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Issar U, Arora R, Kakkar R. In silico studies of the interaction of the minor groove binder Hoechst 33258 with B-DNA. J Biomol Struct Dyn 2024; 42:4537-4552. [PMID: 37301606 DOI: 10.1080/07391102.2023.2220807] [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: 02/23/2022] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Interaction of the minor groove binder, Hoechst 33258, with the Dickerson-Drew DNA dodecamer sequence has been investigated using docking, MM/QM, MM/GBSA and molecular dynamics computations to study the modes of binding and the interactions responsible for the binding. Besides the original Hoechst 33258 ligand (HT), a total of 12 ionization and stereochemical states for the ligand are obtained at the physiological pH and have been docked into B-DNA. These states have one or the other or both benzimidazole rings in protonated states, apart from the piperazine nitrogen, which has a quaternary nitrogen in all the states. Most of these states are found to exhibit good docking scores and free energy of binding with B-DNA. The best docked state has been taken further for molecular dynamics simulations and compared with the original HT. This state is protonated at both benzimidazole rings besides the piperazine ring and hence has very highly negative coulombic interaction energy. In both cases, there are strong coulombic interactions, but these are offset by the almost equally unfavorable solvation energies. Thus, the nonpolar forces, particularly van der Waals contacts, dominate the interaction, and the polar interactions highlight subtle changes in the binding energies, leading to more highly protonated states having more negative binding energies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Upasana Issar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Kalindi College, University of Delhi, Delhi, India
| | - Richa Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Shivaji College, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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DNA sequence-specific ligands. XX. Synthesis, spectral properties, virological and biochemical studies of fluorescent dimeric trisbenzimidazoles DB3P(n). Med Chem Res 2023. [DOI: 10.1007/s00044-023-03017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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3
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Dale AG, Porcu A, Mann J, Neidle S. The mechanism of resistance in Escherichia coli to ridinilazole and other antibacterial head-to-head bis-benzimidazole compounds. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02918-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractThe appY gene has been characterised as conferring resistance to a novel series of antimicrobial benzimidazole derivatives in E. coli MC1061 cells when expressed in high copy-number. A microarray approach was used to identify genes involved in the mechanism of appY-mediated antibacterial resistance, that were up- or down-regulated following induction of the gene in the appY knockout strain JW0553. In total, expression of 90 genes was induced and 48 repressed greater than 2.5-fold (P < 0.05), 45 min after appY induction. Over half the genes up-regulated following appY expression had confirmed or putative roles in acid resistance (AR) and response to oxidative and antibiotic stresses. These included the genes for MdtE and MdtF, which form a multi-drug transporter with TolC and have been implicated in resistance to several antibiotics including erythromycin. Amongst the acid resistance genes were gadAB and adiAC encoding the glutamate-dependant (AR2) and arginine-dependant (AR3) acid resistance systems respectively, in addition to the transcriptional activators of these systems gadE and gadX. In agreement with earlier studies, appA, appCB and hyaA-F were also up-regulated following induction of appY. This study has also confirmed that over-expression of mdtEF confers resistance to these antibacterial benzimidazoles, indicating that the observation of appY conferring resistance to these compounds, proceeds through an appY-mediated up-regulation of this efflux transporter. To assess the importance of the AppY enzyme to acid stress responses, the percentage survival of bacteria in acidified media (pH ≤ 2) was measured. From an initial input of 1 × 106 CFU/ml, the wild-type strain MG1655 showed 7.29% and 0.46% survival after 2 and 4 h, respectively. In contrast, strain JW0553 in which appY is deleted was completely killed by the treatment. Transformation of JW0553 with a plasmid carrying appY returned survival to wild-type levels (7.85% and 1.03% survival at 2 and 4 h). Further dissection of the response by prior induction of each of the three AR systems has revealed that AR1 and AR3 were most affected by the absence of appY. This work highlights an important and previously unidentified role for the AppY enzyme in mediating the responses to several stress conditions. It is likely that the appY gene fits into a complex transcriptional regulatory network involving σS and gadE and gadX. Further work to pinpoint its position in such a hierarchy and to assess the contribution of appY to oxidative stress responses should help determine its full significance. This work is also consistent with recent studies in C. difficile showing that the mechanism of action of ridinilazole involves AT-rich DNA minor groove binding.
