing the behavior of calf thymus DNA upon binding to a carboxamide fungicide boscalid: insights from spectroscopic and molecular docking approaches. J Biomol Struct Dyn 2017; 36:2738-2745. [DOI: 10.1080/07391102.2017.1365012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jie-Hua Shi
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan-Yue Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Kai-Li Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Dong-Qi Pan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
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13
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Palinska-Saadi A, Lukasiewicz M, Oszczapowicz J, Lukawska M, Oszczapowicz I, Zwierkowska E, Achmatowicz S, Maj-Zurawska M. Voltammetric and Spectrophotometric Studies on DNA Interacting with Daunorubicin and its Amidino Derivatives. ELECTROANAL 2016. [DOI: 10.1002/elan.201600514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Malgorzata Lukawska
- Institute of Biotechnology and Antibiotics; Staroscinska 5 02-516 Warsaw Poland
| | - Irena Oszczapowicz
- Institute of Biotechnology and Antibiotics; Staroscinska 5 02-516 Warsaw Poland
| | - Elzbieta Zwierkowska
- Institute of Electronic Materials Technology; Wolczynska 133 01-919 Warsaw Poland
| | - Selim Achmatowicz
- Institute of Electronic Materials Technology; Wolczynska 133 01-919 Warsaw Poland
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14
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Top M, Er O, Congur G, Erdem A, Lambrecht FY. Intracellular uptake study of radiolabeled anticancer drug and impedimetric detection of its interaction with DNA. Talanta 2016; 160:157-163. [DOI: 10.1016/j.talanta.2016.06.058] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 12/13/2022]
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15
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Eksin E, Congur G, Mese F, Erdem A. Electrochemical monitoring of surface confined interaction between 6-Thioguanine and DNA by using single-use graphite electrode. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2014.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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MAZHABI RMOTAGHED, ARVAND M. Disposable electrochemical DNA biosensor for environmental monitoring of toxicant 2-aminoanthracene in the presence of chlorine in real samples. J CHEM SCI 2014. [DOI: 10.1007/s12039-014-0658-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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18
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Lei H, Wang X, Wu C. Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J Mol Graph Model 2012; 38:279-89. [PMID: 23079648 DOI: 10.1016/j.jmgm.2012.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 05/06/2012] [Accepted: 05/15/2012] [Indexed: 11/19/2022]
Abstract
The intercalation mode between doxorubicin (an anticancer drug) and two 6-base-pair DNA model fragments (d(CGATCG)₂ and d(CGTACG)₂) has been well studied by X-ray crystallography and NMR experimental methods. Yet, the detailed intercalation pathway at molecular level remains elusive. In this study, we conducted molecular dynamics binding simulations of these two systems using AMBER DNA (parmbsc0) and drug (GAFF) force fields starting from the unbound state. We observed outside binding (minor groove binding or end-binding) in all six independent binding simulations (three for each DNA fragment), followed by the complete intercalation of a drug molecule in two simulations (one for each DNA fragment). First, our data directly supported that the minor groove binding is the dominant pre-intercalation step. Second, we observed that the opening and flipping of a local base pair (A3-T10 for d(CGATCG)₂ and C1-G12 for d(CGTACG)₂) in the two intercalation trajectories. This locally cooperative flipping-intercalation mechanism was different from the previously proposed rise-insertion mechanism by which the distance between two neighboring intact base pairs increases to create a space for the drug insertion. Third, our simulations provided the first set of data to support the applicability of the AMBER DNA and drug force fields in drug-DNA atomistic binding simulations. Implications on the kinetics pathway and drug action are also discussed.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
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19
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Ermer O, Neudörfl J. Crystal Structure of a Hydrated Molecular 1 : 2 Complex of Nicotinamide Adenine Dinucleotide (NAD+) and Gallic Acid: Polar Alignment of the Phenolic Partner Molecules. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Wilhelm M, Mukherjee A, Bouvier B, Zakrzewska K, Hynes JT, Lavery R. Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA. J Am Chem Soc 2012; 134:8588-96. [DOI: 10.1021/ja301649k] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthieu Wilhelm
- Bioinformatics: Structures and
Interactions, Bases Moléculaires et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086,
IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Arnab Mukherjee
- Chemistry Department, Indian Institute of Science Education and Research,
Pune, 411021, India
| | - Benjamin Bouvier
- Bioinformatics: Structures and
Interactions, Bases Moléculaires et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086,
IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Krystyna Zakrzewska
- Bioinformatics: Structures and
Interactions, Bases Moléculaires et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086,
IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - James T. Hynes
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215,
United States
- Chemistry
Department, Ecole
Normale Supérieure, CNRS UMR 8640, 24 rue Lhomond, 75005 Paris, France
| | - Richard Lavery
- Bioinformatics: Structures and
Interactions, Bases Moléculaires et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086,
IBCP, 7 Passage du Vercors, Lyon 69367, France
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21
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Ensafi AA, Rezaei B, Amini M, Heydari-Bafrooei E. A novel sensitive DNA-biosensor for detection of a carcinogen, Sudan II, using electrochemically treated pencil graphite electrode by voltammetric methods. Talanta 2011; 88:244-51. [PMID: 22265494 DOI: 10.1016/j.talanta.2011.10.038] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 09/28/2011] [Accepted: 10/14/2011] [Indexed: 11/15/2022]
Abstract
A simple and inexpensive methodology was used to develop a novel electrochemical sensor for the determination of Sudan II. The interaction of Sudan II with salmon sperm ds-DNA on the surface of salmon sperm ds-DNA-modified pencil graphite electrode (PGE) and in solution phase was studied, using differential pulse voltammetry. The difference between adenine and guanine signals of the ds-DNA after and before interaction with Sudan II was directly proportional to Sudan II concentration, which used for quantitative inspections. Using PGE, a linear calibration curve (R(2)=0.9958) was observed with 0.5-6.0 μg mL(-1) Sudan II. Furthermore, the LOD of 0.4 μg mL(-1) and linear range between 0.5 and 4.0 μg mL(-1) were achieved in solution phase. In the second part, Sudan II was determined on a pretreated pencil graphite electrode by means of adsorptive stripping differential pulse voltammetry. The peak current was linearly dependent on Sudan II concentration over the range of 0.0015-0.30 μg mL(-1), with a detection limit of 0.00007 μg mL(-1) Sudan II. Both ds-DNA-modified PGE and PPGE were applied to analyze Sudan II in real samples.
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Affiliation(s)
- Ali A Ensafi
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran.
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22
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Agrawal P, Barthwal SK, Govil G, Barthwal R. Studies on the interaction of adriamycin with d-(TGATCA)2 by proton nuclear magnetic resonance spectroscopy, time-resolved fluorescence measurement, diffusion ordered spectroscopy followed by structural refinement using restrained molecular dynamics approach. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.05.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Byler KG, Wang C, Setzer WN. Quinoline alkaloids as intercalative topoisomerase inhibitors. J Mol Model 2009; 15:1417-26. [PMID: 19424733 DOI: 10.1007/s00894-009-0501-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 03/06/2009] [Indexed: 11/30/2022]
Abstract
Quinoline alkaloids are abundant in the Rutaceae, and many have exhibited cytotoxic activity. Because structurally related antitumor alkaloids such as camptothecin and fagaronine are known to function as intercalative topoisomerase poisons, it is hypothesized that cytotoxic Stauranthus alkaloids may also serve as intercalative topoisomerase inhibitors. To test this hypothesis theoretically, ten Stauranthus quinoline alkaloids were examined for potential intercalation into DNA using a molecular docking approach. Four of the alkaloids (stauranthine, skimmianine, 3',6'-dihydroxy-3',6'-dihydrostauranthine, and trans-3',4'-dihydroxy-3',4'-dihydrostauranthine) were able to intercalatively dock consistently into DNA. In order to probe the intermolecular interactions that may be responsible for intercalation of these quinoline alkaloids, density functional calculations have been carried out using both the B3LYP and M06 functionals. M06 calculations indicated favorable pi-pi interactions between either skimmianine or stauranthine and the guanine-cytosine base pair. Furthermore, the lowest-energy face-to-face orientation of stauranthine with guanine is consistent with favorable dipole-dipole orientations, favorable electrostatic interactions, and favorable frontier molecular orbital interactions. Likewise, the lowest-energy face-to-face orientation of stauranthine with the guanine-cytosine base pair reveals favorable electrostatic interactions as well as frontier molecular orbital interactions. Thus, not only can quinoline alkaloids dock intercalatively into DNA, but the docked orientations are also electronically favorable.
