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Majzner K, Deckert-Gaudig T, Baranska M, Deckert V. DOX-DNA Interactions on the Nanoscale: In Situ Studies Using Tip-Enhanced Raman Scattering. Anal Chem 2024. [PMID: 38771097 DOI: 10.1021/acs.analchem.3c05372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Chemotherapeutic anthracyclines, like doxorubicin (DOX), are drugs endowed with cytostatic activity and are widely used in antitumor therapy. Their molecular mechanism of action involves the formation of a stable anthracycline-DNA complex, which prevents cell division and results in cell death. It is known that elevated DOX concentrations induce DNA chain loops and overlaps. Here, for the first time, tip-enhanced Raman scattering was used to identify and localize intercalated DOX in isolated double-stranded calf thymus DNA, and the correlated near-field spectroscopic and morphologic experiments locate the DOX molecules in the DNA and provide further information regarding specific DOX-nucleobase interactions. Thus, the study provides a tool specifically for identifying intercalation markers and generally analyzing drug-DNA interactions. The structure of such complexes down to the molecular level provides mechanistic information about cytotoxicity and the development of potential anticancer drugs.
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Affiliation(s)
- Katarzyna Majzner
- Department of Chemical Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tanja Deckert-Gaudig
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, Jena 07743, Germany
- Leibniz Insti-tute of Photonic Technology, Albert-Einstein-Str.9, Jena 07745, Germany
| | - Malgorzata Baranska
- Department of Chemical Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Jagiellonian Centre for Exper-Imental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
| | - Volker Deckert
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, Jena 07743, Germany
- Leibniz Insti-tute of Photonic Technology, Albert-Einstein-Str.9, Jena 07745, Germany
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2
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Alniss HY, Chu C, Ramadan WS, Msallam YA, Srinivasulu V, El-Awady R, Macgregor RB, Al-Tel TH. Interaction of an anticancer benzopyrane derivative with DNA: Biophysical, biochemical, and molecular modeling studies. Biochim Biophys Acta Gen Subj 2023; 1867:130347. [PMID: 36958685 DOI: 10.1016/j.bbagen.2023.130347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND SIMR1281 is a potent anticancer lead candidate with multi- target activity against several proteins; however, its mechanism of action at the molecular level is not fully understood. Revealing the mechanism and the origin of multitarget activity is important for the rational identification and optimization of multitarget drugs. METHODS We have used a variety of biophysical (circular dichroism, isothermal titration calorimetry, viscosity, and UV DNA melting), biochemical (topoisomerase I & II assays) and computational (molecular docking and MD simulations) methods to study the interaction of SIMR1281 with duplex DNA structures. RESULTS The biophysical results revealed that SIMR1281 binds to dsDNA via an intercalation-binding mode with an average binding constant of 3.1 × 106 M-1. This binding mode was confirmed by the topoisomerases' inhibition assays and molecular modeling simulations, which showed the intercalation of the benzopyrane moiety between DNA base pairs, while the remaining moieties (thiazole and phenyl rings) sit in the minor groove and interact with the flanking base pairs adjacent to the intercalation site. CONCLUSIONS The DNA binding characteristics of SIMR1281, which can disrupt/inhibit DNA function as confirmed by the topoisomerases' inhibition assays, indicate that the observed multi-target activity might originate from ligand intervention at nucleic acids level rather than due to direct interactions with multiple biological targets at the protein level. GENERAL SIGNIFICANCE The findings of this study could be helpful to guide future optimization of benzopyrane-based ligands for therapeutic purposes.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Chen Chu
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Wafaa S Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Taleb H Al-Tel
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
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Doxorubicin-An Agent with Multiple Mechanisms of Anticancer Activity. Cells 2023; 12:cells12040659. [PMID: 36831326 PMCID: PMC9954613 DOI: 10.3390/cells12040659] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Doxorubicin (DOX) constitutes the major constituent of anti-cancer treatment regimens currently in clinical use. However, the precise mechanisms of DOX's action are not fully understood. Emerging evidence points to the pleiotropic anticancer activity of DOX, including its contribution to DNA damage, reactive oxygen species (ROS) production, apoptosis, senescence, autophagy, ferroptosis, and pyroptosis induction, as well as its immunomodulatory role. This review aims to collect information on the anticancer mechanisms of DOX as well as its influence on anti-tumor immune response, providing a rationale behind the importance of DOX in modern cancer therapy.