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Neelakantan M, Latha V, Thalamuthu S. Polyaromatic ring containing β-diketone derivatives with antiproliferative activity toward human breast cancer cell lines: Synthesis, structure, DNA binding and molecular docking. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mousivand M, Bagherzadeh K, Anfossi L, Javan-Nikkhah M. Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study. Biotechnol J 2021; 17:e2100280. [PMID: 34800084 DOI: 10.1002/biot.202100280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B1 (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.
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Affiliation(s)
- Maryam Mousivand
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Kowsar Bagherzadeh
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Eye Research Center, the Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Turin, Italy
| | - Mohammad Javan-Nikkhah
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
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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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Caymaz B, Yıldız U, Akkoç S, Gerçek Z, Şengül A, Coban B. Synthesis, Characterization, and Antiproliferative Activity Studies of Novel Benzimidazole‐Imidazopyridine Hybrids as DNA Groove Binders. ChemistrySelect 2020. [DOI: 10.1002/slct.202001580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bahar Caymaz
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Ufuk Yıldız
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Senem Akkoç
- Department of Basic Pharmaceutical SciencesFaculty of PharmacySüleyman Demirel University Isparta 32260 Turkey
| | - Zuhal Gerçek
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Abdurrahman Şengül
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Burak Coban
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
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Khalid S, Rodger P. Molecular Dynamics Simulations of Dna and Its Complexes. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967404777726232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Current address: Laboratory of Molecular Biophysics, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
| | - P.Mark Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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9
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Ziach K, Chollet C, Parissi V, Prabhakaran P, Marchivie M, Corvaglia V, Bose PP, Laxmi-Reddy K, Godde F, Schmitter JM, Chaignepain S, Pourquier P, Huc I. Single helically folded aromatic oligoamides that mimic the charge surface of double-stranded B-DNA. Nat Chem 2018; 10:511-518. [PMID: 29610464 DOI: 10.1038/s41557-018-0018-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/31/2018] [Indexed: 01/15/2023]
Abstract
Numerous essential biomolecular processes require the recognition of DNA surface features by proteins. Molecules mimicking these features could potentially act as decoys and interfere with pharmacologically or therapeutically relevant protein-DNA interactions. Although naturally occurring DNA-mimicking proteins have been described, synthetic tunable molecules that mimic the charge surface of double-stranded DNA are not known. Here, we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA. These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer-protein interactions, whereas sequence-selective enzymes were not inhibited. Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein-DNA interactions.
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Affiliation(s)
- Krzysztof Ziach
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Céline Chollet
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Vincent Parissi
- Univ. Bordeaux - CNRS, Laboratoire de Microbiologie Fondamentale et Pathogénicité (UMR 5234), Bordeaux, France
| | - Panchami Prabhakaran
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | | | - Valentina Corvaglia
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Partha Pratim Bose
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Katta Laxmi-Reddy
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Frédéric Godde
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Jean-Marie Schmitter
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Stéphane Chaignepain
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France
| | - Philippe Pourquier
- INSERM U1194, Institut de Recherche en Cancérologie de Montpellier & Université de Montpellier, Montpellier, France
| | - Ivan Huc
- Univ. Bordeaux - CNRS - IPB, CBMN Laboratory (UMR5248), Institut Européen de Chimie et Biologie, Pessac, France. .,Department of Pharmacy, Ludwig-Maximilians-Universität, München, Germany.
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Kaulage MH, Maji B, Pasadi S, Ali A, Bhattacharya S, Muniyappa K. Targeting G-quadruplex DNA structures in the telomere and oncogene promoter regions by benzimidazole‒carbazole ligands. Eur J Med Chem 2018; 148:178-194. [DOI: 10.1016/j.ejmech.2018.01.091] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/17/2018] [Accepted: 01/27/2018] [Indexed: 10/18/2022]
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11
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Machha VR, Mikek CG, Wellman S, Lewis EA. Temperature and osmotic stress dependence of the thermodynamics for binding linker histone H1 0, Its carboxyl domain (H1 0-C) or globular domain (H1 0-G) to B-DNA. Biochem Biophys Rep 2017; 12:158-165. [PMID: 29090277 PMCID: PMC5645174 DOI: 10.1016/j.bbrep.2017.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
Linker histones (H1) are the basic proteins in higher eukaryotes that are responsible for the final condensation of chromatin. In contrast to the nucleosome core histone proteins, the role of H1 in compacting DNA is not clearly understood. In this study ITC was used to measure the binding constant, enthalpy change, and binding site size for the interactions of H10, or its C-terminal (H10-C) and globular (H10-G) domains to highly polymerized calf-thymus DNA at temperatures from 288 K to 308 K. Heat capacity changes, ΔCp, for these same H10 binding interactions were estimated from the temperature dependence of the enthalpy changes. The enthalpy changes for binding H10, H10-C, or H10-G to CT-DNA are all endothermic at 298 K, becoming more exothermic as the temperature is increased. The ΔH for binding H10-G to CT-DNA is exothermic at temperatures above approximately 300 K. Osmotic stress experiments indicate that the binding of H10 is accompanied by the release of approximately 35 water molecules. We estimate from our naked DNA titration results that the binding of the H10 to the nucleosome places the H10 protein in close contact with approximately 41 DNA bp. The breakdown is that the H10 carboxyl terminus interacts with 28 bp of linker DNA on one side of the nucleosome, the H10 globular domain binds directly to 7 bp of core DNA, and shields another 6 linker DNA bases, 3 bp on either side of the nucleosome where the linker DNA exits the nucleosome core.