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Affiliation(s)
- Kendall G Byler
- Department of Chemistry, University of Alabama in Huntsville, 35899, USA
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24
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Agrawal P, Govil G, Barthwal R. Studies on drug-DNA complexes, adriamycin-d-(TGATCA)(2) and 4'-epiadriamycin-d-(CGATCG)(2), by phosphorus-31 nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:390-397. [PMID: 19170249 DOI: 10.1002/mrc.2398] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The complexes of adriamycin-d-(TGATCA)(2) and 4'-epiadriamycin-d-(CGATCG)(2) are studied by one- and two-dimensional (31)P nuclear magnetic resonance spectroscopy (NMR) at 500 MHz in the temperature range 275-328 K and as a function of drug to DNA ratio (0.0-2.0). The binding of drug to DNA is clearly evident in (31)P-(31)P exchange NOESY spectra that shows two sets of resonances in slow chemical exchange. The phosphate resonances at the intercalating steps, T1pG2/C1pG2 and C5pA6/C5pG6, shift downfield up to 1.7 ppm and that at the adjacent step shift downfield up to 0.7 ppm, whereas the central phosphate A3pT4 is relatively unaffected. The variations of chemical shift with drug to DNA ratio and temperature as well as linewidths are different in each of the two complexes. These observations reflect change in population of B(I)/B(II) conformation, stretching of backbone torsional angle zeta, and distortions in O-P-O bond angles that occur on binding of drug to DNA. To the best of our knowledge, there are no solution studies on 4'-epiadriamycin, a better tolerated drug, and binding of daunomycin or its analogue to d-(TGATCA)(2) hexamer sequence. The studies report the use of (31)P NMR as a tool to differentiate various complexes. The specific differences may well be the reasons that are responsible for different antitumor action of these drugs due to different binding ability and distortions in DNA.
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Affiliation(s)
- Prashansa Agrawal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
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25
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Agrawal P, Barthwal SK, Govil G, Barthwal R. Solution studies on the complex of 4'-epiadriamycin-d-(CGATCG)2 followed by time-resolved fluorescence measurement, diffusion ordered spectroscopy and restrained molecular dynamics simulations. Bioorg Med Chem 2009; 17:2793-811. [PMID: 19285415 DOI: 10.1016/j.bmc.2009.02.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 02/14/2009] [Accepted: 02/18/2009] [Indexed: 11/26/2022]
Abstract
4'-Epiadriamycin is a better-tolerated anthracycline drug, due to lesser cardiotoxicity. We report here a study of the 2:1 complex of 4'-epiadriamycin-d-(CGATCG)(2) by proton Nuclear Magnetic Resonance Spectroscopy which show the absence of sequential connectivities between C1pG2 and C5pG6 base pair steps and presence of intermolecular cross peaks of the drug and DNA. Our studies establish the role of 9OH, NH3+, 7O, 4OCH(3) groups in binding to DNA. Time-resolved fluorescence measurement and diffusion ordered spectroscopic studies reveal the formation of complex. The nonspecific interactions as well as those essential for biological activity are discussed along with its medicinal importance.
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Affiliation(s)
- Prashansa Agrawal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
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26
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Mirmomtaz E, Ensafi AA, Soleimanian-Zad S. Determination of amiloride using a ds-DNA-modified pencil graphite electrode based on guanine and adenine signals. Electrochim Acta 2009. [DOI: 10.1016/j.electacta.2008.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Barone G, Guerra CF, Gambino N, Silvestri A, Lauria A, Almerico AM, Bickelhaupt FM. Intercalation of Daunomycin into Stacked DNA Base Pairs. DFT Study of an Anticancer Drug. J Biomol Struct Dyn 2008; 26:115-30. [DOI: 10.1080/07391102.2008.10507229] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Barthwal R, Agrawal P, Tripathi A, Sharma U, Jagannathan N, Govil G. Structural elucidation of 4′-epiadriamycin by nuclear magnetic resonance spectroscopy and comparison with adriamycin and daunomycin using quantum mechanical and restrained molecular dynamics approach. Arch Biochem Biophys 2008; 474:48-64. [DOI: 10.1016/j.abb.2008.02.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Revised: 02/25/2008] [Accepted: 02/25/2008] [Indexed: 11/30/2022]
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29
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Shi X, Macgregor RB. Volume and hydration changes of DNA–ligand interactions. Biophys Chem 2007; 125:471-82. [PMID: 17112653 DOI: 10.1016/j.bpc.2006.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 10/25/2006] [Accepted: 10/25/2006] [Indexed: 10/23/2022]
Abstract
We report the volumetric and other thermodynamic properties of ethidium bromide (EB), propidium iodide (PI) and daunomycin (DAU) intercalating with poly(dA).poly(dT), poly[d(A-T)].poly[d(A-T)], and poly[d(G-C)].poly[d(G-C)], respectively, as well as minor groove binder Hoechst 33258 binding with poly[d(A-T)].poly[d(A-T)]. The data were obtained using fluorescence titration and hydrostatic pressure measurements. Our thermodynamic data are combined with enthalpies from literature reports to analyze the thermodynamic characteristics of the different interactions. The differences are interpreted based on three processes related to hydration: I. burial of non-polar hydrophobic solvent accessible surface, II. burial of polar surface and formation of solute-solute H-bonds, and III. disruption of "structural" hydration. Sequence dependent conformational changes may also be important when comparing ligand binding to different DNA sequences. We conclude that a combination of different thermodynamic parameters, especially volume change, is essential in order to understand the role of hydration in the energetics of DNA-ligand interactions.
