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Deng YR, Li YF, Yang H, Fan YR, Huang Y. Synthesis, DNA binding of bis-naphthyl ferrocene derivatives and the application as new electroactive indicators for DNA biosensor. J Inorg Biochem 2024; 257:112615. [PMID: 38772187 DOI: 10.1016/j.jinorgbio.2024.112615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/29/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
A series of bis-naphthyl ferrocene derivatives were synthesized and characterized. Based on the results obtained from UV-visible absorption titration and ethidium bromide (EB) displacement experiments, it was observed that the synthesized compounds exhibited a strong binding ability to dsDNA. In comparison to the viscosity curve of EB, the tested compounds demonstrated a bisintercalation binding mode when interacting with CT-DNA. Differential pulse voltammetry (DPV) was employed to assess the binding specificity of these indicators towards ssDNA and dsDNA. All tested indicators displayed more pronounced signal differences before and after hybridization between probe nucleic acids and target nucleic acids compared to Methylene Blue (MB). Among the evaluated compounds, compound 3j containing an ether chain showed superior performance as an indicator, making it suitable for constructing DNA-based biosensors. Under optimized conditions including probe ssDNA concentration and indicator concentration, this biosensor exhibited good sensitivity, reproducibility, stability, and selectivity. The limit of detection was calculated as 4.53 × 10-11 mol/L. Furthermore, when utilizing 3j as the indicator in serum samples, the biosensor achieved satisfactory recovery rates for detecting the BRCA1 gene.
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Affiliation(s)
- Ya-Ru Deng
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China; Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area Ministry of Education, Ningxia Medical University, Yinchuan 750004, PR China
| | - Ya-Fei Li
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China; Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area Ministry of Education, Ningxia Medical University, Yinchuan 750004, PR China
| | - Hao Yang
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China; Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area Ministry of Education, Ningxia Medical University, Yinchuan 750004, PR China; Collaborative Innovation Center for Ningxia Characteristic Traditional Chinese Medicine by Ningxia Hui Autonomous Region & Education Ministry of P.R. China, Ningxia Characteristic Traditional Chinese Medicine Modern Engineering and Technique Research Center, Ningxia Key Laboratory of Drug Development and Generic Drug Research, Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Yinchuan 750004, PR China
| | - Yan-Ru Fan
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China; Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area Ministry of Education, Ningxia Medical University, Yinchuan 750004, PR China; Collaborative Innovation Center for Ningxia Characteristic Traditional Chinese Medicine by Ningxia Hui Autonomous Region & Education Ministry of P.R. China, Ningxia Characteristic Traditional Chinese Medicine Modern Engineering and Technique Research Center, Ningxia Key Laboratory of Drug Development and Generic Drug Research, Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Yinchuan 750004, PR China.
| | - Yu Huang
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China; Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area Ministry of Education, Ningxia Medical University, Yinchuan 750004, PR China; Collaborative Innovation Center for Ningxia Characteristic Traditional Chinese Medicine by Ningxia Hui Autonomous Region & Education Ministry of P.R. China, Ningxia Characteristic Traditional Chinese Medicine Modern Engineering and Technique Research Center, Ningxia Key Laboratory of Drug Development and Generic Drug Research, Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Yinchuan 750004, PR China.
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2
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Venugopal S, Sharma V, Anuradha M, Singh I, Singh G. DNA Intercalators as Anticancer Agents. Chem Biol Drug Des 2022; 100:580-598. [PMID: 35822451 DOI: 10.1111/cbdd.14116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
Cancer is one of the most prevailing disease conditions which occurs due to uncontrolled cell division either due to natural mutation to the genes or due to changes induced by physical, chemical, or biological carcinogens. According to WHO, it is the second leading cause of death worldwide and has reported 10 million deaths in 2020. Hence there arises the need for better chemotherapies and DNA intercalators are one such emerging therapy for cancer. DNA intercalating agents reversibly intercalate with the double-helical structure of DNA by interacting with adjacent base pairs and disrupting the structure of DNA and thereby causing cell death. Here we discuss the different classes of organo-intercalators used in cancer therapy describing their anticancer and intercalation ability by different methods along with their structure-activity relationship and mechanism of action.