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Affiliation(s)
- V R Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - C G Mikek
- Department of Chemistry, Mississippi State University, Mississippi, MS 39762, USA
| | - S Wellman
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2500 N. State Street, Jackson, MS 39216, USA
| | - E A Lewis
- Department of Chemistry, Mississippi State University, Mississippi, MS 39762, USA
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences; Academia Sinica; 128 Sec. 2, Academia Rd. Nankang Taipei Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center; College of Science; National Taiwan University; No.1, Sec. 4, Roosevelt Rd. Taipei Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology; Chi Mei Medical Center; No.901, Zhonghua Rd. Tainan Taiwan
| | - Stephen Neidle
- The School of Pharmacy; University College London; London WC1N 1AX UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
- Institute of Biotechnology; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
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13
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017; 56:8761-8765. [PMID: 28544401 DOI: 10.1002/anie.201703989] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 01/23/2023]
Abstract
Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII (Chro)2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.
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Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Rd. Nankang, Taipei, Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, College of Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology, Chi Mei Medical Center, No.901, Zhonghua Rd., Tainan, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
- Institute of Biotechnology, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
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Dar AM, Uzzaman S, Ahmad MS, Khan Y. Steroidal imidazoles: Synthesis, characterization, molecular docking studies with DNA and in vitro cytotoxicity. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1755-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Feng Y, Yang D, Chen H, Cheng W, Wang L, Sun H, Tang Y. Stabilization of G-quadruplex DNA and inhibition of Bcl-2 expression by a pyridostatin analog. Bioorg Med Chem Lett 2016; 26:1660-3. [PMID: 26923693 DOI: 10.1016/j.bmcl.2016.02.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 11/27/2022]
Abstract
The G-quadruplexes located in the P1 promoter of B-cell lymphoma-2 (Bcl-2) gene are implicated to regulate Bcl-2 expression. Here, we designed a new pyridostatin analog named PDF, which exhibited high specificity and stabilizing effect toward G-quadruplexes. The luciferase assay demonstrated that PDF could significantly suppress Bcl-2 transcriptional activation in human laryngeal squamous carcinoma cells (Hep-2) cells. Besides, PDF also induced cell apoptosis in vitro assays. These results provide an excellent G-quadruplex specific ligand as an efficient Bcl-2 inhibitor. These results also implicate that PDF may be a potential anticancer drug to head neck cancer.
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Affiliation(s)
- Yun Feng
- Otolaryngology Department, China-Japan Friendship Hospital, Beijing 100029, PR China.
| | - Dazhang Yang
- Otolaryngology Department, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Hongbo Chen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
| | - Wenli Cheng
- Cardiology Department, China-Japan Friendship Hospital, Beijing 100029, PR China.
| | - Lixia Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China.
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China.