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Zhu X, Iyengar SS. Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol. J Chem Theory Comput 2022; 18:5125-5144. [PMID: 35994592 DOI: 10.1021/acs.jctc.1c01241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over a series of publications we have introduced a graph-theoretic description for molecular fragmentation. Here, a system is divided into a set of nodes, or vertices, that are then connected through edges, faces, and higher-order simplexes to represent a collection of spatially overlapping and locally interacting subsystems. Each such subsystem is treated at two levels of electronic structure theory, and the result is used to construct many-body expansions that are then embedded within an ONIOM-scheme. These expansions converge rapidly with many-body order (or graphical rank) of subsystems and have been previously used for ab initio molecular dynamics (AIMD) calculations and for computing multidimensional potential energy surfaces. Specifically, in all these cases we have shown that CCSD and MP2 level AIMD trajectories and potential surfaces may be obtained at density functional theory cost. The approach has been demonstrated for gas-phase studies, for condensed phase electronic structure, and also for basis set extrapolation-based AIMD. Recently, this approach has also been used to derive new quantum-computing algorithms that enormously reduce the quantum circuit depth in a circuit-based computation of correlated electronic structure. In this publication, we introduce (a) a family of neural networks that act in parallel to represent, efficiently, the post-Hartree-Fock electronic structure energy contributions for all simplexes (fragments), and (b) a new k-means-based tessellation strategy to glean training data for high-dimensional molecular spaces and minimize the extent of training needed to construct this family of neural networks. The approach is particularly useful when coupled cluster accuracy is desired and when fragment sizes grow in order to capture nonlocal interactions accurately. The unique multidimensional k-means tessellation/clustering algorithm used to determine our training data for all fragments is shown to be extremely efficient and reduces the needed training to only 10% of data for all fragments to obtain accurate neural networks for each fragment. These fully connected dense neural networks are then used to extrapolate the potential energy surface for all molecular fragments, and these are then combined as per our graph-theoretic procedure to transfer the learning process to a full system energy for the entire AIMD trajectory at less than one-tenth the cost as compared to a regular fragmentation-based AIMD calculation.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
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5
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Kumar A, DeGregorio N, Iyengar SS. Graph-Theory-Based Molecular Fragmentation for Efficient and Accurate Potential Surface Calculations in Multiple Dimensions. J Chem Theory Comput 2021; 17:6671-6690. [PMID: 34623129 DOI: 10.1021/acs.jctc.1c00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a multitopology molecular fragmentation approach, based on graph theory, to calculate multidimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory but at the density functional theory cost. A molecular assembly is coarse-grained into a set of graph-theoretic nodes that are then connected with edges to represent a collection of locally interacting subsystems up to an arbitrary order. Each of the subsystems is treated at two levels of electronic structure theory, the result being used to construct many-body expansions that are embedded within an ONIOM scheme. These expansions converge rapidly with the many-body order (or graphical rank) of subsystems and capture many-body interactions accurately and efficiently. However, multiple graphs, and hence multiple fragmentation topologies, may be defined in molecular configuration space that may arise during conformational sampling or from reactive, bond breaking and bond formation, events. Obtaining the resultant potential surfaces is an exponential scaling proposition, given the number of electronic structure computations needed. We utilize a family of graph-theoretic representations within a variational scheme to obtain multidimensional potential surfaces at a reduced cost. The fast convergence of the graph-theoretic expansion with increasing order of many-body interactions alleviates the exponential scaling cost for computing potential surfaces, with the need to only use molecular fragments that contain a fewer number of quantum nuclear degrees of freedom compared to the full system. This is because the dimensionality of the conformational space sampled by the fragment subsystems is much smaller than the full molecular configurational space. Additionally, we also introduce a multidimensional clustering algorithm, based on physically defined criteria, to reduce the number of energy calculations by orders of magnitude. The molecular systems benchmarked include coupled proton motion in protonated water wires. The potential energy surfaces and multidimensional nuclear eigenstates obtained are shown to be in very good agreement with those from explicit post-Hartree-Fock calculations that become prohibitive as the number of quantum nuclear dimensions grows. The developments here provide a rigorous and efficient alternative to this important chemical physics problem.
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Affiliation(s)
- Anup Kumar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicole DeGregorio
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Ternary Copper Complex of L-Glutamine and Phenanthroline as Counterions of Cyclo-Tetravanadate Anion: Experimental–Theoretical Characterization and Potential Antineoplastic Activity. METALS 2021. [DOI: 10.3390/met11101541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last decade, therapeutic metallodrugs have become substantially effective in the treatment of cancer. Thus, developing new effective anticancer drugs is a significant research area against the continuing increase in cancers worldwide. In the search for heterobimetallic prodrugs containing V/Cu, a new cyclo-tetravanadate was synthesized and characterized by UV-visible and FTIR spectroscopies and single-crystal X-ray diffraction. L-Glutamine and 1,10-phenanthroline allow the crystallization of [Cu(L-Gln)(phen)(H2O)]4[V4O12]∙8(H2O) (1), in which the cyclo-tetravanadate acts as a free anion. Density functional theory (DFT) calculations were carried out to characterize the frontier molecular orbitals and molecular electrostatic potential. Global reactivity indexes were calculated and analyzed to give insight into the cyclo-tetravanadate anion and complex counterions interactions. Also, using Bader’s theory of atoms in molecules (AIM), non-covalent interactions were analyzed. Docking analysis with the Casiopeina-like complex resulting from the hydrolysis of compound 1 provided insights into these complex potential anticancer activities by interacting with DNA/tRNA via H-bonds and hydrophobic interactions. The release of both components could act together or separately, acting as prodrugs with potential dual antineoplastic activities.
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Zhang JH, Ricard TC, Haycraft C, Iyengar SS. Weighted-Graph-Theoretic Methods for Many-Body Corrections within ONIOM: Smooth AIMD and the Role of High-Order Many-Body Terms. J Chem Theory Comput 2021; 17:2672-2690. [PMID: 33891416 DOI: 10.1021/acs.jctc.0c01287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a weighted-graph-theoretic approach to adaptively compute contributions from many-body approximations for smooth and accurate post-Hartree-Fock (pHF) ab initio molecular dynamics (AIMD) of highly fluxional chemical systems. This approach is ONIOM-like, where the full system is treated at a computationally feasible quality of treatment (density functional theory (DFT) for the size of systems considered in this publication), which is then improved through a perturbative correction that captures local many-body interactions up to a certain order within a higher level of theory (post-Hartree-Fock in this publication) described through graph-theoretic techniques. Due to the fluxional and dynamical nature of the systems studied here, these graphical representations evolve during dynamics. As a result, energetic "hops" appear as the graphical representation deforms with the evolution of the chemical and physical properties of the system. In this paper, we introduce dynamically weighted, linear combinations of graphs, where the transition between graphical representations is smoothly achieved by considering a range of neighboring graphical representations at a given instant during dynamics. We compare these trajectories with those obtained from a set of trajectories where the range of local many-body interactions considered is increased, sometimes to the maximum available limit, which yields conservative trajectories as the order of interactions is increased. The weighted-graph approach presents improved dynamics trajectories while only using lower-order many-body interaction terms. The methods are compared by computing dynamical properties through time-correlation functions and structural distribution functions. In all cases, the weighted-graph approach provides accurate results at a lower cost.