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Affiliation(s)
- Sneha Venugopal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Vikas Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Mehra Anuradha
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Iqubal Singh
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Gurdeep Singh
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
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3
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Goswami S, Ghosh R, Prasanthan P, Kishore N. Mode of interaction of altretamine with calf thymus DNA: biophysical insights. J Biomol Struct Dyn 2022; 41:3728-3740. [PMID: 35343872 DOI: 10.1080/07391102.2022.2054472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 103 M-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK-1 mol-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.
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Affiliation(s)
- Sathi Goswami
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Pooja Prasanthan
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
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4
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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5
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Mikulin I, Ljubić I, Piantanida I, Vasilev A, Mondeshki M, Kandinska M, Uzelac L, Martin-Kleiner I, Kralj M, Tumir LM. Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality-Strong Affinity Nucleic Acids Binders. Biomolecules 2021; 11:biom11081075. [PMID: 34439741 PMCID: PMC8391988 DOI: 10.3390/biom11081075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents.
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Affiliation(s)
- Ivana Mikulin
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Ivana Ljubić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Aleksey Vasilev
- Faculty of Chemistry and Pharmacy, Department of Pharmaceutical and Applied Organic Chemistry, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria;
- Correspondence: (A.V.); (L.-M.T.); Tel.: +359-98-836-6528 (A.V.); +385-1-457-1220 (L.-M.T.)
| | - Mihail Mondeshki
- Department of Chemistry, Johannes Gutenberg Universität Mainz, Duesbergweg 10–14, 55128 Mainz, Germany;
| | - Meglena Kandinska
- Faculty of Chemistry and Pharmacy, Department of Pharmaceutical and Applied Organic Chemistry, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria;
| | - Lidija Uzelac
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Irena Martin-Kleiner
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Marijeta Kralj
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
- Correspondence: (A.V.); (L.-M.T.); Tel.: +359-98-836-6528 (A.V.); +385-1-457-1220 (L.-M.T.)
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6
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Rowell KN, Thomas DS, Ball GE, Wakelin LPG. Molecular dynamic simulations of diacridine binding to DNA: Indications that C6 diacridine can bisintercalate spanning two base pairs. Biopolymers 2020; 112:e23409. [PMID: 33207389 DOI: 10.1002/bip.23409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/27/2020] [Accepted: 11/03/2020] [Indexed: 11/06/2022]
Abstract
Dimers of 9-aminoacridine linked via the 9-amino group with polymethylene chains, termed diacridines, are known to bisintercalate into DNA when the linker comprises 6 or more methylene units. There are no literature reports of crystal or NMR solution structures for bisintercalated diacridine-DNA complexes, and the issue of the structure of the C6 ([CH2 ]n linker where n = 6) diacridine complex remains unresolved. Previously, based on simple geometric considerations, it was proposed that C6 diacridine could only span a single base pair, which requires that its bifunctional reaction violates the widely-observed "neighbor exclusion principle" where bound intercalators are separated by at least 2 base pairs. Here we have explored the structure of diacridine-DNA complexes using unrestrained molecular dynamics in explicit solvent using the parmbsc0 forcefield in AMBER14. We studied the C4 to C8 dimers, intercalated via both the minor and major DNA grooves, to a variety of nucleotide sequences. We find that C6, C7, and C8 diacridine are able to form 2 base pair bisintercalated complexes from either groove, whereas the C4 and C5 homologues cannot. We conclude that C6 diacridine does have the capacity to bisintercalate without violating neighbor exclusion, and that the previous proposed binding model needs revision.