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16
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X-ray characterization and in vitro biological evaluation of 1-(4-amidophenyl)-3-(4-acetylphenyl)triazene and the gold(I) triazenide complex {Au(I)[RPhNNNPhR′][PPh3]} [R = (C O)NH2, R′ = (C O)CH3]. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.10.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Kamran MZ, Ranjan A, Kaur N, Sur S, Tandon V. Radioprotective Agents: Strategies and Translational Advances. Med Res Rev 2016; 36:461-93. [PMID: 26807693 DOI: 10.1002/med.21386] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 12/15/2015] [Accepted: 01/01/2016] [Indexed: 01/08/2023]
Abstract
Radioprotectors are agents required to protect biological system exposed to radiation, either naturally or through radiation leakage, and they protect normal cells from radiation injury in cancer patients undergoing radiotherapy. It is imperative to study radioprotectors and their mechanism of action comprehensively, looking at their potential therapeutic applications. This review intimately chronicles the rich intellectual, pharmacological story of natural and synthetic radioprotectors. A continuous effort is going on by researchers to develop clinically promising radioprotective agents. In this article, for the first time we have discussed the impact of radioprotectors on different signaling pathways in cells, which will create a basis for scientific community working in this area to develop novel molecules with better therapeutic efficacy. The bright future of exceptionally noncytotoxic derivatives of bisbenzimidazoles is also described as radiomodulators. Amifostine, an effective radioprotectant, has been approved by the FDA for limited clinical use. However, due to its adverse side effects, it is not routinely used clinically. Recently, CBLB502 and several analog of a peptide are under clinical trial and showed high success against radiotherapy in cancer. This article reviews the different types of radioprotective agents with emphasis on the strategies for the development of novel radioprotectors for drug development. In addition, direction for future strategies relevant to the development of radioprotectors is also addressed.
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Affiliation(s)
- Mohammad Zahid Kamran
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Atul Ranjan
- Kansas University of Medical Center, Kansas City, KS, 66160
| | - Navrinder Kaur
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Souvik Sur
- Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.,Department of Chemistry, University of Delhi, Delhi, 110007, India
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18
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Spectroscopic, Viscositic, DNA Binding and Cytotoxic Studies of Newly Synthesized Steroidal Imidazolidines. J Fluoresc 2015; 26:639-49. [DOI: 10.1007/s10895-015-1750-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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19
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In vitro cytotoxcity and interaction of new steroidal oxadiazinanones with calf thymus DNA using molecular docking, gel electrophoresis and spectroscopic techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 148:340-350. [DOI: 10.1016/j.jphotobiol.2015.04.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/23/2022]
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20
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Banik M, Basu T. Calcium phosphate nanoparticles: a study of their synthesis, characterization and mode of interaction with salmon testis DNA. Dalton Trans 2014; 43:3244-59. [PMID: 24356414 DOI: 10.1039/c3dt52522h] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calcium phosphate nanoparticles (CPNPs) are presently emerging as a second generation vector for efficient delivery and stabilization of nucleic acids inside cells, although the detailed mode of interaction between CPNPs and DNA is still obscure. This study discloses some features of the interaction. For this study, we synthesized CPNPs by a modified co-precipitation method and characterized the particles by different techniques such as dynamic light scattering, X-ray diffraction, electron dispersive spectroscopy, Fourier transform infra-red spectroscopy, differential thermal and thermo-gravimetric analysis, and atomic force, scanning and transmission electron microscopy. The characterization studies showed that the nanoparticles were spherical in shape, about 45 nm in size and were composed of the hydroxyapatite form of calcium phosphate; almost 90% of the starting materials were converted to nanoparticles (NPs). The different aspects of the interaction between CPNPs and salmon testis DNA were investigated using techniques such as UV-Vis spectrophotometry, circular dichroism, Fourier transform infra-red spectrometry, thermal denaturation, microviscometry, agarose gel electrophoresis, cyclic voltammetry and atomic force microscopy. The results revealed that CPNPs interacted with DNA with ~1 : 3.3 stoichiometry with a binding constant of the order of 10(4) M(-1) through groove-interacting mode and a single nanoparticle covered about 6.2 base pairs of the DNA chain. Moreover, the binding interaction was spontaneous, cooperative, exothermic and enthalpy-driven and some electrostatic nature of the binding was also evident; however, the non-polyelectrolyte contribution was dominant. The binding interaction finally caused an increase in the melting temperature of DNA from 70.8 °C to 75 °C and alteration of its secondary structure from the naturally occurring B-form to C-form.
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Affiliation(s)
- Milon Banik
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani - 741235, West Bengal, India.