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Affiliation(s)
- Xuesong Shi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
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30
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Pandyra A, Tsankov D, Andrushchenko V, van de Sande JH, Wieser H. Intercalation of daunomycin into d(CG)4 oligomer duplex containing G x T mismatches by vibrational circular dichroism and infrared absorption spectroscopy. Biopolymers 2006; 82:189-98. [PMID: 16312022 DOI: 10.1002/bip.20416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The vibrational circular dichroism (VCD) and infrared absorption (IR) spectra of the mismatched octamer oligonucleotides d(CGTGCGCG)(2) (CGT) and d(CGCGTGCG)(2) (CGC) and their complexes with the antitumor drug daunomycin were measured in D(2)O, interpreted, and compared to the octamer d(CGCGCGCG)(2) (CG). The IR spectra of the mismatched octamers in the carbonyl-stretching region are similar to those of the parent CG, whereas the VCD spectra differ in several respects between each other. The main VCD feature due to carbonyl stretching is informative for the mismatches and CG. Vibrational modes in the sugar-phosphate region remain essentially unchanged especially for PO(2) (-) symmetric stretching. Differences between the free and complexed mismatch octamers occurred mainly in the carbonyl-stretching region (1,700-1,600 cm(-1)). The absorption intensity of the C==O peak of G is more prominent for CGC than CGT and resembles CG in this respect. The detailed composition of this doublet is clearly visible, indicating the geometric rearrangement of the base pairs in the presence of the mismatch and upon forming the daunomycin complex.
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Affiliation(s)
- A Pandyra
- Department of Chemistry, Faculty of Science, University of Calgary, Calgary, AB, T2N 1N4, Canada
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31
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Jain M, Barthwal SK, Barthwal R, Govil G. Restrained molecular dynamics studies on complex of adriamycin with DNA hexamer sequence d-CGATCG. Arch Biochem Biophys 2005; 439:12-24. [PMID: 15946641 DOI: 10.1016/j.abb.2005.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 05/05/2005] [Accepted: 05/06/2005] [Indexed: 11/30/2022]
Abstract
Adriamycin is an anthracycline anticancer drug used widely for solid tumors in spite of its adverse side effects. The solution structure of 2:1 adriamycin-d-(CGATCG)(2) complex has been studied by restrained molecular dynamics simulations. The restraint data set consists of several intramolecular and intermolecular nuclear Overhauser enhancement cross-peaks obtained from two-dimensional nuclear magnetic resonance spectroscopy data. The drug is found to intercalate between CG and GC base pairs at two d-CpG sites. The drug-DNA complex is stabilized via specific hydrogen bonding and van der Waal's interactions involving 4OCH(3), O5, 6OH, and NH(3)(+) moiety of daunosamine sugar, and rings A protons. The O-glycosidic bond C7-O7-C1'-C2' lies in the range 138 degrees -160 degrees during the course of simulations. The O6-H6...O5 hydrogen bond is stable while O11-H11...O12 hydrogen bond is not favored. The intercalating base pairs are buckled and minor groove is wider in the complex. The phosphate on one strand at intercalation site C1pG2 is in B(I) conformation and the phosphates directly lying on opposite strand is in B(II) conformation. The phosphorus on adjacent site G2pA3 is in B(II) conformation and hence a distinct pattern of B(I) and B(II) conformations is induced and stabilized. The role of various functional groups by which the molecular action is mediated has been discussed and correlated to the available biochemical evidence.
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Affiliation(s)
- Monica Jain
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
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32
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Barthwal R, Awasthi P, Kaur M, Sharma U, Srivastava N, Barthwal SK, Govil G. Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics. J Struct Biol 2005; 148:34-50. [PMID: 15363786 DOI: 10.1016/j.jsb.2004.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Revised: 05/24/2004] [Indexed: 11/20/2022]
Abstract
The 5' d-TpG 3' element is a part of DNA sequences involved in regulation of gene expression and is also a site for intercalation of several anticancer drugs. Solution conformation of DNA duplex d-TGATCA containing this element has been investigated by two-dimensional NMR spectroscopy. Using a total of 12 torsional angles and 121 distance constraints, structural refinement has been carried out by restrained molecular dynamics (rMDs) in vacuum up to 100 ps. The structure is characterized by a large positive roll at TpG/CpA base pair step and large negative propeller twist for AT and TA base pairs. The backbone torsional angle, gamma(O5'-C5'-C4'-C3'), of T1 residue adopts a trans-conformation which is corroborated by short intra nucleotide T1H6-T1H5' (3.7A) distance in nuclear overhauser effect spectroscopy (NOESY) spectra while the backbone torsional angle, beta(P-O5'-C5'-C4'), exists in trans as well as gauche state for T1 and C5 residues. There is evidence of significant flexibility of the sugar-phosphate backbone with rapid inter-conversion between two different conformers at TpG/CpA base pair step. The base sequence dependent variations and local structural heterogeneity have important implications in specific recognition of DNA by ligands.