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Affiliation(s)
- Keiran N Rowell
- School of Chemistry, UNSW Sydney, Sydney, New South Wales, Australia
| | - Donald S Thomas
- NMR Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Graham E Ball
- School of Chemistry, UNSW Sydney, Sydney, New South Wales, Australia
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7
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8
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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9
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Bhattacharya P, Mukherjee S, Mandal SM. Fluoroquinolone antibiotics show genotoxic effect through DNA-binding and oxidative damage. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117634. [PMID: 31756649 DOI: 10.1016/j.saa.2019.117634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
The fluoroquinolones (FQs) are one the most successful class of synthetic antibiotics that primarily target the type II topoisomerases. With a pursuit to evaluate their genotoxicity, the present work established moderate to good DNA-damaging properties of some of the well-known and clinically prescribed fluoroquinolone antibiotics (2nd and 3rd generation). Hypochromic shift in UV-Vis absorption titration, fluorescence quenching in competitive ethidium bromide displacement assay (with calf-thymus DNA) and in-silico studies established DNA-intercalation with binding constants of the order 104. A basic Structure Activity Relationship (SAR) has been derived from the docking results. MTT assay has been also done to evaluate the effect of these antibiotics on cell viability. The expression level of specific DNA-glycosylase enzymes responsible for repairing the oxidized DNA bases are quantified through western blot analysis. The studies revealed that fluoroquinolone antibiotics initiate the genotoxic effect at a concentration of above 50 μg/mL. Recruitment of APE1 and NEIL1 was found to be significantly increased to remove the oxidized nucleobases.
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Affiliation(s)
| | - Srasta Mukherjee
- Department of Chemistry, Adamas University, Kolkata, 700126, India
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology, Kharagpur, 721302, WB, India.
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10
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A Garratt-Braverman cyclization route towards the synthesis of phenanthridine derivatives and their DNA-binding studies. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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Portugal J. Challenging transcription by DNA-binding antitumor drugs. Biochem Pharmacol 2018; 155:336-345. [PMID: 30040927 DOI: 10.1016/j.bcp.2018.07.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022]
Abstract
Cancer has been associated with altered gene expression. Therefore, transcription and its regulation by transcription factors are considered key points to be explored in the pursuit of more efficient antitumor agents. This paper reviews the effects of DNA-binding drugs on the interaction between transcription factors and DNA, and it discusses recent advances in the understanding of the mechanisms by which small compounds interfere with the activity of transcription factors and gene expression. Many DNA-binding drugs, some of them in clinical use, can compete with a variety of transcription factors for their preferred binding sites in gene promoters, or they can covalently modify DNA, thus preventing transcription factors from recognizing their binding sites. On the other hand, transcription factor activity can be impaired through modification of the protein factors or their complexes. Several "omic" tools have been developed to explore the genome-wide changes in gene expression induced by DNA-binding drugs, which reveal details of the mechanisms of action. Transcriptomic profiles obtained from drug-treated cells and of samples collected from patients upon treatment provide insights into the in vivo mechanisms of drug action related to the inhibition of gene transcription. The information available about the molecular structure and mechanisms of action of both transcription factors and DNA-binding drugs, together with the new opportunities provided by functional genomics, should encourage the development of new more-selective DNA-binding antitumor drugs to target a single gene with little effect on others.
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Affiliation(s)
- José Portugal
- Instituto de Diagnóstico Ambiental y Estudios del Agua, CSIC, E-08034 Barcelona, Spain.
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12
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Hormann J, Malina J, Lemke O, Hülsey MJ, Wedepohl S, Potthoff J, Schmidt C, Ott I, Keller BG, Brabec V, Kulak N. Multiply Intercalator-Substituted Cu(II) Cyclen Complexes as DNA Condensers and DNA/RNA Synthesis Inhibitors. Inorg Chem 2018; 57:5004-5012. [DOI: 10.1021/acs.inorgchem.8b00027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Hormann
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
| | - Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
| | - Oliver Lemke
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Max J. Hülsey
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Stefanie Wedepohl
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Jan Potthoff
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
| | - Claudia Schmidt
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, 38106 Braunschweig, Germany
| | - Ingo Ott
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, 38106 Braunschweig, Germany
| | - Bettina G. Keller
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
| | - Nora Kulak
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
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13
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Liu X, Wu C, Zhang J, Shi Y, Zhang S, Geng Y, Tung CH, Wang W. Cobalt-catalyzed radical cyclization of isocyanides forming phenanthridine derivatives. Org Chem Front 2018. [DOI: 10.1039/c8qo00887f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A neutral cobalt(ii) compound catalyzes the radical cyclization of 2-isocyano-biphenyls with various alkyl halides, providing a series of phenanthridine-fused polycycles.