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21
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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22
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Ramos JP, Le VH, Lewis EA. Role of Water in Netropsin Binding to an A2T2 Hairpin DNA Site: Osmotic Stress Experiments. J Phys Chem B 2013; 117:15958-65. [DOI: 10.1021/jp408077m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph P. Ramos
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Vu H. Le
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Edwin A. Lewis
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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23
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Ju XH, Wang WJ, Qiu L, Xiao HM. Ab Initioand DFT Studies on the Structure, Infrared Spectrum, and Thermodynamic Properties of Hoechst 33258. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200500063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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24
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Yaku H, Murashima T, Tateishi-Karimata H, Nakano SI, Miyoshi D, Sugimoto N. Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition. Methods 2013; 64:19-27. [PMID: 23562626 DOI: 10.1016/j.ymeth.2013.03.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/21/2013] [Accepted: 03/25/2013] [Indexed: 01/24/2023] Open
Abstract
The telomere G-quadruplex-binding and telomerase-inhibiting capacity of two cationic (TMPyP4 and PIPER) and two anionic (phthalocyanine and Hemin) G-quadruplex-ligands were examined under conditions of molecular crowding (MC). Osmotic experiments showed that binding of the anionic ligands, which bind to G-quadruplex DNA via π-π stacking interactions, caused some water molecules to be released from the G-quadruplex/ligand complex; in contrast, a substantial number of water molecules were taken up upon electrostatic binding of the cationic ligands to G-quadruplex DNA. These behaviors of water molecules maintained or reduced the binding affinity of the anionic and the cationic ligands, respectively, under MC conditions. Consequently, the anionic ligands (phthalocyanine and Hemin) robustly inhibited telomerase activity even with MC; in contrast, the inhibition of telomerase caused by cationic TMPyP4 was drastically reduced by MC. These results allow us to conclude that the binding of G-quadruplex-ligands to G-quadruplex via non-electrostatic interactions is preferable for telomerase inhibition under physiological conditions.
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Key Words
- 5,10,15,20-tetra-(N-methyl-4-pyridyl)porphyrin
- Cancer
- Cu-APC
- EG
- Fe(III)-protoporphyrin IX
- G-quadruplex-ligand
- Hemin
- MC
- Molecular crowding
- N,N′-bis[2-(1-piperidino)ethyl]-3,4,9,10-perylenetetracarboxylic diimide
- PEG
- PIPER
- TMPyP4
- Telomerase
- Water molecule
- copper(II) phthalocyanine 3,4′,4′′,4′′′-tetrasulfonic acid tetrasodium salt
- double-stranded DNA
- dsDNA
- ethylene glycol
- molecular crowding
- poly ethylene glycol
- tsTRAP assay
- two-step telomere repeat amplification protocol assay
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Affiliation(s)
- Hidenobu Yaku
- Advanced Technology Research Laboratories, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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25
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Selvaraju M, Shiu WS, Kulkarni MV, Sun CM. Ionic liquid supported synthesis of tricyclic pyrimido[1,2-a]benzimidazoles by a telescoped Michael/hetero annulation strategy. RSC Adv 2013. [DOI: 10.1039/c3ra42658k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Dale AG, Hinds J, Mann J, Taylor PW, Neidle S. Symmetric Bis-benzimidazoles Are Potent Anti-Staphylococcal Agents with Dual Inhibitory Mechanisms against DNA Gyrase. Biochemistry 2012; 51:5860-71. [DOI: 10.1021/bi300645n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Aaron G. Dale
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square,
London WC1N 1AX, U.K
| | - Jason Hinds
- Bacterial
Microarray Group,
Division of Cellular and Molecular Medicine, St. George’s, University of London, Cranmer Terrace, London SW17
0RE, U.K
| | - John Mann
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square,
London WC1N 1AX, U.K
| | - Peter W. Taylor
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square,
London WC1N 1AX, U.K
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square,
London WC1N 1AX, U.K
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27
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Parveen S, Arjmand F. De novo design, synthesis and spectroscopic characterization of chiral benzimidazole-derived amino acid Zn(II) complexes: Development of tryptophan-derived specific hydrolytic DNA artificial nuclease agent. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 85:53-60. [PMID: 22000640 DOI: 10.1016/j.saa.2011.09.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/18/2011] [Accepted: 09/04/2011] [Indexed: 05/31/2023]
Abstract
Novel ternary dizinc(II) complexes 1-3, derived from 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol and l-form of amino acids (viz., tryptophan, leucine and valine) were synthesized and characterized by spectroscopic (IR, (1)H NMR, UV-vis, ESI-MS) and other analytical methods. To evaluate the biological preference of chiral drugs for inherently chiral target DNA, interaction of 1-3 with calf thymus DNA in Tris-HCl buffer was studied by various biophysical techniques which reveal that all these complexes bind to CT DNA non-covalently via electrostatic interaction. The higher K(b) value of L-tryptophan complex 1 suggested greater DNA binding propensity. Further, to evaluate the mode of action at the molecular level, interaction studies of complexes 1 and 2 with nucleotides (5'-GMP and 5'-TMP) were carried out by UV-vis titrations, (1)H and (31)P NMR which implicates the preferential selectivity of these complexes to N3 of thymine rather than N7 of guanine. Furthermore, complex 1 exhibits efficient DNA cleavage with supercoiled pBR322. The complex 1 cleaves DNA efficiently involving hydrolytic cleavage pathway. Such chiral synthetic hydrolytic nucleases with asymmetric centers are gaining considerable attention owing to their importance in biotechnology and drug design, in particular to cleave DNA with sequence selectivity different from that of the natural enzymes.
