1
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Preparation of graphene-based nanocomposites with spinel ferrite nanoparticles: Their cytotoxic levels in different human cell lines and molecular docking studies. J Organomet Chem 2023. [DOI: 10.1016/j.jorganchem.2023.122660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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2
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DNA, a target of mixed chelate copper(II) compounds (Casiopeinas®) studied by electrophoresis, UV–vis and circular dichroism techniques. J Inorg Biochem 2022; 231:111772. [DOI: 10.1016/j.jinorgbio.2022.111772] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 11/22/2022]
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3
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Yahyazadehfar M, Sheikhhosseini E, Ahmadi SA, Ghazanfari D. One Pot Unexpected Isocyanide-based Three-component Synthesis of Pyrrole-3-carboxamides Containing Ether Groups. ORG PREP PROCED INT 2021. [DOI: 10.1080/00304948.2021.1973275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | | | - Sayed Ali Ahmadi
- Department of Chemistry, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Dadkhoda Ghazanfari
- Department of Chemistry, Kerman Branch, Islamic Azad University, Kerman, Iran
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4
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Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis. Molecules 2021; 26:molecules26195871. [PMID: 34641414 PMCID: PMC8510488 DOI: 10.3390/molecules26195871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.
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5
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Biolayer interferometry provides a robust method for detecting DNA binding small molecules in microbial extracts. Anal Bioanal Chem 2020; 413:1159-1171. [PMID: 33236226 DOI: 10.1007/s00216-020-03079-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/24/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022]
Abstract
DNA replication is an exceptional point of therapeutic intervention for many cancer types and several small molecules targeting DNA have been developed into clinically used antitumor agents. Many of these molecules are naturally occurring metabolites from plants and microorganisms, such as the widely used chemotherapeutic doxorubicin. While natural product sources contain a vast number of DNA binding small molecules, isolating and identifying these molecules is challenging. Typical screening campaigns utilize time-consuming bioactivity-guided fractionation approaches, which use sequential rounds of cell-based assays to guide the isolation of active compounds. In this study, we explore the use of biolayer interferometry (BLI) as a tool for rapidly screening natural product sources for DNA targeting small molecules. We first verified that BLI robustly detected DNA binding using designed GC- and AT-rich DNA oligonucleotides with known DNA intercalating, groove binding, and covalent binding agents including actinomycin D (1), doxorubicin (2), ethidium bromide (3), propidium iodide (4), Hoechst 33342 (5), and netropsin (6). Although binding varied with the properties of the oligonucleotides, measured binding affinities agreed with previously reported values. We next utilized BLI to screen over 100 bacterial extracts from our microbial library for DNA binding activity and found three highly active extracts. Binding-guided isolation was used to isolate the active principle component from each extract, which were identified as echinomycin (8), actinomycin V (9), and chartreusin (10). This biosensor-based DNA binding screen is a novel, low-cost, easy to use, and sensitive approach for medium-throughput screening of complex chemical libraries. Graphical abstract.
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6
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Soni MN, Kumar SP, S. R. KJ, Rawal RM, Pandya HA. An integrated computational approach to identify GC minor groove binders using various molecular docking scoring functions, dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2020; 38:3838-3855. [DOI: 10.1080/07391102.2019.1664331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Mehul N. Soni
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Sivakumar Prasanth Kumar
- Department of Life Sciences, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Kaid Johar S. R.
- Department of Zoology, Bio-Medical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Rakesh M. Rawal
- Department of Life Sciences, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Himanshu A. Pandya
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, University School of Sciences, Gujarat University, Ahmedabad, India
- Department of Life Sciences, University School of Sciences, Gujarat University, Ahmedabad, India
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7
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Fudickar W, Linker T. Structural motives controlling the binding affinity of 9,10-bis(methylpyridinium)anthracenes towards DNA. Bioorg Med Chem 2020; 28:115432. [DOI: 10.1016/j.bmc.2020.115432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
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8
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Sahle FF, Lowe TL. Design strategies for programmable oligonucleotide nanotherapeutics. Drug Discov Today 2020; 25:73-88. [PMID: 31525462 PMCID: PMC6980509 DOI: 10.1016/j.drudis.2019.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/02/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
Abstract
A systematic review on how to design different programmable nanotherapeutics using oligonucleotides as building blocks or as surface and matrix modifiers for controlled and targeted delivery of various therapeutic agents in presented.
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Affiliation(s)
- Fitsum Feleke Sahle
- Department of Pharmaceutical Sciences, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
| | - Tao L Lowe
- Department of Pharmaceutical Sciences, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA.
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9
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Copper bis-Dipyridoquinoxaline Is a Potent DNA Intercalator that Induces Superoxide-Mediated Cleavage via the Minor Groove. Molecules 2019; 24:molecules24234301. [PMID: 31779066 PMCID: PMC6930674 DOI: 10.3390/molecules24234301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/25/2023] Open
Abstract
Herein, we report the synthesis, characterisation, X-ray crystallography, and oxidative DNA binding interactions of the copper artificial metallo-nuclease [Cu(DPQ)2(NO3)](NO3), where DPQ = dipyrido[3,2-f:2',3'-h]quinoxaline. The cation [Cu(DPQ)2]2+ (Cu-DPQ), is a high-affinity binder of duplex DNA and presents an intercalative profile in topoisomerase unwinding and viscosity experiments. Artificial metallo-nuclease activity occurs in the absence of exogenous reductant but is greatly enhanced by the presence of the reductant Na-L-ascorbate. Mechanistically, oxidative DNA damage occurs in the minor groove, is mediated aerobically by the Cu(I) complex and is dependent on both superoxide and hydroxyl radical generation. To corroborate cleavage at the minor groove, DNA oxidation of a cytosine-guanine (5'-CCGG-3')-rich oligomer was examined in tandem with a 5-methylcytosine (5'-C5mCGG-3') derivative where 5mC served to sterically block the major groove and direct damage to the minor groove. Overall, both the DNA binding affinity and cleavage mechanism of Cu-DPQ depart from Sigman's reagent [Cu(1,10-phenanthroline)2]2+; however, both complexes are potent oxidants of the minor groove.