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Affiliation(s)
- Xiangyu Liu
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Chengjuan Wu
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Jing Zhang
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Yihan Shi
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Shengnan Zhang
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Yan Geng
- College of Chemistry
- Chemical Engineering and Materials Science
- Shandong Normal University
- Jinan 250014
- P. R. China
| | - Chen-Ho Tung
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Wenguang Wang
- Key Lab of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
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14
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Kukowska M. Amino acid or peptide conjugates of acridine/acridone and quinoline/quinolone-containing drugs. A critical examination of their clinical effectiveness within a twenty-year timeframe in antitumor chemotherapy and treatment of infectious diseases. Eur J Pharm Sci 2017; 109:587-615. [PMID: 28842352 DOI: 10.1016/j.ejps.2017.08.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/16/2017] [Accepted: 08/19/2017] [Indexed: 01/10/2023]
Abstract
Acridines/acridones, quinolines/quinolones (chromophores) and their derivatives constitute extremely important family of compounds in current medicine. Great significance of the compounds is connected with antimicrobial and antitumor activities. Combining these features together in one drug seems to be long-term benefit, especially in oncology therapy. The attractiveness of the chromophore drugs is still enhanced by elimination their toxicity and improvement not only selectivity, specificity but also bioavailability. The best results are reached by conjugation to natural peptides. This paper highlights significant advance in the study of amino acid or peptide chromophore conjugates that provide highly encouraging data for novel drug development. The structures and clinical significance of amino acid or peptide chromophore conjugates are widely discussed.
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Affiliation(s)
- Monika Kukowska
- Chair & Department of Chemical Technology of Drugs, Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland.
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15
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Conformational Preferences of π–π Stacking Between Ligand and Protein, Analysis Derived from Crystal Structure Data Geometric Preference of π–π Interaction. Interdiscip Sci 2015; 7:211-20. [DOI: 10.1007/s12539-015-0263-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 04/01/2014] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
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16
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Sankappa Rai U, Isloor A, Shetty P, Pai K, Fun H. Synthesis and in vitro biological evaluation of new pyrazole chalcones and heterocyclic diamides as potential anticancer agents. ARAB J CHEM 2015. [DOI: 10.1016/j.arabjc.2014.01.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Rescifina A, Zagni C, Mineo PG, Giofrè SV, Chiacchio U, Tommasone S, Talotta C, Gaeta C, Neri P. DNA Recognition with Polycyclic-Aromatic-Hydrocarbon-Presenting Calixarene Conjugates. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Interactions with polynucleotides and antitumor activity of amidino and imidazolinyl substituted 2-phenylbenzothiazole mesylates. Eur J Med Chem 2014; 86:406-19. [PMID: 25194933 DOI: 10.1016/j.ejmech.2014.08.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/12/2014] [Accepted: 08/30/2014] [Indexed: 11/23/2022]
Abstract
Based on previously reported antiproliferative activity screening, four most promising disubstituted 2-phenylbenzothiazole hydrochlorides were chosen for detailed study. Water solubility, as well as liphophilicity/hydrophilicity balance of organic core were modified by conversion to mesylate salts. For purpose of structure/activity studies their structures were determined by X-ray structure analysis. Detailed analysis of interactions of new compounds with double stranded (ds-) DNA/RNA by UV/Vis and CD titrations, thermal melting and viscometry experiments revealed that most of studied compounds intercalate into ds-RNA but bind into minor groove of AT-DNA, and agglomerate along GC-DNA. Furthermore, compounds also interact with ss-RNA, but only amino-imidazolinyl 2-phenylbenzothiazole, 4b displayed well defined orientation and dominant binding mode (by induced CD signals) with poly A and poly G. Besides, in vitro investigations revealed moderate to high antiproliferative activity of benzothiazoles against seven human cancer cell lines, while in some cases (HTC 116, SW620, MIA PaCa-2) high correlation between the type of the amidino group and cytotoxic activity was observed.
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19
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Hu C, Xi Q, Ge J, Luo FY, Tang LJ, Jiang JH, Yu RQ. Graphene–hemin hybrid nanosheets as a label-free colorimetric platform for DNA and small molecule assays. RSC Adv 2014. [DOI: 10.1039/c4ra08789e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel colorimetric platform has been developed for detecting DNA and small molecules based on a graphene–hemin hybrid nanosheet in a homogenous solution.