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Affiliation(s)
- Ritu Barthwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247 667.
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33
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Fox KR, Webster R, Phelps RJ, Fokt I, Priebe W. Sequence selective binding of bis-daunorubicin WP631 to DNA. ACTA ACUST UNITED AC 2004; 271:3556-66. [PMID: 15317591 DOI: 10.1111/j.0014-2956.2004.04292.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have used footprinting techniques on a wide range of natural and synthetic footprinting substrates to examine the sequence-selective interaction of the bis-daunorubicin antibiotic WP631 with DNA. The ligand produces clear DNase I footprints that are very different from those seen with other anthracycline antibiotics such as daunorubicin and nogalamycin. Footprints are found in a diverse range of sequences, many of which are rich in GT (AC) or GA (TC) residues. As expected, the ligand binds well to the sequences CGTACG and CGATCG, but clear footprints are also found at hexanucleotide sequences such GCATGC and GCTAGC. The various footprints do not contain any particular unique di-, tri- or tetranucleotide sequences, but are frequently contain the sequence (G/C)(A/T)(A/T)(G/C). All sequences with this composition are protected by the ligand, though it can also bind to some sites that differ from this consensus by one base pair.
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Affiliation(s)
- Keith R Fox
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, UK.
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34
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Ozkan D, Karadeniz H, Erdem A, Mascini M, Ozsoz M. Electrochemical genosensor for Mitomycin C–DNA interaction based on guanine signal. J Pharm Biomed Anal 2004; 35:905-12. [PMID: 15193735 DOI: 10.1016/j.jpba.2004.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Revised: 03/01/2004] [Accepted: 03/02/2004] [Indexed: 11/19/2022]
Abstract
The interaction of mitomycin C (MC) with fish sperm or calf thymus DNA immobilized onto carbon screen-printed electrodes (CSPE) and carbon paste electrode (CPE) have been studied by using electrochemical techniques as square wave voltammetry (SWV) and differential pulse voltammetry (DPV). After the interaction was occurred between DNA and MC on electrode surface, it was observed that the guanine signal was higher with bare electrode than DNA-modified one. The changes in the experimental parameters such as the concentration of MC, and the accumulation time of MC were studied by using SWV and DPV. In addition, reproducibility, and detection limit parameters were determined using both electrodes. The partition coefficient of MC was also calculated before and after interaction of MC with dsDNA at CPE surface. These results showed that these two different DNA biosensors could be used for the sensitive, rapid and cost effective detection of MC-DNA interaction.
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Affiliation(s)
- Dilsat Ozkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, 35100 Bornova-Izmir, Turkey
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35
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Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedl KR. Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA. J Biomol Struct Dyn 2004; 21:713-24. [PMID: 14769064 DOI: 10.1080/07391102.2004.10506961] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG)2 in the B-form with two putative intercalation sites at the 5'-CGA-3' step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5'-CGA-3' steps. Thereby--in contrast to X-ray structures--a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5'-CG-3' bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of BI and BII around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.
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Affiliation(s)
- Michael Trieb
- Institute of General Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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36
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Karadeniz H, Gulmez B, Sahinci F, Erdem A, Kaya GI, Unver N, Kivcak B, Ozsoz M. Disposable electrochemical biosensor for the detection of the interaction between DNA and lycorine based on guanine and adenine signals. J Pharm Biomed Anal 2003; 33:295-302. [PMID: 12972094 DOI: 10.1016/s0731-7085(03)00283-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interaction of lycorine (LYC) with calf thymus double stranded DNA (dsDNA) and calf thymus single stranded DNA (ssDNA) was studied electrochemically based on the oxidation signals of guanine and adenine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE) and pencil graphite electrode (PGE). As a result of the interaction of LYC with DNA, the voltammetric signal of guanine and adenine greatly decreased. The changes in the experimental parameters such as the concentration of LYC, and the accumulation time of LYC were studied by using DPV with PGE. The interaction of LYC with synthetic polynucleotides, such as poly[G] was also observed. The interaction of LYC with dsDNA was also observed at PGE in solution phase. In addition, the detection limit and the reproducibility was determined by using both electrochemical transducers. The application of electrochemical methods on the interactions between DNA and DNA targeted agent were explored.