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Affiliation(s)
- Juncheng Harry Zhang
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Timothy C Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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8
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Sachar HS, Chava BS, Pial TH, Das S. Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Harnoor Singh Sachar
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bhargav Sai Chava
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Turash Haque Pial
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
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Corona-Motolinia ND, Martínez-Valencia B, Noriega L, Sánchez-Gaytán BL, Méndez-Rojas MÁ, Melendez FJ, Castro ME, González-Vergara E. Synthesis, Crystal Structure, and Computational Methods of Vanadium and Copper Compounds as Potential Drugs for Cancer Treatment. Molecules 2020; 25:E4679. [PMID: 33066356 PMCID: PMC7587343 DOI: 10.3390/molecules25204679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/23/2020] [Accepted: 10/02/2020] [Indexed: 12/24/2022] Open
Abstract
Transition metal-based compounds have shown promising uses as therapeutic agents. Among their unique characteristics, these compounds are suitable for interaction with specific biological targets, making them important potential drugs to treat various diseases. Copper compounds, of which Casiopeinas® are an excellent example, have shown promising results as alternatives to current cancer therapies, in part because of their intercalative properties with DNA. Vanadium compounds have been extensively studied for their pharmacological properties and application, mostly in diabetes, although recently, there is a growing interest in testing their activity as anti-cancer agents. In the present work, two compounds, [Cu(Metf)(bipy)Cl]Cl·2H2O and [Cu(Impy)(Gly)(H2O)]VO3, were obtained and characterized by visible and FTIR spectroscopies, single-crystal X-ray diffraction, and theoretical methods. The structural and electronic properties of the compounds were calculated through the density functional theory (DFT) using the Austin-Frisch-Petersson functional with dispersion APFD, and the 6-311 + G(2d,p) basis set. Non-covalent interactions were analyzed using Hirshfeld surface analysis (HSA) and atom in molecules analysis (AIM). Additionally, docking analysis to test DNA/RNA interactions with the Casiopeina-like complexes were carried out. The compounds provide metals that can interact with critical biological targets. In addition, they show interesting non-covalent interactions that are responsible for their supramolecular arrangements.
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Affiliation(s)
- Nidia D. Corona-Motolinia
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (N.D.C.-M.); (B.M.-V.); (B.L.S.-G.)
| | - Beatriz Martínez-Valencia
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (N.D.C.-M.); (B.M.-V.); (B.L.S.-G.)
| | - Lisset Noriega
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (L.N.); (F.J.M.)
| | - Brenda L. Sánchez-Gaytán
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (N.D.C.-M.); (B.M.-V.); (B.L.S.-G.)
| | - Miguel Ángel Méndez-Rojas
- Departamento de Ciencias Químico Biológicas, Universidad de las Américas. Puebla, Sta. Catarina Mártir, Cholula Puebla C.P. 72820, Mexico;
| | - Francisco J. Melendez
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (L.N.); (F.J.M.)
| | - María Eugenia Castro
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (N.D.C.-M.); (B.M.-V.); (B.L.S.-G.)
| | - Enrique González-Vergara
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San Claudio, Col. San Manuel, Puebla C. P. 72570, Mexico; (N.D.C.-M.); (B.M.-V.); (B.L.S.-G.)
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Martínez-Valencia B, Corona-Motolinia ND, Sánchez-Lara E, Noriega L, Sánchez-Gaytán BL, Castro ME, Meléndez-Bustamante F, González-Vergara E. Cyclo-tetravanadate bridged copper complexes as potential double bullet pro-metallodrugs for cancer treatment. J Inorg Biochem 2020; 208:111081. [PMID: 32531543 DOI: 10.1016/j.jinorgbio.2020.111081] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 03/21/2020] [Accepted: 03/21/2020] [Indexed: 02/07/2023]
Abstract
Over the last decade, copper and vanadium complexes have shown promising properties for the treatment of several types of cancer. In particular, Casiopeinas®, a group of copper-based complexes, has received specific attention, and their mechanism of action has been extensively studied since their structure is simple and their synthesis may be affordable. Similarly, vanadium-containing compounds in the form of complexes and simple polyoxovanadates have also been studied as antitumor agents. Here, potential prodrugs that would release the two metals, V and Cu, in usable form to act in conjunction against cancer cells are reported. The new series of Casiopeinas-like compounds are bridged by a cyclotetravanadate ion with the generic formula [Cu(N,N')(AA)]2•(V4O12), where (N,N') represent 1,10-phenanthroline and 2,2'-bipyridine, and (AA) are aminoacidate ions (Lysine and Ornithine). The compounds were characterized by elemental analysis, single-crystal X-ray diffraction and Visible, FTIR, and Raman spectroscopies, as well as 51V NMR, EPR, and Thermogravimetric Analysis. Additionally, theoretical calculations based on the Density Functional Theory (DFT) were carried out to model the compounds. Optimized structures, theoretical IR, and Raman spectra were also obtained, as well as docking analysis to test DNA interactions with the casiopeina-like complexes. The compounds may act as prodrugs by providing acting molecules that have showed potential pharmacological properties for the treatment of several types of cancer.