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Affiliation(s)
- Cui Hu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Qiang Xi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Jia Ge
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Feng-Yan Luo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
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20
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W. Gribble G, D. Mosher M, D. Jaycox G, Cory M, A. Fairley T. Potential DNA Bis-Intercalating Agents. Synthesis and Antitumor Activity of N,N'-(Methylenedi-4,1-cyclohexanediyl-bis(9-acridinamine) Isomers. HETEROCYCLES 2014. [DOI: 10.3987/com-13-s(s)77] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Jahromi AH, Fu Y, Miller KA, Nguyen L, Luu LM, Baranger AM, Zimmerman SC. Developing bivalent ligands to target CUG triplet repeats, the causative agent of myotonic dystrophy type 1. J Med Chem 2013; 56:9471-9481. [PMID: 24188018 DOI: 10.1021/jm400794z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An expanded CUG repeat transcript (CUG(exp)) is the causative agent of myotonic dystrophy type 1 (DM1) by sequestering muscleblind-like 1 protein (MBNL1), a regulator of alternative splicing. On the basis of a ligand (1) that was previously reported to be active in an in vitro assay, we present the synthesis of a small library containing 10 dimeric ligands (4-13) that differ in length, composition, and attachment point of the linking chain. The oligoamino linkers gave a greater gain in affinity for CUG RNA and were more effective when compared to oligoether linkers. The most potent in vitro ligand (9) was shown to be aqueous-soluble and both cell- and nucleus-permeable, displaying almost complete dispersion of MBNL1 ribonuclear foci in a DM1 cell model. Direct evidence for the bioactivity of 9 was observed in its ability to disperse ribonuclear foci in individual live DM1 model cells using time-lapse confocal fluorescence microscopy.
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Affiliation(s)
- Amin Haghighat Jahromi
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA.,Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Yuan Fu
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Kali A Miller
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lien Nguyen
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Long M Luu
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Anne M Baranger
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Steven C Zimmerman
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA.,Department of Chemistry, University of Illinois, Urbana, IL, USA
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22
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Willner I, Eichen Y, Doron A, Marx S. Effects of Electrostatic and π-π Interactions on the Stabilities of Xanthene Dye-4,4′-Bipyridinium Complexes: Structural Design of a Geared Supramolecular Machine. Isr J Chem 2013. [DOI: 10.1002/ijch.199200008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Tulla-Puche J, Auriemma S, Falciani C, Albericio F. Orthogonal chemistry for the synthesis of thiocoraline-triostin hybrids. Exploring their structure-activity relationship. J Med Chem 2013; 56:5587-600. [PMID: 23746132 DOI: 10.1021/jm4006093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The natural compounds triostin and thiocoraline are potent antitumor agents that act as DNA bisintercalators. From a pharmaceutical point of view, these compounds are highly attractive although they present a low pharmacokinetic profile, in part due to their low solubility. Synthetically, they represent a tour de force because no robust strategies have been developed to access a broad range of these bicyclic (depsi)peptides in a straightforward manner. Here we describe solid-phase strategies to synthesize new bisintercalators, such as thiocoraline-triostin hybrids, as well as analogues bearing soluble tags. Orthogonal protection schemes (up to five from: Fmoc, Boc Alloc, pNZ, o-NBS, and Troc), together with the right concourse of the coupling reagents (HOSu, HOBt, HOAt, Oxyma, EDC, DIPCDI, PyAOP, PyBOP, HATU, COMU), were crucial to establish the synthetic plan. In vitro studies and structure-activity relationships have been shown trends in the structure-activity relationship that will facilitate the design of new bisintercalators.