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10
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Sánchez MI, Rama G, Calo-Lapido R, Ucar K, Lincoln P, López MV, Melle-Franco M, Mascareñas JL, Vázquez ME. Canonical DNA minor groove insertion of bisbenzamidine-Ru(ii) complexes with chiral selectivity. Chem Sci 2019; 10:8668-8674. [PMID: 31803441 PMCID: PMC6849638 DOI: 10.1039/c9sc03053k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/30/2019] [Indexed: 11/24/2022] Open
Abstract
We report the first Ru(ii) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites.
We report the first Ru(ii) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis-benzamidine minor groove DNA-binding agent with a ruthenium(ii) complex. Importantly, one of the enantiomers (Δ-[Ru(bpy)2b4bpy]2+, Δ-4Ru) shows a considerably higher DNA affinity than the parent organic ligand and the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.
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Affiliation(s)
- Mateo I Sánchez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Gustavo Rama
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Inorgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Renata Calo-Lapido
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Kübra Ucar
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , SE 412 96 Gothenburg , Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , SE 412 96 Gothenburg , Sweden
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Inorgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Manuel Melle-Franco
- Ciceco - Aveiro Institute of Materials , University of Aveiro Campus Universitario de Santiago , Aveiro , 3810-193 , Portugal
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
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11
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Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors. J Antibiot (Tokyo) 2019; 73:5-27. [PMID: 31578455 PMCID: PMC7102388 DOI: 10.1038/s41429-019-0240-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 12/17/2022]
Abstract
The development of new mechanisms of resistance among pathogens, the occurrence and transmission of genes responsible for antibiotic insensitivity, as well as cancer diseases have been a serious clinical problem around the world for over 50 years. Therefore, intense searching of new leading structures and active substances, which may be used as new drugs, especially against strain resistant to all available therapeutics, is very important. Dihydrofolate reductase (DHFR) has attracted a lot of attention as a molecular target for bacterial resistance over several decades, resulting in a number of useful agents. Trimethoprim (TMP), (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidine) is the well-known dihydrofolate reductase inhibitor and one of the standard antibiotics used in urinary tract infections (UTIs). This review highlights advances in design, synthesis, and biological evaluations in structural modifications of TMP as DHFR inhibitors. In addition, this report presents the differences in the active site of human and pathogen DHFR. Moreover, an excellent review of DHFR inhibition and their relevance to antimicrobial and parasitic chemotherapy was presented.
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12
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Krafcikova M, Dzatko S, Caron C, Granzhan A, Fiala R, Loja T, Teulade-Fichou MP, Fessl T, Hänsel-Hertsch R, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. J Am Chem Soc 2019; 141:13281-13285. [PMID: 31394899 DOI: 10.1021/jacs.9b03031] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studies on DNA-ligand interactions in the cellular environment are problematic due to the lack of suitable biophysical tools. To address this need, we developed an in-cell NMR-based approach for monitoring DNA-ligand interactions inside the nuclei of living human cells. Our method relies on the acquisition of NMR data from cells electroporated with preformed DNA-ligand complexes. The impact of the intracellular environment on the integrity of the complexes is assessed based on in-cell NMR signals from unbound and ligand-bound forms of a given DNA target. This technique was tested on complexes of two model DNA fragments and four ligands, namely, a representative DNA minor-groove binder (netropsin) and ligands binding DNA base-pairing defects (naphthalenophanes). In the latter case, we demonstrate that two of the three in vitro-validated ligands retain their ability to form stable interactions with their model target DNA in cellulo, whereas the third one loses this ability due to off-target interactions with genomic DNA and cellular metabolites. Collectively, our data suggest that direct evaluation of the behavior of drug-like molecules in the intracellular environment provides important insights into the development of DNA-binding ligands with desirable biological activity and minimal side effects resulting from off-target binding.