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Affiliation(s)
- Beatriz Martínez-Valencia
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico
| | - Nidia D Corona-Motolinia
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico
| | - Eduardo Sánchez-Lara
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico
| | - Lisset Noriega
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico
| | - Brenda L Sánchez-Gaytán
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico
| | - María Eugenia Castro
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico
| | | | - Enrique González-Vergara
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Puebla, Mexico.
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11
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Yao F, An Y, Li X, Li Z, Duan J, Yang XD. Targeted Therapy of Colon Cancer by Aptamer-Guided Holliday Junctions Loaded with Doxorubicin. Int J Nanomedicine 2020; 15:2119-2129. [PMID: 32280210 PMCID: PMC7125415 DOI: 10.2147/ijn.s240083] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Chemotherapy is the primary treatment for advanced colon cancer, but its efficacy is often limited by severe toxicities. Targeted therapy in the form of selectively drug delivery system (SDDS) is an important strategy to reduce adverse effects. Here, we aim to design a novel SDDS with potential for practical application using biocompatible components and scalable production process, for targeted delivery of doxorubicin (Dox) to colon cancer cells. Methods The SDDS was made of a self-assembled DNA nano-cross (Holliday junction, or HJ) functionalized by four AS1411 aptamers (Apt-HJ) and loaded with Dox. Results Apt-HJ had an average size of 12.45 nm and a zeta potential of −11.6 mV. Compared with the monovalent AS1411 aptamer, the quadrivalent Apt-HJ showed stronger binding to target cancer cells (CT26). A complex of Apt-HJ and doxorubicin (Apt-HJ-Dox) was formed by intercalating Dox into the DNA structure of Apt-HJ, with each complex carrying approximately 17 Dox molecules. Confocal microscopy revealed that Apt-HJ-Dox selectively delivered Dox into CT26 colon cancer cells but not the control cells. Moreover, Apt-HJ-Dox achieved targeted killing of CT26 cancer cells in vitro and reduced the damage to control cells. Importantly, compared with free Dox, Apt-HJ-Dox significantly enhanced the antitumor efficacy in vivo without boosting the adverse effects. Conclusion These results suggest that Apt-HJ-Dox has application potential in targeted treatment of colon cancer.
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Affiliation(s)
- Fengjiao Yao
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Yacong An
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Xundou Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhaoyi Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jinhong Duan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Xian-Da Yang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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12
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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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13
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Calvo F. Conformational diversity in deprotonated water clusters and anharmonic infrared spectra. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2018.1513653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- F. Calvo
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
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14
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Mathivathanan L, Yang G, Leng F, Raptis RG. Crystal structure and conformational analysis of doxorubicin nitrate. Acta Crystallogr E Crystallogr Commun 2018; 74:400-405. [PMID: 29765732 PMCID: PMC5947812 DOI: 10.1107/s2056989018002955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/19/2018] [Indexed: 11/13/2023]
Abstract
Crystal structure determination of doxorubicin nitrate, (DoxH)NO3, systematic name (7S,9S)-7-{[(2R,4S,5S,6S)-4-azaniumyl-5-hy-droxy-6-methyl-oxan-2-yl]-oxy}-6,9,11-trihy-droxy-9-(2-hy-droxy-acet-yl)-4-meth-oxy-8,10-di-hydro-7H-tetra-cen-5,12-dione nitrate, shows two formula units present in the asymmetric unit. In the crystal lattice, hydrogen-bonded pairs of (DoxH+) cations and segregation of the aglycone and sugar moieties are observed. Inspection of mol-ecular overlays reveals that the conformation of (DoxH)NO3 resembles that of DNA-inter-calated, but not of protein-docked (DoxH)+. The structure was refined as a two-component twin.
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Affiliation(s)
- Logesh Mathivathanan
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Guang Yang
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan, 450001, People’s Republic of China
| | - Fenfei Leng
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Raphael G. Raptis
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
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15
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Haycraft C, Li J, Iyengar SS. Efficient, “On-the-Fly”, Born–Oppenheimer and Car–Parrinello-type Dynamics with Coupled Cluster Accuracy through Fragment Based Electronic Structure. J Chem Theory Comput 2017; 13:1887-1901. [DOI: 10.1021/acs.jctc.6b01107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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16
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Li J, Haycraft C, Iyengar SS. Hybrid Extended Lagrangian, Post-Hartree–Fock Born–Oppenheimer ab Initio Molecular Dynamics Using Fragment-Based Electronic Structure. J Chem Theory Comput 2016; 12:2493-508. [DOI: 10.1021/acs.jctc.6b00001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
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17
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Eissa IH, El-Naggar AM, El-Hashash MA. Design, synthesis, molecular modeling and biological evaluation of novel 1H-pyrazolo[3,4-b]pyridine derivatives as potential anticancer agents. Bioorg Chem 2016; 67:43-56. [PMID: 27253830 DOI: 10.1016/j.bioorg.2016.05.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 11/16/2022]
Abstract
In trying to develop new anticancer agents, a series of 1H-pyrazolo[3,4-b]pyridine derivatives was designed and synthesized. Fifteen compounds were evaluated in vitro for their anti-proliferative activity against HePG-2, MCF-7, HCT-116, and PC-3 cell lines. Additionally, DNA binding affinity of the synthesized derivatives was investigated as a potential mechanism for the anticancer activity using DNA/methyl green assay and association constants assay. Compounds 19, 20, 21, 24 and 25 exhibited good activity against the four cancer cells comparable to that of doxorubicin. Interestingly, DNA binding assay results were in agreement with that of the cytotoxicity assays where the most potent anticancer compounds showed good DNA binding affinity comparable to that of doxorubicin and daunorubicin. Furthermore, a molecular docking of the tested compounds was carried out to investigate their binding pattern with the prospective target, DNA (PDB-code: 152d).