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Affiliation(s)
- Judit Tulla-Puche
- Institute for Research in Biomedicine Barcelona , Baldiri Reixac 10, 08028 Barcelona, Spain
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24
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Grabar Branilović M, Tomić S, Tumir LM, Piantanida I. The bis-phenanthridinium system flexibility and position of covalently bound uracil finely tunes the interaction with polynucleotides. MOLECULAR BIOSYSTEMS 2013; 9:2051-62. [PMID: 23681361 DOI: 10.1039/c3mb25578f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of structurally similar bis-phenanthridinium derivatives, some with uracil at different positions, revealed different interactions with various polynucleotides. The uniform binding of mononucleotides to all studied compounds by "cyclobisintercaland" binding type indicated that compound-polynucleotide interaction selectivity was the consequence of polynucleotide secondary structure and not direct nucleobase recognition. Although affinity and fluorimetric response of all studied compounds toward ds-DNA/RNA was similar, the thermal denaturation and ICD signal-based sensing was highly sensitive to polynucleotide basepair composition and secondary structure. In particular, for the specific poly rAH(+)-poly rAH(+) double helix MD parameters are newly developed and used for analysis of its complexes. The highly sensitive orientation of phenanthridinium as well as the role of the uracil substituent, both binding interactions finely tuned by the steric and binding properties of the DNA/RNA-ligand interaction site, offer novel structural information about binding and steric properties of particular DNA-RNA systems.
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Affiliation(s)
- Marina Grabar Branilović
- Laboratory for Chemical and Biological Crystallography, Division of Physical Chemistry, Ruđer Bošković Institute, HR 10002 Zagreb, P.O.B. 180, Croatia.
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25
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Doughty B, Rao Y, Kazer SW, Kwok SJJ, Turro NJ, Eisenthal KB. Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation. J Phys Chem B 2013; 117:15285-9. [DOI: 10.1021/jp311634a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Benjamin Doughty
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Yi Rao
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Samuel W. Kazer
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Sheldon J. J. Kwok
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Nicholas J. Turro
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Kenneth B. Eisenthal
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
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26
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Synthesis of novel bis-anthraquinone derivatives and their biological evaluation as antitumor agents. Arch Pharm Res 2013; 36:573-8. [DOI: 10.1007/s12272-013-0074-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 02/24/2013] [Indexed: 11/27/2022]
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27
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Duskova K, Sierra S, Fernández MJ, Gude L, Lorente A. Synthesis and DNA interaction of ethylenediamine platinum(II) complexes linked to DNA intercalants. Bioorg Med Chem 2012; 20:7112-8. [DOI: 10.1016/j.bmc.2012.09.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
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28
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Liu Y, Chai Y, Kumar A, Tidwell RR, Boykin DW, Wilson WD. Designed compounds for recognition of 10 base pairs of DNA with two at binding sites. J Am Chem Soc 2012; 134:5290-9. [PMID: 22369366 DOI: 10.1021/ja211628j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Short AT base pair sequences that are separated by a small number of GCs are common in eukaryotic parasite genomes. Cell-permeable compounds that bind effectively and selectively to such sequences present an attractive therapeutic approach. Compounds with linked, one or two amidine-benzimidazole-phenyl (ABP) motifs were designed, synthesized, and evaluated for binding to adjacent AT sites by biosensor-surface plasmon resonance (SPR). A surprising feature of the linked ABP motifs is that a set of six similar compounds has three different minor groove binding modes with the target sequences. Compounds with one ABP bind independently to two separated AT sites. Unexpectedly, compounds with two ABP motifs can bind strongly either as monomers or as cooperative dimers to the full site. The results are supported by mass spectrometry and circular dichroism, and models to explain the different binding modes are presented.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, United States
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29
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Wang M, Yang Z, Li Y, Li H. Lanthanide complex of 1-phenyl-3-methyl-5-hydroxypyrazole-4-carbaldehyde-(isonicotinoyl) hydrazone: crystal structure and DNA-binding properties. J COORD CHEM 2011. [DOI: 10.1080/00958972.2011.610102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Mingfang Wang