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Affiliation(s)
- Hakan Karadeniz
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, 35100 Bornova, Izmir, Turkey
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Shinomiya M, Chu W, Carlson RG, Weaver RF, Takusagawa F. Structural, Physical, and Biological Characteristics of RNA.cntdot.DNA Binding Agent N8-Actinomycin D. Biochemistry 2002. [DOI: 10.1021/bi00026a032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zargar SJ, Rabbani A. Interaction of daunomycin antibiotic with histone H(1): ultraviolet spectroscopy and equilibrium dialysis studies. Int J Biol Macromol 2002; 30:113-7. [PMID: 11911902 DOI: 10.1016/s0141-8130(02)00009-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Using ultraviolet spectroscopy and equilibrium dialysis techniques, we have investigated the interaction of anticancer drug, daunomycin with calf thymus histone H(1) chromosomal protein in 20 mM phosphate buffer, pH 7.0, 1 mM EDTA at room temperature. The UV spectroscopy results show that daunomycin (5.0-100 microM) decreases the absorbance of histone H(1) at 210-230 nm and induces hypochromicity in the absorption spectrum of the protein. The equilibrium dialysis data show that daunomycin binds to histone H(1) and the binding process is positive cooperative with two binding sites as Scatchard plot and Hill coefficient confirm it. The results suggest that daunomycin binds to histone H(1) and changes its conformation.
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Affiliation(s)
- Seyed Jalal Zargar
- Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran
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Zargar SJ, Rabbani A. The effects of daunomycin antibiotic on histone H(1): thermal denaturation and fluorescence spectroscopy studies. Int J Biol Macromol 2000; 28:75-9. [PMID: 11033180 DOI: 10.1016/s0141-8130(00)00146-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Using thermal denaturation and fluorescence spectroscopy, we have investigated the interaction of antitumor antibiotic, daunomycin, with calf thymus histone H(1) under several ionic strengths. The results show that daunomycin binds to histone H(1) and increases its melting temperature. Increasing ionic strength elevates this effect. Fluorescence emission data show that the interaction of daunomycin with histone H(1) decreases the emission intensity at 325 nm and induces hyperchromicity in the emission spectrum of the drug. The results suggest that histone H(1) can be considered as a new target for drug action at the chromatin level.
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Affiliation(s)
- S J Zargar
- Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145, 1384, Tehran, Iran
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41
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Davies DB, Eaton RJ, Baranovsky SF, Veselkov AN. NMR investigation of the complexation of daunomycin with deoxytetranucleotides of different base sequence in aqueous solution. J Biomol Struct Dyn 2000; 17:887-901. [PMID: 10798533 DOI: 10.1080/07391102.2000.10506577] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
500 MHz NMR spectroscopy has been used to investigate the complexation of the anthracycline antibiotic daunomycin (DAU) with self-complementary deoxytetranucleotides, 5'-d(CGCG), 5'-d(GCGC), 5'-d(TGCA), 5'-d(ACGT) and 5'-d(AGCT), of different base sequence in aqueous salt solution. 2D homonuclear 1H NMR spectroscopy (TOCSY and NOESY) and heteronuclear 1H - 31P NMR spectroscopy (HMBC) have been used for complete assignment of the non-exchangeable protons and the phosphorus resonance signals, respectively, and for a qualitative determination of the preferred binding sites of the drug. Analysis shows that DAU intercalates preferentially into the terminal sites of each of the tetranucleotides and that the aminosugar of the antibiotic is situated in the minor groove of the tetramer duplex, partly eclipsing the third base pair. A quantitative determination of the complexation of DAU with the deoxytetranucleotides has been made using the experimental concentration and temperature dependences of the drug proton chemical shifts; these have been analysed in terms of the equilibrium reaction constants, limiting proton chemical shifts and thermodynamical parameters (enthalpies deltaH, entropies deltaS) of different drug-DNA complexes (1:1, 1:2, 2:1, 2:2) in aqueous solution. It is found that DAU interacts with sites containing three adjacent base pairs but does not show any significant sequence specificity of binding with either single or double-stranded tetranucleotides, in contrast with other intercalating drugs such as proflavine, ethidium bromide and actinomycin D. The most favourable structures of the 1:2 complexes have been derived from the induced limiting proton chemical shifts of the drug in the intercalated complexes with the tetranucleotide duplex, in conjunction with 2D NOE data. It has been found that the conformational parameters of the double helix and the orientation of the DAU chromophore in the intercalated complexes depend on base sequence at the binding site of the tetramer duplexes in aqueous solution.
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Affiliation(s)
- D B Davies
- School of Biological and Chemical Sciences, Birkbeck College, University of London, UK.