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Affiliation(s)
- Shazia Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
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28
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Li L, Cao W, Zheng W, Fan C, Chen T. Ruthenium complexes containing 2,6-bis(benzimidazolyl)pyridine derivatives induce cancer cell apoptosis by triggering DNA damage-mediated p53 phosphorylation. Dalton Trans 2012; 41:12766-72. [DOI: 10.1039/c2dt30665d] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Štefanišinová M, Tomečková V, Kožurková M, Ostró A, Mareková M. Study of DNA interactions with cyclic chalcone derivatives by spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 81:666-671. [PMID: 21778103 DOI: 10.1016/j.saa.2011.06.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/21/2011] [Accepted: 06/26/2011] [Indexed: 05/31/2023]
Abstract
A series of chalcone derivatives (1-4) were studied. The interaction between these ligands and calf thymus DNA was studied with UV-vis spectrophotometry, fluorescence and circular dichroism spectroscopy. The binding constants K were estimated at 0.5-4.6×10(5) M(-1). All these measurements indicated that the compounds behave as effective DNA-intercalating agents. Electrophoretic separation proved that ligands inhibited topoisomerase I at a concentration of 60 μM.
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Affiliation(s)
- M Štefanišinová
- Department of Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Košice, Trieda SNP 1, Košice 040 66, Slovak Republic.
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30
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Koonammackal MV, Nellipparambil UVN, Sudarsanakumar C. Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin. J Mol Model 2011; 17:2805-16. [DOI: 10.1007/s00894-011-0954-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 01/03/2011] [Indexed: 12/27/2022]
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31
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Stolić I, Mišković K, Piantanida I, Lončar MB, Glavaš-Obrovac L, Bajić M. Synthesis, DNA/RNA affinity and antitumour activity of new aromatic diamidines linked by 3,4-ethylenedioxythiophene. Eur J Med Chem 2011; 46:743-55. [PMID: 21227551 DOI: 10.1016/j.ejmech.2010.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 12/04/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
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32
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Selective binding of small molecules to DNA: Application and perspectives. Colloids Surf B Biointerfaces 2010; 79:1-4. [DOI: 10.1016/j.colsurfb.2010.03.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 03/31/2010] [Indexed: 11/22/2022]
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33
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Anuradha, Alam MS, Chaudhury NK. Osmolyte Changes the Binding Affinity and Mode of Interaction of Minor Groove Binder Hoechst 33258 with Calf Thymus DNA. Chem Pharm Bull (Tokyo) 2010; 58:1447-54. [DOI: 10.1248/cpb.58.1447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Anuradha
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
| | | | - Nabo Kumar Chaudhury
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
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34
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Huang J, Li G, Wu Z, Song Z, Zhou Y, Shuai L, Weng X, Zhou X, Yang G. Bisbenzimidazole to benzobisimidazole: from binding B-form duplex DNA to recognizing different modes of telomereG-quadruplex. Chem Commun (Camb) 2009:902-4. [DOI: 10.1039/b819789j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Buurma NJ, Haq I. Calorimetric and spectroscopic studies of Hoechst 33258: self-association and binding to non-cognate DNA. J Mol Biol 2008; 381:607-21. [PMID: 18617189 DOI: 10.1016/j.jmb.2008.05.073] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 05/04/2008] [Accepted: 05/30/2008] [Indexed: 10/22/2022]
Abstract
Sequence and structure-specific molecular recognition of DNA by small molecules is an important goal in biophysical chemistry and drug discovery. Many candidate ligands possess flat aromatic surfaces and other molecular features that allow them to self-associate. In addition, non-specific binding to the target is a complicating feature of these interactions. Therefore, multiple equilibria are present and need to be accounted for in data analysis in order to obtain meaningful thermodynamic parameters. In order to address these issues we have systematically examined the bis-benzimidazole dye Hoechst 33258 (H33258) in terms of self-aggregation and binding to DNA oligonucleotides lacking any cognate minor groove A.T sites. This model system has been interrogated using isothermal titration calorimetry (ITC), circular dichroism (CD), fluorescence spectroscopy and pulsed gradient spin echo NMR. Three distinct binding events and ligand self-aggregation have been identified and, where possible, quantified. H33258 self-aggregation involves a step-wise aggregation mechanism, driven by stacking interactions. The DNA binding process includes two specific binding modes and non-specific DNA-templated H33258 stacking. We have written novel ITC data-fitting software (IC-ITC; freely available to the biophysics community), which simultaneously fits ligand aggregation and ligand-DNA binding. Here, this numerical analysis, which uses simulated annealing of complex calorimetric data representing multiple coupled equilibria, is described.