- a Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000 , P.R. China
| | - Zhengyin Yang
- a Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000 , P.R. China
| | - Yong Li
- a Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000 , P.R. China
| | - Hongge Li
- a Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000 , P.R. China
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30
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Guin M, Patwari GN, Karthikeyan S, Kim KS. Do N-heterocyclic aromatic rings prefer π-stacking? Phys Chem Chem Phys 2011; 13:5514-25. [DOI: 10.1039/c0cp02015j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Radić Stojković M, Miljanić S, Mišković K, Glavaš-Obrovac L, Piantanida I. The phenanthridine biguanides efficiently differentiate between dGdC, dAdT and rArU sequences by two independent, sensitive spectroscopic methods. MOLECULAR BIOSYSTEMS 2011; 7:1753-65. [DOI: 10.1039/c1mb05030c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Maity S, Patwari GN, Sedlak R, Hobza P. A π-stacked phenylacetylene dimer. Phys Chem Chem Phys 2011; 13:16706-12. [DOI: 10.1039/c1cp20677j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Szumilak M, Szulawska-Mroczek A, Koprowska K, Stasiak M, Lewgowd W, Stanczak A, Czyz M. Synthesis and in vitro biological evaluation of new polyamine conjugates as potential anticancer drugs. Eur J Med Chem 2010; 45:5744-51. [PMID: 20974504 DOI: 10.1016/j.ejmech.2010.09.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
Abstract
The synthesis of new polyamine derivatives containing dimeric quinoline (3a-c), cinnoline (4a-c) and phthalimide (7a-c and 8a-c) moieties is described. Three different polyamines: (1,4-bis(3-aminopropyl)piperazine (a), 4,9-dioxa-1,12-dodecanediamine (b), 3,3'-diamino-N-methyldipropylamine (c) were used as linkers. The new compounds were obtained according to known procedures. Their biological activity was assessed in vitro in a highly aggressive melanoma cell line A375. Polyamine diimides containing phthalimide moieties demonstrated no inhibitory activities against melanoma cells. Quinoline diamides were more efficient than cinnoline ones. Mainly cytostatic activity exerted as altered cell cycle profiles was observed at the concentrations causing about 50% reduction of adherent cell proliferation. Based on their structure as well as their biological activity, we assume that some of the newly synthesized compounds may act as DNA bisintercalators. This study might be useful for further designing and developing anticancer drugs with potent activities.
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Affiliation(s)
- Marta Szumilak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland
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Dukši M, Baretić D, Čaplar V, Piantanida I. Novel bis-phenanthridine derivatives with easily tunable linkers, study of their interactions with DNA and screening of antiproliferative activity. Eur J Med Chem 2010; 45:2671-6. [DOI: 10.1016/j.ejmech.2010.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 12/28/2009] [Accepted: 02/04/2010] [Indexed: 10/19/2022]
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35
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Galisteo J, Navarro P, Campayo L, Yunta MJR, Gómez-Contreras F, Villa-Pulgarin JA, Sierra BG, Mollinedo F, Gonzalez J, Garcia-España E. Synthesis and cytotoxic activity of a new potential DNA bisintercalator: 1,4-Bis{3-[N-(4-chlorobenzo[g]phthalazin-1-yl)aminopropyl]}piperazine. Bioorg Med Chem 2010; 18:5301-9. [PMID: 20538470 DOI: 10.1016/j.bmc.2010.05.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/14/2010] [Accepted: 05/18/2010] [Indexed: 11/25/2022]
Abstract
The synthesis of new 1,4-bisalkylamino (2-4) and 1-alkylamino-4-chloro (5-6) substituted benzo[g]phthalazines is reported. Compounds 2-4 and 6 were prepared both in the free and heteroaromatic ring protonated forms. Bifunctional 6 contains the 1,4-bisaminopropylpiperazine chain as a linker between the two heteroaromatic units, whereas 5 is its monofunctional analogue. The in vitro antitumour activity of the synthesized compounds has been tested against human colon, breast and lung carcinoma cells, and also against human glioblastoma cells. Results obtained show that all of them are active in all cases, but bifunctional 6.2HCl is remarkably effective against the four cell lines tested, exhibiting IC50 values in the range of 10(-7) M, similar to those found for doxorubicin. The bifunctional structure of 6.2HCl enhances activity with respect to the monofunctional related compounds 5 and 7, leading to the highest activity among all the compounds tested. Molecular modelling of 6 suggests that those results could be indicative of DNA bisintercalation, which should be specially favoured in the diprotonated form 6.2HCl, a compound suitable for being studied more in depth in further biological tests. Measure of the DNA thermal melting curves show that the linear rise in Tm for bifunctional 6.2HCl is nearly twice than that one obtained for monofunctional 5, and supports the DNA-binding hypothesis.