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Affiliation(s)
- Ibrahim H Eissa
- Pharmaceutical Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt.
| | - Abeer M El-Naggar
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassiya, Cairo 11566, Egypt
| | - Maher A El-Hashash
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassiya, Cairo 11566, Egypt
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18
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Li J, Iyengar SS. Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique. J Chem Theory Comput 2015; 11:3978-91. [DOI: 10.1021/acs.jctc.5b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
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19
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Akhter MZ, Luthra K, Rajeswari MR. Molecular aspects on adriamycin interaction with hmga1 regulatory region and its inhibitory effect on HMGA1 expression in human cervical cancer. J Biomol Struct Dyn 2015; 34:877-91. [PMID: 26084422 DOI: 10.1080/07391102.2015.1057617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High mobility group A1 (HMGA1), a non-histone chromosomal protein, is highly expressed in a wide range of human cancers including cervical, breast, and prostate cancers. Therefore, hmga1 gene is considered as an attractive potential target for anticancer drugs. We have chosen 27 bp DNA sequence from a regulatory region of hmga1 promoter and studied its interaction with adriamycin (ADM) and in vitro expression of HMGA1 in the presence of ADM in HeLa cell line. A variety of biophysical techniques were employed to understand the characteristics of [DNA-ADM] complex. Spectrophotometric titration data, DNA denaturation profiles, and quenching of fluorescence of ADM in the presence of DNA demonstrated a strong complexation between DNA and ADM with a high binding affinity (Ka) of 1.3 × 10(6) M(-1) and a stoichiometry of 1:3 (drug:nucleotide). The energetics of binding obtained from isothermal titration calorimetry and differential scanning calorimetry suggest the binding to be exothermic and enthalpy (∆H, -6.7 ± 2.4 kcal M(-1)) and entropy (TΔS, 18.5 ± 6.4 kcal M(-1)) driven (20°C), which is typical of intercalative mode of binding. Further, results on decreased expression (by ~70%) of HMGA1 both at mRNA and protein levels in association with the observed cell death (by ~75%) in HeLa cell line, clearly confirm that ADM does target hmga1; however, the effect of ADM on genes other than hmga1 either directly or via hmga1-mediated pathways cannot be ruled out in the observed cytotoxicity. Therefore, hmga1 in general and particularly the regulatory region is a promising target for therapeutic strategy in combating cancer.
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Affiliation(s)
- Md Zahid Akhter
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| | - Kalpana Luthra
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
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20
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Hartlieb KJ, Witus LS, Ferris DP, Basuray AN, Algaradah MM, Sarjeant AA, Stern CL, Nassar MS, Botros YY, Stoddart JF. Anticancer activity expressed by a library of 2,9-diazaperopyrenium dications. ACS NANO 2015; 9:1461-1470. [PMID: 25555133 PMCID: PMC4344210 DOI: 10.1021/nn505895j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/02/2015] [Indexed: 06/04/2023]
Abstract
Polyaromatic compounds are well-known to intercalate DNA. Numerous anticancer chemotherapeutics have been developed upon the basis of this recognition motif. The compounds have been designed such that they interfere with the role of the topoisomerases, which control the topology of DNA during the cell-division cycle. Although many promising chemotherapeutics have been developed upon the basis of polyaromatic DNA intercalating systems, these candidates did not proceed past clinical trials on account of their dose-limiting toxicity. Herein, we discuss an alternative, water-soluble class of polyaromatic compounds, the 2,9-diazaperopyrenium dications, and report in vitro cell studies for a library of these dications. These investigations reveal that a number of 2,9-diazaperopyrenium dications show similar activities as doxorubicin toward a variety of cancer cell lines. Additionally, we report the solid-state structures of these dications, and we relate their tendency to aggregate in solution to their toxicity profiles. The addition of bulky substituents to these polyaromatic dications decreases their tendency to aggregate in solution. The derivative substituted with 2,6-diisopropylphenyl groups proved to be the most cytotoxic against the majority of the cell lines tested. In the solid state, the 2,6-diisopropylphenyl-functionalized derivative does not undergo π···π stacking, while in aqueous solution, dynamic light scattering reveals that this derivative forms very small (50-100 nm) aggregates, in contrast with the larger ones formed by dications with less bulky substituents. Alteration of the aromaticitiy in the terminal heterocycles of selected dications reveals a drastic change in the toxicity of these polyaromatic species toward specific cell lines.
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Affiliation(s)
- Karel J. Hartlieb
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Leah S. Witus
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Daniel P. Ferris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Ashish N. Basuray
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Mohammed M. Algaradah
- Joint Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6068, Riyadh 11442, Kingdom of Saudia Arabia
| | - Amy A. Sarjeant
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Charlotte L. Stern
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Majed S. Nassar
- Joint Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6068, Riyadh 11442, Kingdom of Saudia Arabia
| | - Youssry Y. Botros
- University Research Office, Intel Corporation, Building RNB-6-61, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - J. Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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21
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Akhter MZ, Rajeswari MR. Interaction of doxorubicin with a regulatory element of hmga1 and its in vitro anti-cancer activity associated with decreased HMGA1 expression. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:36-46. [DOI: 10.1016/j.jphotobiol.2014.08.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 11/26/2022]
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22
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Lohani N, Narayan Singh H, Agarwal S, Mehrotra R, Rajeswari MR. Interaction of adriamycin with a regulatory element ofhmgb1: spectroscopic and calorimetric approach. J Biomol Struct Dyn 2014; 33:1612-23. [DOI: 10.1080/07391102.2014.967301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Shaaban S, Negm A, Ibrahim EE, Elrazak AA. Chemotherapeutic agents for the treatment of hepatocellular carcinoma: efficacy and mode of action. Oncol Rev 2014; 8:246. [PMID: 25992234 PMCID: PMC4419609 DOI: 10.4081/oncol.2014.246] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/06/2014] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a dreaded malignancy that every year causes half a million deaths worldwide. Being an aggressive cancer, its incidence exceeds 700,000 new cases per year worldwide with a median survival of 6-8 months. Despite advances in prognosis and early detection, effective HCC chemoprevention or treatment strategies are still lacking, therefore its dismal survival rate remains largely unchanged. This review will characterize currently available chemotherapeutic drugs used in the treatment of HCC. The respective mode(s) of action, side effects and recommendations will be also described for each drug.