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Affiliation(s)
- Michaela Krafcikova
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
| | - Simon Dzatko
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Coralie Caron
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Tomas Loja
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Tomas Fessl
- Faculty of Science , University of South Bohemia , Ceske Budejovice CZ-370 05 , Czech Republic
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute , University of Cambridge , Cambridge CB2 0RE , United Kingdom
| | - Jean-Louis Mergny
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
| | | | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
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13
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Tavakkoli H, Attaran R, Khosravi A, Salari Z, Salarkia E, Dabiri S, Mosallanejad SS. Vascular alteration in relation to fosfomycine: In silico and in vivo investigations using a chick embryo model. Biomed Pharmacother 2019; 118:109240. [PMID: 31401391 DOI: 10.1016/j.biopha.2019.109240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 02/08/2023] Open
Abstract
Fosfomycin residues are found in the egg following administration in the layer hen. In this regard, some aspects of embryo-toxicity of fosfomycin have been documented previously. The exact mechanism by which fosfomycin causes embryo-toxicity is not clearly understood. We hypothesis that fosfomycin may alter vasculature as well as normal expression of genes, which are associated with vascular development. Therefore, the present study aimed to address these issues through in silico and in vivo investigations. At first, embryo-toxicity and anti-angiogenic effects of fosfomycin were tested using computerized programs. After that, fertile chicken eggs were treated with fosfomycin and chorioallantoic membrane vasculature was assessed through morphometric, molecular and histopathological assays. The results showed that fosfomycin not only interacted with VEGF-A protein and promoter, but also altered embryonic vasculature and decreased expression level of VEGF-A. Reticulin staining of treated group was also confirmed decreased vasculature. The minor groove of DNA was the preferential binding site for fosfomycin with its selective binding to GC-rich sequences. We suggested that the affinity of fosfomycin for VEGF-A protein and promoter as well as alteration of the angiogenic signaling pathway may cause vascular damage during embryonic growth. Hence, veterinarians should be aware of such effects and limit the use of this drug during the developmental stages of the embryo, particularly in breeder farms. Considering the anti-angiogenic activity and sequence selectivity of fosfomycin, a major advantage that seems to be very promising is the fact that it is possible to achieve a sequence-selective binding drug for cancer.
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Affiliation(s)
- Hadi Tavakkoli
- Department of Clinical Science, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Reza Attaran
- Department of Clinical Science, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ahmad Khosravi
- Leishmaniasis Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Zohreh Salari
- Obstetrics and Gynecology Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ehsan Salarkia
- Leishmaniasis Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Shahriar Dabiri
- Afzalipour School of Medicine & Pathology and Stem Cells Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyedeh Saedeh Mosallanejad
- Afzalipour School of Medicine & Biochemistry Department, Kerman University of Medical Sciences, Kerman, Iran
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14
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Sustained Release of Minor-Groove-Binding Antibiotic Netropsin from Calcium-Coated Groove-Rich DNA Particles. Pharmaceutics 2019; 11:pharmaceutics11080387. [PMID: 31382405 PMCID: PMC6724015 DOI: 10.3390/pharmaceutics11080387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/14/2019] [Accepted: 07/22/2019] [Indexed: 12/02/2022] Open
Abstract
Control of the release properties of drugs has been considered a key factor in the development of drug delivery systems (DDSs). However, drug delivery has limitations including cytotoxicity, low loading efficiency, and burst release. To overcome these challenges, nano or micro-particles have been suggested as carrier systems to deliver chemical drugs. Herein, nano-sized DNA particles (DNAp) were manufactured to deliver netropsin, which is known to bind to DNA minor grooves. The rationally designed particles with exposed rich minor grooves were prepared by DNAp synthesis via rolling circle amplification (RCA). DNAp could load large quantities of netropsin in its minor grooves. An analytical method was also developed for the quantification of netropsin binding to DNAp by UV–visible spectrometry. Moreover, controlled release of netropsin was achieved by forming a layer of Ca2+ on the DNAp (CaDNAp). As a proof of concept, the sustained release of netropsin by CaDNAp highlights the potential of the DNAp-based delivery approach.
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15
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Arciszewska K, Pućkowska A, Wróbel A, Drozdowska D. Carbocyclic Analogues of Distamycin and Netropsin. Mini Rev Med Chem 2019; 19:98-113. [PMID: 30626311 DOI: 10.2174/1389557518666181009143203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 11/22/2022]
Abstract
The DNA as the depository of genetic information is a natural target for chemotherapy. A lot of anticancer and antimicrobial agents derive their biological activity from their selective interaction with DNA in the minor groove and from their ability to interfere with biological processes such as enzyme catalysis, replication and transcription. The discovery of the details of minor groove binding drugs, such as netropsin and distamycin A, oligoamides built of 4-amino-1-methylpyrrole-2-carboxylic acid residues, allowed to develop various DNA sequence-reading molecules, named lexitropsins, capable of interacting with DNA precisely, strongly and with a high specificity, and at the same time exhibiting significant cytotoxic potential. Among such compounds, lexitropsins built of carbocyclic sixmembered aromatic rings occupy a quite prominent place in drug research. This work is an attempt to present current findings in the study of carbocyclic lexitropins, their structures, syntheses and biological investigations such as DNA-binding and antiproliferative activity.
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Affiliation(s)
| | - Anna Pućkowska
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
| | - Agnieszka Wróbel
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
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16
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Kollmann F, Ramakrishnan S, Shen B, Grundmeier G, Kostiainen MA, Linko V, Keller A. Superstructure-Dependent Loading of DNA Origami Nanostructures with a Groove-Binding Drug. ACS OMEGA 2018; 3:9441-9448. [PMID: 31459078 PMCID: PMC6644410 DOI: 10.1021/acsomega.8b00934] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/03/2018] [Indexed: 05/26/2023]
Abstract
DNA origami nanostructures are regarded as powerful and versatile vehicles for targeted drug delivery. So far, DNA origami-based drug delivery strategies mostly use intercalation of the therapeutic molecules between the base pairs of the DNA origami's double helices for drug loading. The binding of nonintercalating drugs to DNA origami nanostructures, however, is less studied. Therefore, in this work, we investigate the interaction of the drug methylene blue (MB) with different DNA origami nanostructures under conditions that result in minor groove binding. We observe a noticeable effect of DNA origami superstructure on the binding affinity of MB. In particular, non-B topologies as for instance found in designs using the square lattice with 10.67 bp/turn may result in reduced binding affinity because groove binding efficiency depends on groove dimensions. Also, mechanically flexible DNA origami shapes that are prone to structural fluctuations may exhibit reduced groove binding, even though they are based on the honeycomb lattice with 10.5 bp/turn. This can be attributed to the induction of transient over- and underwound DNA topologies by thermal fluctuations. These issues should thus be considered when designing DNA origami nanostructures for drug delivery applications that employ groove-binding drugs.