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42
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Hudson BP, Barton JK. Solution Structure of a Metallointercalator Bound Site Specifically to DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja974134x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian P. Hudson
- Contribution from the Division of Chemistry & Chemical Engineering and the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Jacqueline K. Barton
- Contribution from the Division of Chemistry & Chemical Engineering and the Beckman Institute, California Institute of Technology, Pasadena, California 91125
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Wang J, Ozsoz M, Cai X, Rivas G, Shiraishi H, Grant DH, Chicharro M, Fernandes J, Paleček E. Interactions of antitumor drug daunomycin with DNA in solution and at the surface. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0302-4598(98)00075-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Depew KM, Zeman SM, Boyer SH, Denhart DJ, Ikemoto N, Danishefsky SJ, Crothers DM. Synthese und DNA-Bindungseigenschaften von Hybriden aus der Kohlenhydrat-Einheit von Calicheamicin γ1I und den Aglycon von Daunorubicin: Calichearubicine A und B. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961082317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Cruse WB, Saludjian P, Leroux Y, Léger G, Manouni DE, Prangé T. A continuous transition from A-DNA to B-DNA in the 1:1 complex between nogalamycin and the hexamer dCCCGGG. J Biol Chem 1996; 271:15558-67. [PMID: 8662899 DOI: 10.1074/jbc.271.26.15558] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The antibiotic nogalamycin, a drug with high specificity for TG and CG steps in double-stranded DNA, has been crystallized as a 1:1 complex with the hexamer d(CCCGGG). The antibiotic is inserted at the central CG step of the duplex, with the two sugars oriented in the same direction and with strong interactions with the DNA within the grooves. The amino-glucose residue makes an integral part of a well defined major groove hydration network with van der Waals contacts and several strong hydrogen bonds to the duplex. The nogalose residue resides in the minor groove, making primarily van der Waals contacts. The single site allows an accurate molecular description of the intercalation, without perturbations from end effects observed previously. The local unwinding induced by nogalamycin is completely relaxed 2 base pairs away from the intercalation site. The two strands of the DNA show a continuous deformation from the A to the B form: 1) the cytosines toward the 5' end of the nogalomycin site in each strand have c3'-endo conformations while 5 guanosines toward the 3' ends have c2'-endo conformations; 2) within each strand, the phosphate-phosphate distances increase in a continuous manner from 5.7 A (A-form) to 7.1 A (B-form).
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Affiliation(s)
- W B Cruse
- "Chimie Structurale et Spectroscopie Biomoléculaire" (URA 1430 CNRS) UFR-Biomédicale, 74, rue M. Cachin, 93012 Bobigny Cedex, France
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Barthwal R, Mujeeb A, Srivastava N, Sharma U. A proton nuclear magnetic resonance investigation of the conformation of daunomycin. Chem Biol Interact 1996; 100:125-39. [PMID: 8646786 DOI: 10.1016/0009-2797(96)03693-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The 500 MHz proton NMR spectra of 4.95 mM daunomycin in D2O have been investigated in the temperature range 277-350 K. Down field shifts of approximately 0.15 to 0.20 ppm in 1H, 2H and 3H protons with increasing temperature indicate that daunomycin exists in aggregated form at 277 K which is stabilized by stacking of aromatic rings. The 7H, 10axH and 10eqH protons show a change in chemical shift of 0.12 to 0.16 ppm, while other ring A/sugar protons shift by 0.0 to 0.08 ppm due to self association. The drug exists in monomer state at about 350 K. The conformational features have been ascertained from NOESY spectra at 297 K. The 7H proton is found to be strongly coupled to 8axH (J = 5 Hz) as compared to 8eqH (J = 2 Hz), while the 4'H-5'H connectivity is not observed in the COSY spectra. Besides the NOESY cross peaks between the spin-spin coupled protons, several intramolecular NOEs are seen. The 8axH and 8eqH are equally distant from 5'H proton. The distances of 3'H and 4'H daunosamine sugar protons from the ring A protons--7H, 8eqH, 9COCH3--are in the range 2.9-3.1 A, giving moderate cross peaks in NOESY spectra. The observed results imply the existence of predominantly 9H8 half chair conformation of ring A in aqueous solution, which is marginally different from that obtained by X-ray crystal analysis.