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Affiliation(s)
- Saad Shaaban
- Department of Chemistry, Mansoura University , Egypt
| | - Amr Negm
- Department of Biochemistry, Mansoura University , Egypt
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24
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Marciante M, Calvo F. Modelling infrared action spectra of protonated water clusters. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.844804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. Marciante
- ILM, CNRS UMR 5306, Université Lyon 1, Bâtiment Kastler, 43 Bd du 11 Novembre 1918, F69622, Villeurbanne Cedex, France
| | - F. Calvo
- ILM, CNRS UMR 5306, Université Lyon 1, Bâtiment Kastler, 43 Bd du 11 Novembre 1918, F69622, Villeurbanne Cedex, France
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25
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Tiwari S, Pitre KS. Anticancer Drug Modified GCFE, for the Study of ItsIn-VivoInteraction Mechanism. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200800172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Heler R, Bell JK, Boland LM. Homology model and targeted mutagenesis identify critical residues for arachidonic acid inhibition of Kv4 channels. Channels (Austin) 2013; 7:74-84. [PMID: 23334377 PMCID: PMC3667888 DOI: 10.4161/chan.23453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Polyunsaturated fatty acids such as arachidonic acid (AA) exhibit inhibitory modulation of Kv4 potassium channels. Molecular docking approaches using a Kv4.2 homology model predicted a membrane-embedded binding pocket for AA comprised of the S4-S5 linker on one subunit and several hydrophobic residues within S3, S5 and S6 from an adjacent subunit. The pocket is conserved among Kv4 channels. We tested the hypothesis that modulatory effects of AA on Kv4.2/KChIP channels require access to this site. Targeted mutation of a polar residue (K318) and a nonpolar residue (G314) within the S4-S5 linker as well as a nonpolar residue in S3 (V261) significantly impaired the effects of AA on K (+) currents in Xenopus oocytes. These residues may be important in stabilizing (K318) or regulating access to (V261, G314) the negatively charged carboxylate moiety on the fatty acid. Structural specificity was supported by the lack of disruption of AA effects observed with mutations at residues located near, but not within the predicted binding pocket. Furthermore, we found that the crystal structure of the related Kv1.2/2.1 chimera lacks the structural features present in the proposed AA docking site of Kv4.2 and the Kv1.2/2.1 K (+) currents were unaffected by AA. We simulated the mutagenic substitutions in our Kv4.2 model to demonstrate how specific mutations may disrupt the putative AA binding pocket. We conclude that AA inhibits Kv4 channel currents and facilitates current decay by binding within a hydrophobic pocket in the channel in which K318 within the S4-S5 linker is a critical residue for AA interaction.
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Affiliation(s)
- Robert Heler
- Department of Biology, University of Richmond, Richmond, VA, USA
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27
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Pirolli D, Giardina B, Mordente A, Ficarra S, De Rosa MC. Understanding the binding of daunorubicin and doxorubicin to NADPH-dependent cytosolic reductases by computational methods. Eur J Med Chem 2012; 56:145-54. [PMID: 22982121 DOI: 10.1016/j.ejmech.2012.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/02/2012] [Accepted: 08/16/2012] [Indexed: 10/28/2022]
Abstract
The anthracycline anticancer agents daunorubicin (DAUN) and doxorubicin (DOX) are reduced by different NADPH-dependent cytosolic reductases into their corresponding alcohol metabolites daunorubicinol (DAUNol) and doxorubicinol (DOXol), which have been implicated in the development of chronic cardiomyopathy. To better understand the individual importance of each enzyme in the reduction and to provide deeper insight into the binding at atomic level we performed molecular docking and dynamics simulations of DAUN and DOX into the active sites of human carbonyl reductase 1 (CBR1) and human aldehyde reductase (AKR1A1). Such simulations evidenced a different behavior between the reductases with respect to DAUN and DOX suggesting major contribution of CBR1 in the reduction. The results are in agreement with available experimental data and for each enzyme and anthracycline pair provided the identification of key residues involved in the interactions. The structural models that we have derived could serve as a useful tool for structure-guided drug design studies.
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Affiliation(s)
- Davide Pirolli
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy.
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28
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Meng L, Yang L, Zhao X, Zhang L, Zhu H, Liu C, Tan W. Targeted delivery of chemotherapy agents using a liver cancer-specific aptamer. PLoS One 2012; 7:e33434. [PMID: 22558072 PMCID: PMC3338807 DOI: 10.1371/journal.pone.0033434] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/08/2012] [Indexed: 11/18/2022] Open
Abstract
Background Using antibody/aptamer-drug conjugates can be a promising method for decreasing toxicity, while increasing the efficiency of chemotherapy. Methodology/Principal Findings In this study, the antitumor agent Doxorubicin (Dox) was incorporated into the modified DNA aptamer TLS11a-GC, which specifically targets LH86, a human hepatocellular carcinoma cell line. Cell viability tests demonstrated that the TLS11a-GC-Dox conjugates exhibited both potency and target specificity. Importantly, intercalating Dox into the modified aptamer inhibited nonspecific uptake of membrane-permeable Dox to the non-target cell line. Since the conjugates are selective for cells that express higher amounts of target proteins, both criteria noted above are met, making TLS11a-GC-Dox conjugates potential candidates for targeted delivery to liver cancer cells. Conclusions/Significance Considering the large number of available aptamers that have specific targets for a wide variety of cancer cells, this novel aptamer-drug intercalation method will have promising implications for chemotherapeutics in general.