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Affiliation(s)
- Fabian Kollmann
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger
Str. 100, 33098 Paderborn, Germany
| | - Saminathan Ramakrishnan
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger
Str. 100, 33098 Paderborn, Germany
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Guido Grundmeier
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger
Str. 100, 33098 Paderborn, Germany
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Veikko Linko
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger
Str. 100, 33098 Paderborn, Germany
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Adrian Keller
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger
Str. 100, 33098 Paderborn, Germany
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17
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Kıbrız İE, Saçmacı M, Yıldırım İ, Abbas Ali Noma S, Taşkın Tok T, Ateş B. Xanthine oxidase inhibitory activity of new pyrrole carboxamide derivatives:In vitroandin silicostudies. Arch Pharm (Weinheim) 2018; 351:e1800165. [DOI: 10.1002/ardp.201800165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 01/24/2023]
Affiliation(s)
- İbrahim Evren Kıbrız
- Faculty of Arts and Sciences, Department of Chemistry; Bozok University; Yozgat Turkey
| | - Mustafa Saçmacı
- Faculty of Arts and Sciences, Department of Chemistry; Bozok University; Yozgat Turkey
| | - İsmail Yıldırım
- Faculty of Sciences, Department of Chemistry; Erciyes University; Kayseri Turkey
| | - Samir Abbas Ali Noma
- Faculty of Arts and Sciences, Department of Chemistry; Inonu University; Malatya Turkey
| | - Tuğba Taşkın Tok
- Faculty of Arts and Sciences, Department of Chemistry; Gaziantep University; Gaziantep Turkey
| | - Burhan Ateş
- Faculty of Arts and Sciences, Department of Chemistry; Inonu University; Malatya Turkey
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18
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Hebenbrock M, González-Abradelo D, Strassert CA, Müller J. DNA Groove-binding Ability of Luminescent Platinum(II) Complexes based on a Family of Tridentate N^N^C Ligands Bearing Differently Substituted Alkyl Tethers. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 30 48149 Münster Germany
| | - Darío González-Abradelo
- CeNTech and Physikalisches Institut; Westfälische Wilhelms-Universität Münster; Heisenbergstraße 11 48149 Münster Germany
| | - Cristian A. Strassert
- CeNTech and Physikalisches Institut; Westfälische Wilhelms-Universität Münster; Heisenbergstraße 11 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 30 48149 Münster Germany
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19
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20
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Das S, Purkayastha P. Selective Binding of Thioflavin T in Sequence-Exchanged Single Strand DNA Oligomers and Further Interaction with Phospholipid Membranes. ChemistrySelect 2017. [DOI: 10.1002/slct.201700194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shrabanti Das
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
| | - Pradipta Purkayastha
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
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21
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Synthesis of crescent shaped heterocycle-fused aromatics via Garratt-Braverman cyclization and their DNA-binding studies. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Deiana M, Mettra B, Matczyszyn K, Piela K, Pitrat D, Olesiak-Banska J, Monnereau C, Andraud C, Samoc M. Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA. Phys Chem Chem Phys 2016; 17:30318-27. [PMID: 26506886 DOI: 10.1039/c5cp05381a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Bastien Mettra
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Katarzyna Piela
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Delphine Pitrat
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Cyrille Monnereau
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Chantal Andraud
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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23
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Czarnomysy R, Bielawski K, Muszynska A, Bielawska A, Gornowicz A. Biological evaluation of dimethylpyridine-platinum complexes with potent antiproliferative activity. J Enzyme Inhib Med Chem 2016; 31:150-165. [PMID: 27488500 DOI: 10.1080/14756366.2016.1212191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
This study investigates the effect of three new platinum complexes: Pt2(2,4-dimethylpyridine)4(berenil)2 (Pt14), Pt2(3,4-dimethylpyridine)4(berenil)2 (Pt15) and Pt2(3,5-dimethylpyridine)4(berenil)2 (Pt16) on growth and viability of breast cancer cells and their putative mechanism(s) of cytotoxicity. Cytotoxicity was measured with MTT assay and inhibition of [3H]thymidine incorporation into DNA in both breast cancer cells. Results revealed that Pt14-Pt16 exhibit substantially greater cytotoxicity than cisplatin against MCF-7 and MDA-MB-231 breast cancer cells. In the case of human skin fibroblast cell, cytotoxicity assays demonstrated that these compounds are less toxic to normal cells than cisplatin. In addition, the effects of Pt14-Pt16 are investigated using the flow cytometry assessment of annexin V binding, analysis of mitochondrial potential, markers of apoptosis such as caspase-3, caspase-8, caspase-9, caspase-10 and defragmentation of DNA by TUNEL assay. These results indicate that Pt14-Pt16 induce apoptosis by the mitochondrial and external pathway.