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Affiliation(s)
- Juan Galisteo
- Instituto de Química Médica, Centro de Química Orgánica Manuel Lora-Tamayo, CSIC, c/Juan de la Cierva 3, E-28006 Madrid, Spain
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36
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Ramisetty SR, Baranger AM. Cooperative binding of a quinoline derivative to an RNA stem loop containing a dangling end. Bioorg Med Chem Lett 2010; 20:3134-7. [DOI: 10.1016/j.bmcl.2010.03.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 03/23/2010] [Accepted: 03/26/2010] [Indexed: 11/25/2022]
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37
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Tumir LM, Grabar M, Tomić S, Piantanida I. The interactions of bis-phenanthridinium–nucleobase conjugates with nucleotides: adenine-conjugate recognizes UMP in aqueous medium. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Stojković MR, Marjanović M, Pawlica D, Dudek L, Eilmes J, Kralj M, Piantanida I. Cationic side-chains control DNA/RNA binding properties and antiproliferative activity of dicationic dibenzotetraaza[14]annulene derivatives. NEW J CHEM 2010. [DOI: 10.1039/b9nj00490d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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39
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Tewari AK, Srivastava P, Puerta C, Valerga P. Stacking in 5-[3-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-propoxy]-3-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid ethyl ester through C–H···π, C–H···O and C–H···N networks. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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KARUP GUNNAR, MELDAL MORTEN, NIELSEN PETERE, BUCHARDT OLE. 9-Acridinylpeptides and 9-acridinyl-4-nitrophenylsulfonylpeptides. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1988.tb01268.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Intercalating, cytotoxic, antitumour activity of 8-chloro and 4-morpholinopyrimido [4′,5′:4,5]thieno(2,3-b)quinolines. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 94:13-9. [DOI: 10.1016/j.jphotobiol.2008.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Revised: 09/02/2008] [Accepted: 09/07/2008] [Indexed: 11/22/2022]
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42
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Ligand binding to nucleic acids and proteins: Does selectivity increase with strength? Eur J Med Chem 2008; 43:2307-15. [DOI: 10.1016/j.ejmech.2008.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2007] [Revised: 01/30/2008] [Accepted: 02/08/2008] [Indexed: 11/21/2022]
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43
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44
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Solvothermal Synthesis, Crystal Structure and DNA Binding Studies of a 3D Supramolecular Complex {[Cu(phen)CN][Cu(phen)][Cu(CN)2]} n Assembled by Double Curvy Chains. J Inorg Organomet Polym Mater 2008. [DOI: 10.1007/s10904-008-9211-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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He Z, Bu X, Eleftheriou A, Zihlif M, Qing Z, Stewart BW, Wakelin LP. DNA threading bis(9-aminoacridine-4-carboxamides): Effects of piperidine sidechains on DNA binding, cytotoxicity and cell cycle arrest. Bioorg Med Chem 2008; 16:4390-400. [DOI: 10.1016/j.bmc.2008.02.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 02/17/2008] [Accepted: 02/19/2008] [Indexed: 11/25/2022]
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Navarrete-Vázquez G, Moreno-Diaz H, Estrada-Soto S, Tlahuext H. 2-(2-Benzyl-oxyphen-yl)-1H-benzimid-azole. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o608. [PMID: 21201944 PMCID: PMC2960883 DOI: 10.1107/s1600536808004510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 02/14/2008] [Indexed: 05/26/2023]
Abstract
The asymmetric unit of the title compound, C20H16N2O, contains two molecules. The dihedral angles between the benzimidazole ring systems and the attached benzene rings are 10.6 (5) and 13.7 (5)°. The conformers are linked by bifurcated three-centre hydrogen bonds, forming chains along the diagonal of the ab plane. The packing is further stabilized by π–π and C—H⋯π interactions.
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Hill JG, Platts JA. Calculating stacking interactions in nucleic acid base-pair steps using spin-component scaling and local second order Møller–Plesset perturbation theory. Phys Chem Chem Phys 2008; 10:2785-91. [DOI: 10.1039/b718691f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Biron E, Voyer N. Towards sequence selective DNA binding: design, synthesis and DNA binding studies of novel bis-porphyrin peptidic nanostructures. Org Biomol Chem 2008; 6:2507-15. [DOI: 10.1039/b803281e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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