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Affiliation(s)
- Ling Meng
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Liu Yang
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Xiangxuan Zhao
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Lucy Zhang
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Haizhen Zhu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, People’s Republic of China
| | - Chen Liu
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (WT); (CL)
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (WT); (CL)
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Li T, Huang XH, Zhao YF, Li HH, Wu ST, Huang CC. An unusual double T5(2) water tape trapped in silver(i) coordination polymer hosts: influence of the solvent on the assembly of Ag(i)-4,4′-bipyridine chains with trans-cyclohexanedicarboxylate and their luminescent properties. Dalton Trans 2012; 41:12872-81. [DOI: 10.1039/c2dt31847d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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30
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Guza R, Kotandeniya D, Murphy K, Dissanayake T, Lin C, Giambasu GM, Lad RR, Wojciechowski F, Amin S, Sturla SJ, Hudson RH, York DM, Jankowiak R, Jones R, Tretyakova NY. Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA. Nucleic Acids Res 2011; 39:3988-4006. [PMID: 21245046 PMCID: PMC3089471 DOI: 10.1093/nar/gkq1341] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023] Open
Abstract
Endogenous 5-methylcytosine ((Me)C) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational 'hotspots' for smoking induced lung cancer. (Me)C enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5'-CCCGGCACCC GC[(15)N(3),(13)C(1)-G]TCCGCG-3', + strand) were prepared containing [(15)N(3), (13)C(1)]-guanine opposite unsubstituted cytosine, (Me)C, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2'-deoxynucleosides, N(2)-BPDE-dG adducts formed at the [(15)N(3), (13)C(1)]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N(2)-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE-DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N(2) position of guanine.
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MESH Headings
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/analogs & derivatives
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry
- Base Pairing
- Chromatography, High Pressure Liquid
- Cytosine/analogs & derivatives
- DNA Adducts/chemistry
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Genes, p53
- Guanine/chemistry
- Isotope Labeling
- Models, Molecular
- Oligodeoxyribonucleotides/chemical synthesis
- Oligodeoxyribonucleotides/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Rebecca Guza
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Delshanee Kotandeniya
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Kristopher Murphy
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Thakshila Dissanayake
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Chen Lin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - George Madalin Giambasu
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Rahul R. Lad
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Filip Wojciechowski
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shantu Amin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shana J. Sturla
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Robert H.E. Hudson
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ryszard Jankowiak
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Roger Jones
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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31
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Akhter MZ, Sharma A, Rajeswari MR. Interaction of adriamycin with a promoter region of hmga1 and its inhibitory effect on HMGA1 expression in A431 human squamous carcinoma cell line. MOLECULAR BIOSYSTEMS 2011; 7:1336-46. [DOI: 10.1039/c0mb00247j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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Conformational diversity of anthracycline anticancer antibiotics: A density functional theory calculation. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Differences in accumulation of anthracyclines daunorubicin, doxorubicin and epirubicin in rat tissues revealed by immunocytochemistry. Histochem Cell Biol 2010; 133:677-82. [DOI: 10.1007/s00418-010-0700-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2010] [Indexed: 10/19/2022]
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34
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Detection of DNA damage induced by styrene oxide in dsDNA layer-by-layer films using adriamycin as electroactive probe. Colloids Surf B Biointerfaces 2010; 76:334-9. [DOI: 10.1016/j.colsurfb.2009.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 11/20/2009] [Accepted: 11/23/2009] [Indexed: 11/18/2022]
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35
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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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36
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Douady J, Calvo F, Spiegelman F. Structure, stability, and infrared spectroscopy of (H2O)nNH4+ clusters: A theoretical study at zero and finite temperature. J Chem Phys 2008; 129:154305. [DOI: 10.1063/1.2987304] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Yu H, Ren J, Chaires JB, Qu X. Hydration of drug-DNA complexes: greater water uptake for adriamycin compared to daunomycin. J Med Chem 2008; 51:5909-11. [PMID: 18788722 PMCID: PMC2663378 DOI: 10.1021/jm800826y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water is an integral part of DNA, and the conserved water molecules at the binding sites can modulate drug binding to DNA or protein. We report here that anthracycline antitumor antibiotics, adriamycin (AM) and daunomycin (DM), binding to DNA is accompanied by different hydration changes, with AM binding resulting in the uptake of about twice as many water molecules as DM. These results indicate that water is playing an important role in drug binding to DNA.