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Affiliation(s)
| | | | | | - Anna Bielawska
- b Department of Biotechnology , Medical University of Bialystok , Bialystok , Poland
| | - Agnieszka Gornowicz
- b Department of Biotechnology , Medical University of Bialystok , Bialystok , Poland
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24
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Chaires JB. A small molecule--DNA binding landscape. Biopolymers 2016; 103:473-9. [PMID: 25913470 DOI: 10.1002/bip.22660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/16/2015] [Indexed: 02/03/2023]
Abstract
This brief account traces the development of a "competition dialysis" method used to characterize the structural and sequence selectivity of DNA binding compounds. The method was inspired by a simple "differential dialysis" method pioneered by Don Crothers to explore base-selective intercalator binding. Results from compiled competition dialysis studies provide a small-molecule DNA binding landscape that shows a rich diversity of interactions and molecular recognition.
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Affiliation(s)
- Jonathan B Chaires
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
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25
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Ivanov AA, Salyanov VI, Zhuze AL. DNA sequence-specific ligands: XV. Synthesis and spectral characteristics of a new series of dimeric bisbenzimidazoles DB(1, 2, 6, 8, 9, 10, 12). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016020059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Surovaya AN, Bazhulina NP, Lepehina SY, Andronova VL, Galegov GA, Moiseeva ED, Grokhovsky SL, Gursky GV. Interaction of a dimeric distamycin analog with poly(dA)poly(dT), poly[d(A–T)]poly[d(A–T)], and duplex O23 at the origin of replication of the herpes simplex virus. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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28
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Chi S, Li L, Wu Y. Novel mono-cationic fluorescent probes based on different central π-conjugated bridges for two-photon bioimaging of cellular nuclei. RSC Adv 2016. [DOI: 10.1039/c6ra12193d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A series of novel pyridine mono-cationic two-photon fluorescent probes based on different central π-conjugated bridges, fluorenone (W-pyI), dibenzothiophene (S-pyI), and dibenzofuran (F-pyI), were prepared and studied for improving photostability in bioimaging applications.
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Affiliation(s)
- Shuheng Chi
- Key Laboratory of Material Science and Technology for High Power Lasers
- Shanghai Institute of Optics and Fine Mechanics
- Chinese Academy of Sciences
- Shanghai 201800
- PR China
| | - Liang Li
- Key Laboratory of Material Science and Technology for High Power Lasers
- Shanghai Institute of Optics and Fine Mechanics
- Chinese Academy of Sciences
- Shanghai 201800
- PR China
| | - Yiqun Wu
- Key Laboratory of Material Science and Technology for High Power Lasers
- Shanghai Institute of Optics and Fine Mechanics
- Chinese Academy of Sciences
- Shanghai 201800
- PR China
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29
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Chakravorty A, Sugden B. The AT-hook DNA binding ability of the Epstein Barr virus EBNA1 protein is necessary for the maintenance of viral genomes in latently infected cells. Virology 2015; 484:251-258. [PMID: 26122471 DOI: 10.1016/j.virol.2015.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/02/2015] [Accepted: 05/20/2015] [Indexed: 02/01/2023]
Abstract
Epstein Barr Virus (EBV) is a human tumor virus that is causally linked to malignancies such as Burkitt׳s lymphoma, and gastric and nasopharyngeal carcinomas. Tethering of EBV genomes to cellular chromosomes is required for the synthesis and persistence of viral plasmids in tumor cells. However, it is not established how EBV genomes are tethered to cellular chromosomes. We test the hypothesis that the viral protein EBNA1 tethers EBV genomes to chromosomes specifically through its N-terminal AT-hook DNA-binding domains by using a small molecule, netropsin, that has been shown to inhibit the AT-hook DNA-binding of EBNA1 in vitro. We show that netropsin forces the loss of EBV genomes from epithelial and lymphoid cells in an AT-hook dependent manner and that EBV-positive lymphoma cells are significantly more inhibited in their growth by netropsin than are corresponding EBV-negative cells.
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Affiliation(s)
- Adityarup Chakravorty
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States.
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30
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Abouzeid LA, El-Subbagh HI. DNA binding of ethyl 2-substituted aminothiazole-4-carboxylate analogues: A molecular modeling approach to predict their antitumor activity. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2015. [DOI: 10.1016/j.fjps.2015.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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31
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Vijayalakshmi P, Selvaraj C, Shafreen RMB, Singh SK, Pandian SK, Daisy P. Ligand-based pharmacophore modelling and screening of DNA minor groove binders targeting Staphylococcus aureus. J Mol Recognit 2015; 27:429-37. [PMID: 24895275 DOI: 10.1002/jmr.2363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/07/2022]
Abstract
The recognition of DNA by small molecules is of special importance in the design of new drugs. Many natural and synthetic compounds have the ability to interact with the minor groove of DNA. In the present study, identification of minor groove binding compounds was attained by the combined approach of pharmacophore modelling, virtual screening and molecular dynamics approach. Experimentally reported 32 minor groove binding compounds were used to develop the pharmacophore model. Based on the fitness score, best three pharmacophore hypotheses were selected and used as template for screening the compounds from drug bank database. This pharmacophore-based screening provides many compounds with the same pharmacological properties. All these compounds were subjected to four phases of docking protocols with combined Glide-quantum-polarized ligand docking approach. Molecular dynamics results indicated that selected compounds are more active and showed good interaction in the binding site of DNA. Based on the scoring parameters and energy values, the best compounds were selected, and antibacterial activity of these compounds was identified using in vitro antimicrobial techniques.