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Affiliation(s)
- R Barthwal
- Department of Biosciences and Biotechnology, University of Roorkee, India. biost%
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Windsor SA, Tinker MH. Binding of biologically important molecules to DNA, probed using electro-fluorescence polarization spectroscopy. Biophys Chem 1996; 58:141-50. [PMID: 8679917 DOI: 10.1016/0301-4622(95)00093-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
When small fluorescent tag molecules are bound with a single geometry to larger carrier molecules the fluorescence excited using polarized light may itself be partially polarized. If this is the case then alignment of the carrier molecules changes the fluorescence polarization. Electro-fluorescence polarization spectrometry (EFPS) makes use of the fluorescence polarization changes which occur when the carrier molecules are aligned by an electric field. EFPS allows the determination of the binding geometry of the small tag molecules to the larger carrier molecules. In this study, EFPS has been used to probe the interactions between DNA and a series of chromosomal stains and anti-neoplastic (anti-cancer) agents. Results are presented for calf thymus DNA, treated with the dyes acridine orange, ethidium bromide, proflavine, Hoechst 33258, Hoechst 33342, 4',6-diamidino-2-phenylindole and the anti-tumour agents, doxorubicin, daunomycin, actinomycin C and actinomycin V.
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Affiliation(s)
- S A Windsor
- JJ Thomson Physical Laboratory, University of Reading, Whiteknights, UK
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Berger I, Su L, Spitzner JR, Kang C, Burke TG, Rich A. Molecular structure of the halogenated anti-cancer drug iododoxorubicin complexed with d(TGTACA) and d(CGATCG). Nucleic Acids Res 1995; 23:4488-94. [PMID: 7501474 PMCID: PMC307408 DOI: 10.1093/nar/23.21.4488] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
4'-Deoxy-4'-iododoxorubicin, a halogenated anthracycline derivative, is an anticancer agent currently under Phase II clinical trials. In preclinical studies, it has demonstrated significantly reduced levels of cardiotoxicity compared to currently employed anthracyclines. It also has modified pharmacological properties resulting in an altered spectrum of experimental antitumor activity. The iodine atom at the 4' position of the sugar ring reduces the basicity and enhances the lipophilicity of this compound as compared to related anthracycline drugs. We report here single crystal X-ray diffraction studies of the complexes of 4'-deoxy-4'-iododoxorubicin with the hexanucleotide duplex sequences d(TGTACA) and d(CGATCG) at 1.6 and 1.5 A, respectively. The iodine substituent does not alter the geometry of intercalation as compared to previously solved anthracycline complexes, but appears to markedly affect the solvent environment of the structures. This could have consequences for the interaction of this drug with DNA and DNA binding proteins in cells.
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Affiliation(s)
- I Berger
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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Hansen M, Yun S, Hurley L. Hedamycin intercalates the DNA helix and, through carbohydrate-mediated recognition in the minor groove, directs N7-alkylation of guanine in the major groove in a sequence-specific manner. CHEMISTRY & BIOLOGY 1995; 2:229-40. [PMID: 9383425 DOI: 10.1016/1074-5521(95)90273-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The pluramycins are a class of antitumor antibiotics that exert their biological activity through interaction with DNA. Recent studies with the analog altromycin B have determined that these agents intercalate into the DNA molecule, position carbohydrate substituents into both major and minor grooves, and alkylate the DNA molecule by epoxide-mediated electrophilic attack on N7 of guanine located to the 3' side of the drug molecule. Alkylation is sequence dependent and appears to be modulated by glycoside substituents attached at the corners of a planar chromophore. The altromycin B-like analogs preferentially alkylate 5'AG sequences; hedamycin-like analogs prefer 5'TG and 5'CG sequences. Although the mechanism of guanine modification by altromycin B has been extensively studied, the mechanism of action of hedamycin has not been previously determined. RESULTS Using high-field NMR, we have shown that hedamycin stacks to the 5' side of the guanine nucleotide at the site of intercalation in a DNA decamer, positioning both aminosaccharides into the minor groove to direct alkylation by the epoxide moiety on N7 of guanine. The C10 linked N,N-dimethylvancosamine sugar moiety interacts to the 5' side of the intercalation site, while the C8 linked anglosamine moiety interacts to the 3' side. The binding interactions of the two aminosugars steer the C2 double epoxide located in the major groove into the proximity of N7 of guanine. Unexpectedly, it is not the first epoxide that undergoes electrophilic addition to N7 of guanine, which would correspond to altromycin B, but the second, terminal epoxide. CONCLUSIONS We have used two-dimensional NMR to elucidate the sequence-selective recognition of DNA by hedamycin and the mechanism of covalent modification of guanine by this antibiotic. Characterization of the intermolecular interactions between both hedamycin and altromycin B and their targeted DNA sequences has yielded a better understanding of the reasons for variations in sequence selectivity and alkylation reactivity among the pluramycin compounds.
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Affiliation(s)
- M Hansen
- Drug Dynamics Institute, College of Pharmacy, University of Texas at Austin 78712-1074, USA
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