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Affiliation(s)
- Haijia Yu
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jinsong Ren
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, 529 S. Jackson St., Louisville, KY 40202
| | - Xiaogang Qu
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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38
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Sumner I, Iyengar SS. Combining quantum wavepacketab initiomolecular dynamics with QM/MM and QM/QM techniques: Implementation blendingONIOMand empirical valence bond theory. J Chem Phys 2008; 129:054109. [DOI: 10.1063/1.2956496] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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39
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Li X, Moore DT, Iyengar SS. Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: Case study of the proton-bound dimethyl ether dimer. J Chem Phys 2008; 128:184308. [DOI: 10.1063/1.2903446] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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40
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Smolin N, Daggett V. Formation of Ice-like Water Structure on the Surface of an Antifreeze Protein. J Phys Chem B 2008; 112:6193-202. [DOI: 10.1021/jp710546e] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nikolai Smolin
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5013
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5013
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41
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Komorsky-Lovrić S. Redox kinetics of adriamycin adsorbed on the surface of graphite and mercury electrodes. Bioelectrochemistry 2006; 69:82-7. [PMID: 16443398 DOI: 10.1016/j.bioelechem.2005.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 10/13/2005] [Accepted: 10/18/2005] [Indexed: 10/25/2022]
Abstract
Kinetics of the surface redox reactions of adriamycin (doxorubicin hydrochloride) adsorbed on paraffin-impregnated graphite electrode (PIGE) and on mercury electrode is measured by square-wave voltammetry. In 0.9 mol/L KNO3 buffered to pH 4.65, the standard electrode reaction rate constants of the first quinone/hydroquinone redox couple (see Scheme 2) on PIGE and mercury are k(s1)=49+/-12 s(-1) and k(s1)=147+/-36 s(-1), respectively. Under the same conditions, the standard rate constant of the second redox couple on the PIGE is smaller than 4 s(-1) and the electron transfer coefficient of the reduction is alpha2=0.35.
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Affiliation(s)
- Sebojka Komorsky-Lovrić
- Center for Marine and Environmental Research Ruder Bosković Institute, P.O. Box 180 10002, Zagreb, Croatia.
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42
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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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43
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Iyengar SS, Petersen MK, Day TJF, Burnham CJ, Teige VE, Voth GA. The properties of ion-water clusters. I. The protonated 21-water cluster. J Chem Phys 2005; 123:084309. [PMID: 16164293 DOI: 10.1063/1.2007628] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ab initio atom-centered density-matrix propagation approach and the multistate empirical valence bond method have been employed to study the structure, dynamics, and rovibrational spectrum of a hydrated proton in the "magic" 21 water cluster. In addition to the conclusion that the hydrated proton tends to reside on the surface of the cluster, with the lone pair on the protonated oxygen pointing "outwards," it is also found that dynamical effects play an important role in determining the vibrational properties of such clusters. This result is used to analyze and complement recent experimental and theoretical studies.
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Affiliation(s)
- Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, USA.
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44
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Tumir LM, Piantanida I, Juranović I, Meić Z, Tomić S, Zinić M. Recognition of homo-polynucleotides containing adenine by a phenanthridinium bis-uracil conjugate in aqueous media. Chem Commun (Camb) 2005:2561-3. [PMID: 15900326 DOI: 10.1039/b500617a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Among novel bis-nucleobase-phenanthridinium conjugates bis-uracil analogue stabilized significantly more effective poly-dA-poly-dT and poly-AH(+)-poly-AH(+) than adenine analogue and reference compound . For the alternating poly-dAdT-poly-dAdT however, the binding preference is lost, pointing to the importance of specific interactions of uracils of with homopolynucleotides containing consecutive adenines.
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Affiliation(s)
- Lidija-Marija Tumir
- Laboratory of Supramolecular and Nucleoside Chemistry, Department of Chemistry and Biochemistry, Ruder Bosković Institute, HR 10002 Zagreb, P.O.B. 180, Croatia
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45
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Smolin N, Winter R. Molecular Dynamics Simulations of Staphylococcal Nuclease: Properties of Water at the Protein Surface. J Phys Chem B 2004. [DOI: 10.1021/jp047579y] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nikolai Smolin
- Department of Chemistry, Physical Chemistry I, University of Dortmund, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- Department of Chemistry, Physical Chemistry I, University of Dortmund, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
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46
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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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47
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Howerton SB, Nagpal A, Williams LD. Surprising roles of electrostatic interactions in DNA-ligand complexes. Biopolymers 2003; 69:87-99. [PMID: 12717724 DOI: 10.1002/bip.10319] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The positions of cations in x-ray structures are modulated by sequence, conformation, and ligand interactions. The goal here is to use x-ray diffraction to help resolve structural and thermodynamic roles of specifically localized cations in DNA-anthracycline complexes. We describe a 1.34 A resolution structure of a CGATCG(2)-adriamycin(2) complex obtained from crystals grown in the presence of thallium (I) ions. Tl(+) can substitute for biological monovalent cations, but is readily detected by distinctive x-ray scattering, obviating analysis of subtle differences in coordination geometry and x-ray scattering of water, sodium, potassium, and ammonium. Six localized Tl(+) sites are observable adjacent to each CGATCG(2)-adriamycin(2) complex. Each of these localized monovalent cations are found within the G-tract major groove of the intercalated DNA-drug complex. Adriamycin appears to be designed by nature to interact favorably with the electrostatic landscape of DNA, and to conserve the distribution of localized cationic charge. Localized inorganic cations in the major groove are conserved upon binding of adriamycin. In the minor groove, inorganic cations are substituted by a cationic functional group of adriamycin. This partitioning of cationic charge by adriamycin into the major groove of CG base pairs and the minor groove of AT base pairs may be a general feature of sequence-specific DNA-small molecule interactions and a potentially useful important factor in ligand design.
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Affiliation(s)
- Shelley B Howerton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta 30332-0400, USA
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48
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Anodic voltammetry and AFM imaging of picomoles of adriamycin adsorbed onto carbon surfaces. J Electroanal Chem (Lausanne) 2002. [DOI: 10.1016/s0022-0728(02)00944-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Bosma WB, Rhodes MM. Molecular dynamics simulations of structural transitions and phase coexistence in water pentamers. J Chem Phys 2002. [DOI: 10.1063/1.1515764] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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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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