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Affiliation(s)
- Periyasamy Vijayalakshmi
- Bioinformatics Centre (BIF), PG and Research Department of Biotechnology and Bioinformatics, Holy Cross College (Autonomous), Tiruchirappalli, 620002, Tamil Nadu, India
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32
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Wojciechowska A, Gągor A, Zierkiewicz W, Jarząb A, Dylong A, Duczmal M. Metal–organic framework in an l-arginine copper(ii) ion polymer: structure, properties, theoretical studies and microbiological activity. RSC Adv 2015. [DOI: 10.1039/c5ra02790j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel 1D polymeric copper(ii) complex of formula {[Cu(l-Arg)2(μ-4,4′-bpy)]Cl2·3H2O∞} was synthesized and characterized using X-ray diffraction, FT-IR, Raman, electron paramagnetic resonance and NIR-vis-UV spectroscopy, and its microbiological properties were analyzed.
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Affiliation(s)
| | - Anna Gągor
- Institute of Low Temperature and Structure Research
- Polish Academy of Sciences in Wrocław
- 50-422 Wrocław
- Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry
- Wroclaw University of Technology
- 50-370 Wrocław
- Poland
| | - Anna Jarząb
- Institute of Immunology and Experimental Therapy
- Polish Academy of Sciences
- 53-114 Wrocław
- Poland
| | - Agnieszka Dylong
- Faculty of Chemistry
- Wroclaw University of Technology
- 50-370 Wrocław
- Poland
| | - Marek Duczmal
- Faculty of Chemistry
- Wroclaw University of Technology
- 50-370 Wrocław
- Poland
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33
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Szerszenowicz J, Drozdowska D. Semi-automatic synthesis, antiproliferative activity and DNA-binding properties of new netropsin and bis-netropsin analogues. Molecules 2014; 19:11300-15. [PMID: 25090119 PMCID: PMC6271738 DOI: 10.3390/molecules190811300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/16/2022] Open
Abstract
A general route for the semi-automatic synthesis of some new potential minor groove binders was established. Six four-numbered sub-libraries of new netropsin and bis-netropsin analogues have been synthesized using a Syncore Reactor. The structures of the all new substances prepared in this investigation were fully characterized by NMR ((1)H, (13)C), HPLC and LC-MS. The antiproliferative activity of the obtained compounds was tested on MCF-7 breast cancer cells. The ethidium displacement assay using pBR322 confirmed the DNA-binding properties of the new analogues of netropsin and bis-netropsin.
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Affiliation(s)
- Jakub Szerszenowicz
- Saint Brunon Farmacy, Bohaterów Westerplatte 4 Str., 11-500 Giżycko, Poland.
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University, Mickiewicza 2A Str., 15-222 Białystok, Poland.
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34
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Kumar H, Chattopadhyay A, Prasath R, Devaraji V, Joshi R, Bhavana P, Saini P, Ghosh SK. Design, Synthesis, Physicochemical Studies, Solvation, and DNA Damage of Quinoline-Appended Chalcone Derivative: Comprehensive Spectroscopic Approach toward Drug Discovery. J Phys Chem B 2014; 118:7257-66. [DOI: 10.1021/jp5025262] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Himank Kumar
- Department
of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Anjan Chattopadhyay
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - R. Prasath
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Vinod Devaraji
- Department
of Pharmaceutical Chemistry, College of Pharmacy, Madras Medical College, Chennai 600003, India
| | - Ritika Joshi
- Department
of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - P. Bhavana
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Praveen Saini
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Sujit Kumar Ghosh
- Department
of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
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35
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μ-Oxamido binuclear copper (II) complexes: Synthesis, crystal structure, DNA interaction and antibacterial studies. Polyhedron 2014. [DOI: 10.1016/j.poly.2013.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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You X, Xie X, Sun R, Chen H, Li S, Liu Y. Titanium-mediated cross-coupling reactions of 1,3-butadiynes with α-iminonitriles to 3-aminopyrroles: observation of an imino aza-Nazarov cyclization. Org Chem Front 2014. [DOI: 10.1039/c4qo00159a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ti(OiPr)4/2 nBuLi-mediated highly efficient cross-coupling reactions of 1,3-butadiynes with α-iminonitriles are described, which provide convenient access to functionalized 3-aminopyrroles.
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Affiliation(s)
- Xu You
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032, People's Republic of China
| | - Xin Xie
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032, People's Republic of China
| | - Renhong Sun
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032, People's Republic of China
| | - Haoyi Chen
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032, People's Republic of China
| | - Shi Li
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032, People's Republic of China
| | - Yuanhong Liu
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032, People's Republic of China
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37
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Dumat B, Bordeau G, Faurel-Paul E, Mahuteau-Betzer F, Saettel N, Metge G, Fiorini-Debuisschert C, Charra F, Teulade-Fichou MP. DNA Switches on the Two-Photon Efficiency of an Ultrabright Triphenylamine Fluorescent Probe Specific of AT Regions. J Am Chem Soc 2013; 135:12697-706. [DOI: 10.1021/ja404422z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Blaise Dumat
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Guillaume Bordeau
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Elodie Faurel-Paul
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | | | - Nicolas Saettel
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Germain Metge
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
| | | | - Fabrice Charra
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
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38
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Ramos JP, Babu B, Chavda S, Liu Y, Plaunt A, Ferguson A, Savagian M, Lee M, Tzou S, Lin S, Kiakos K, Wang S, Lee M, Hartley JA, Wilson WD. Affinity and kinetic modulation of polyamide-DNA interactions by N-modification of the heterocycles. Biopolymers 2013; 99:497-507. [PMID: 23712486 PMCID: PMC3872963 DOI: 10.1002/bip.22205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 12/27/2022]
Abstract
Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form "stacked" dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f-ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5'-ACGCGT-3'. The synthesis and biophysical characterization of six f-ImPy*Im were determined by CD, ΔTM, DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f-ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5'-ACGCGT-3', and with strong affinity, Keq = 2.8 × 10(8) M(-1) and Keq = 6.2 × 10(7) M(-1), respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development.