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Affiliation(s)
- Niklaas J Buurma
- Centre for Chemical Biology, The Department of Chemistry, The University of Sheffield, Dainton Building, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
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36
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Li G, Huang J, Zhang M, Zhou Y, Zhang D, Wu Z, Wang S, Weng X, Zhou X, Yang G. Bis(benzimidazole)pyridine derivative as a new class of G-quadruplex inducing and stabilizing ligand. Chem Commun (Camb) 2008:4564-6. [DOI: 10.1039/b807916a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC. A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine. J Am Chem Soc 2007; 128:7846-54. [PMID: 16771498 PMCID: PMC2515929 DOI: 10.1021/ja0600936] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within approximately 3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A.T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G.C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G.C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination.
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Affiliation(s)
| | | | | | | | | | | | - Eric C. Long
- * Authors to whom correspondence should be addressed. E-mail: ,
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38
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Freyer MW, Buscaglia R, Hollingsworth A, Ramos J, Blynn M, Pratt R, Wilson WD, Lewis EA. Break in the heat capacity change at 303 K for complex binding of netropsin to AATT containing hairpin DNA constructs. Biophys J 2007; 92:2516-22. [PMID: 17237207 PMCID: PMC1864850 DOI: 10.1529/biophysj.106.098723] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Studies performed in our laboratory demonstrated the formation of two thermodynamically distinct complexes on binding of netropsin to a number of hairpin-forming DNA sequences containing AATT-binding regions. These two complexes were proposed to differ only by a bridging water molecule between the drug and the DNA in the lower affinity complex. A temperature-dependent isothermal titration calorimetry (ITC)-binding study was performed using one of these constructs (a 20-mer hairpin of sequence 5'-CGAATTCGTCTCCGAATTCG) and netropsin. This study demonstrated a break in the heat capacity change for the formation of the complex containing the bridging water molecule at approximately 303 K. In the plot of the binding enthalpy change versus temperature, the slope (DeltaCp) was -0.67 kcal mol-1 K-1 steeper after the break at 303 K. Because of the relatively low melting temperature of the 20-mer hairpin (341 K (68 degrees C)), the enthalpy change for complex formation might have included some energy of refolding of the partially denatured hairpin, giving the suggestion of a larger DeltaCp. Studies done on the binding of netropsin to similar constructs, a 24-mer and a 28-mer, with added GC basepairs in the hairpin stem to increase thermal stability, exhibit the same nonlinearity in DeltaCp over the temperature range of from 275 to 333 K. The slopes (DeltaCp) were -0.69 and -0.64 kcal mol-1 K-1 steeper after 303 K for the 24-mer and 28-mer, respectively. This observation strengthens the argument regarding the presence of a bridging water molecule in the lower affinity netropsin/DNA complex. The DeltaCp data seem to infer that because the break in the heat capacity change function for the lower affinity binding occurs at the isoequilibrium temperature for water, water may be included or trapped in the complex. The fact that this break does not occur in the heat capacity change function for formation of the higher affinity complex can similarly be taken as evidence that water is not included in the higher affinity complex.