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Affiliation(s)
- Joseph P. Ramos
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Balaji Babu
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Sameer Chavda
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Adam Plaunt
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Amanda Ferguson
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Mia Savagian
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Megan Lee
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Samuel Tzou
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Shicai Lin
- Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Moses Lee
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - John A. Hartley
- Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
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39
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Bazhulina NP, Surovaya AN, Gursky YG, Andronova VL, Moiseeva ED, Nikitin CACM, Golovkin MV, Galegov GА, Grokhovsky SL, Gursky GV. Complex of the herpes simplex virus type 1 origin binding protein UL9 with DNA as a platform for the design of a new type of antiviral drugs. J Biomol Struct Dyn 2013; 32:1456-73. [PMID: 23879454 PMCID: PMC4066892 DOI: 10.1080/07391102.2013.820110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The herpes simplex virus type 1 origin-binding protein, OBP, is a DNA helicase encoded by the UL9 gene. The protein binds in a sequence-specific manner to the viral origins of replication, two OriS sites and one OriL site. In order to search for efficient inhibitors of the OBP activity, we have obtained a recombinant origin-binding protein expressed in Escherichia coli cells. The UL9 gene has been amplified by PCR and inserted into a modified plasmid pET14 between NdeI and KpnI sites. The recombinant protein binds to Box I and Box II sequences and possesses helicase and ATPase activities. In the presence of ATP and viral protein ICP8 (single-strand DNA-binding protein), the initiator protein induces unwinding of the minimal OriS duplex (≈80 bp). The protein also binds to a single-stranded DNA (OriS*) containing a stable Box I-Box III hairpin and an unstable AT-rich hairpin at the 3'-end. In the present work, new minor groove binding ligands have been synthesized which are capable to inhibit the development of virus-induced cytopathic effect in cultured Vero cells. Studies on binding of these compounds to DNA and synthetic oligonucleotides have been performed by fluorescence methods, gel mobility shift analysis and footprinting assays. Footprinting studies have revealed that Pt-bis-netropsin and related molecules exhibit preferences for binding to the AT-spacer in OriS. The drugs stabilize structure of the AT-rich region and inhibit the fluctuation opening of AT-base pairs which is a prerequisite to unwinding of DNA by OBP. Kinetics of ATP-dependent unwinding of OriS in the presence and absence of netropsin derivatives have been studied by measuring the efficiency of Forster resonance energy transfer (FRET) between fluorophores attached to 5'- and 3'- ends of an oligonucleotide in the minimal OriS duplex. The results are consistent with the suggestion that OBP is the DNA Holiday junction (HJ) binding helicase. The protein induces conformation changes (bending and partial melting) of OriS duplexes and stimulates HJ formation in the absence of ATP. The antiviral activity of bis-netropsins is coupled with their ability to inhibit the fluctuation opening of АТ base pairs in the А + Т cluster and their capacity to stabilize the structure of the АТ-rich hairpin in the single-stranded oligonucleotide corresponding to the upper chain in the minimal duplex OriS. The antiviral activities of bis-netropsins in cell culture and their therapeutic effects on HSV1-infected laboratory animals have been studied.
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Affiliation(s)
- N P Bazhulina
- a V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , ul. Vavilova 32, 119991 , Moscow , Russia
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40
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Denisiuk A, Schubert V, Wolter FE, Irran E, Trouillas P, Süssmuth RD. Conformational investigation of antibiotic proximicin by X-ray structure analysis and quantum studies suggest a stretched conformation of this type of γ-peptide. Bioorg Med Chem 2013; 21:3582-9. [DOI: 10.1016/j.bmc.2013.02.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/18/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
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Khan RA, Asim A, Kakkar R, Gupta D, Bagchi V, Arjmand F, Tabassum S. A Chloro-Bridged Heterobimetallic (η6-Arene)ruthenium–Organotin Complex as an Efficient Topoisomerase Iα Inhibitor. Organometallics 2013. [DOI: 10.1021/om301223k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Rais Ahmad Khan
- Department
of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Ahmad Asim
- Department
of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Rita Kakkar
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Deepti Gupta
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Vivek Bagchi
- Department of Chemistry, University of Missouri, Rolla, Missouri 65409, United States
| | - Farukh Arjmand
- Department
of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Sartaj Tabassum
- Department
of Chemistry, Aligarh Muslim University, Aligarh 202002, India
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42
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Comprehensive Study on the Binding of Iron Schiff Base Complex with DNA and Determining the Binding Mode. J Fluoresc 2013; 23:813-21. [DOI: 10.1007/s10895-013-1181-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/24/2013] [Indexed: 10/27/2022]
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Sharpless KB, Manetsch R. In situ click chemistry: a powerful means for lead discovery. Expert Opin Drug Discov 2013; 1:525-38. [PMID: 23506064 DOI: 10.1517/17460441.1.6.525] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry and parallel synthesis are important and regularly applied tools for lead identification and optimisation, although they are often accompanied by challenges related to the efficiency of library synthesis and the purity of the compound library. In the last decade, novel means of lead discovery approaches have been investigated where the biological target is actively involved in the synthesis of its own inhibitory compound. These fragment-based approaches, also termed target-guided synthesis (TGS), show great promise in lead discovery applications by combining the synthesis and screening of libraries of low molecular weight compounds in a single step. Of all the TGS methods, the kinetically controlled variant is the least well known, but it has the potential to emerge as a reliable lead discovery method. The kinetically controlled TGS approach, termed in situ click chemistry, is discussed in this article.
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Affiliation(s)
- K Barry Sharpless
- WM Keck Professor, Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-315 La Jolla, CA 92037, USA.
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La Pensée L, Sabbani S, Sharma R, Bhamra I, Shore E, Chadwick AE, Berry NG, Firman J, Araujo NC, Cabral L, Cristiano MLS, Bateman C, Janneh O, Gavrila A, Wu YH, Hussain A, Ward SA, Stocks PA, Cosstick R, O'Neill PM. Artemisinin-polypyrrole conjugates: synthesis, DNA binding studies and preliminary antiproliferative evaluation. ChemMedChem 2013; 8:709-18. [PMID: 23495190 DOI: 10.1002/cmdc.201200536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Indexed: 11/06/2022]
Abstract
Greater than the sum of its parts: Artemisinins are currently in phase I-II clinical trials against breast, colorectal and non-small-cell lung cancers. In an attempt to offer increased specificity, a series of hybrid artemisinin-polypyrrole minor groove binder conjugates are described. DNA binding/modelling studies and preliminary biological evaluation give insights into their mechanism of action and the potential of this strategy.
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Affiliation(s)
- Louise La Pensée
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool L69 7ZD, UK
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Montalbano A, Parrino B, Diana P, Barraja P, Carbone A, Spanò V, Cirrincione G. Synthesis of the new oligopeptide pyrrole derivative isonetropsin and its one pyrrole unit analogue. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.01.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Yang RCK, Huang JTB, Chien SC, Huang R, Jeng KCG, Chen YC, Liao M, Wu JR, Hung WK, Hung CC, Chen YL, Waring MJ, Sheh L. Energetic studies on DNA–peptide interaction in relation to the enthalpy–entropy compensation paradox. Org Biomol Chem 2013; 11:48-61. [DOI: 10.1039/c2ob26320c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Abstract
Molecular docking, molecular mechanics, molecular dynamics and relaxation matrix simulation protocols have been extensively used to generate the structural details of ligand-receptor complexes in order to understand the binding interactions between the two entities. Experimental methods like NMR spectroscopy and X-ray crystallography are known to provide structural information about ligand-receptor complexes. In addition, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular docking have also been utilized to decode the phenomenon of the ligand-DNA interactions, with good correlation between experimental and computational results. The DNA binding affinity was demonstrated by analysing fluorescence spectral data. Structural rigidity of DNA upon ligand binding was identified by CD spectroscopy. Docking is carried out using the DNA-Dock program which results in the binding affinity data along with structural information like interatomic distances and H-bonding, etc. The complete structural analyses of various drug-DNA complexes have afforded results that indicate a specific DNA binding pattern of these ligands. It also exhibited that certain structural features of ligands can make a ligand to be AT- or GC-specific. It was also demonstrated that changing specificity from AT base pairs to GC base pairs further improved the DNA topoisomerase inhibiting activity in certain ligands. Thus, a specific molecular recognition signature encrypted in the structure of ligand can be decoded and can be effectively employed in designing more potent antiviral and antitumour agents.
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Yin YX, Wen JH, Geng ZR, Li YZ, Wang ZL. Two heptadentate Co(III) and Mn(III) complexes with partially deprotonated cyclen derivative bearing four hydroxypropyl pendants: structure, DNA binding and DNA cleavage. Appl Organomet Chem 2012. [DOI: 10.1002/aoc.2905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Jing-Han Wen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing; People's Republic of China
| | - Zhi-Rong Geng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing; People's Republic of China
| | - Yi-Zhi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing; People's Republic of China
| | - Zhi-Lin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing; People's Republic of China
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Tabassum S, Al-Asbahy WM, Afzal M, Arjmand F, Bagchi V. Molecular drug design, synthesis and structure elucidation of a new specific target peptide based metallo drug for cancer chemotherapy as topoisomerase I inhibitor. Dalton Trans 2012; 41:4955-4964. [PMID: 22407358 DOI: 10.1039/c2dt12044e] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
To evaluate the biological preference of metallopeptide drugs in cancer cells, a new dinuclear copper(II) complex [Cu(2)(glygly)(2)(ppz)(H(2)O)(4)]·2H(2)O (1) (glygly = glycyl glycine anion and ppz = piperazine), was designed and synthesized as topoisomerase I inhibitor. The structural elucidation of the complex was done by elemental analysis, spectroscopic methods and single crystal X-ray diffraction. The in vitro DNA binding studies of complex 1 with CT DNA were carried out by employing different optical methods viz. UV-vis, fluorescence and circular dichroism. The molecular docking technique was also utilized to ascertain the mechanism and mode of action towards the molecular target DNA and enzymes. Complex 1 cleaves pBR322 DNA via an oxidative mechanism and strongly binds to the DNA minor groove. Furthermore, complex 1 exhibits significant inhibitory effects on the catalytic activity of topoisomerase I at a very low concentration, ~12.5 μM, in addition to its excellent SOD mimics (IC(50)~0.086 μM).
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Affiliation(s)
- Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh 202201, UP, India.
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Lin CY, Yang YT, Ong CW. Synthesis of Chiral Pyrrolidine Isostere Inserted into Pyrrole Polyamide Skeleton. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201100603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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