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Affiliation(s)
- Matthew W Freyer
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, Arizona 86011-5698, USA
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39
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Freyer MW, Buscaglia R, Cashman D, Hyslop S, Wilson WD, Chaires JB, Lewis EA. Binding of netropsin to several DNA constructs: evidence for at least two different 1:1 complexes formed from an -AATT-containing ds-DNA construct and a single minor groove binding ligand. Biophys Chem 2006; 126:186-96. [PMID: 16837123 DOI: 10.1016/j.bpc.2006.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 06/15/2006] [Indexed: 11/22/2022]
Abstract
Isothermal titration calorimetry, ITC, has been used to determine the thermodynamics (DeltaG, DeltaH, and -TDeltaS) for binding netropsin to a number of DNA constructs. The DNA constructs included: six different 20-22mer hairpin forming sequences and an 8-mer DNA forming a duplex dimer. All DNA constructs had a single -AT-rich netropsin binding with one of the following sequences, (A(2)T(2))(2), (ATAT)(2), or (AAAA/TTTT). Binding energetics are less dependent on site sequence than on changes in the neighboring single stranded DNA (hairpin loop size and tail length). All of the 1:1 complexes exhibit an enthalpy change that is dependent on the fractional saturation of the binding site. Later binding ligands interact with a significantly more favorable enthalpy change (partial differential DeltaH(1-2) from 2 to 6 kcal/mol) and a significantly less favorable entropy change (partial differential (-TDeltaS(1-2))) from -4 to -9 kcal/mol). The ITC data could only be fit within expected experimental error by use of a thermodynamic model that includes two independent binding processes with a combined stoichiometry of 1 mol of ligand per 1 mol of oligonucleotide. Based on the biophysical evidence reported here, including theoretical calculations for the energetics of "trapping" or structuring of a single water molecule and molecular docking computations, it is proposed that there are two modes by which flexible ligands can bind in the minor groove of duplex DNA. The higher affinity binding mode is for netropsin to lay along the floor of the minor groove in a bent conformation and exclude all water from the groove. The slightly weaker binding mode is for the netropsin molecule to have a slightly more linear conformation and for the required curvature to be the result of a water molecule that bridges between the floor of the minor groove and two of the amidino nitrogens located at one end of the bound netropsin molecule.
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Affiliation(s)
- M W Freyer
- Department of Chemistry and Biochemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, AZ 86011, USA
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Kiser JR, Monk RW, Smalls RL, Petty JT. Hydration changes in the association of Hoechst 33258 with DNA. Biochemistry 2005; 44:16988-97. [PMID: 16363812 PMCID: PMC6158785 DOI: 10.1021/bi051769x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of water in the interaction of Hoechst 33258 with the minor groove binding site of the (AATT)2 sequence was investigated using calorimetric and equilibrium constant measurements. Using isothermal titration calorimetry measurements, the heat capacity change for the reaction is -256 +/- 10 cal/(K mol of Hoechst). Comparison with the heat capacity changes based on area models supports the expulsion of water from the interface of the Hoechst-DNA complex. To further consider the role of water, the osmotic stress method was used to determine if the Hoechst association with DNA was coupled with hydration changes. Using four osmolytes with varying molecular weights and chemical properties, the Hoechst affinity for DNA decreases with increasing osmolyte concentration. From the dependence of the equilibrium constant on the solution osmolality, 60 +/- 13 waters are acquired in the complex relative to the reactants. It is proposed that the osmotic stress technique is measuring weakly bound waters that are not measured via the heat capacity changes.
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Affiliation(s)
- John R Kiser
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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41
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Jacquemard U, Routier S, Dias N, Lansiaux A, Goossens JF, Bailly C, Mérour JY. Synthesis of 2,5- and 3,5-diphenylpyridine derivatives for DNA recognition and cytotoxicity. Eur J Med Chem 2005; 40:1087-95. [PMID: 15951061 DOI: 10.1016/j.ejmech.2005.04.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2004] [Revised: 04/25/2005] [Accepted: 04/27/2005] [Indexed: 11/17/2022]
Abstract
A series of 2,5- and 3,5-diphenylpyridine derivatives was synthetised in high yields. A versatile chemical strategy allows the design of diphenylpyridines differently substituted with cationic or neutral side chains. The interaction of the molecules with DNA was investigated by biophysical and biochemical methods and an AT-binder (20) was characterised. A few cytotoxic molecules were identified but their antiproliferative activity does not correlate with DNA binding. Two compounds 18 and 22 showed significant antiproliferative activity and provide a novel route to potential anticancer agents.
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Affiliation(s)
- Ulrich Jacquemard
- Institut de Chimie Organique et Analytique, UMR 6005, Université d'Orléans, B.P. 6759, 45067 Orléans cedex 2, France
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42
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Alemán C, Namba AM, Casanovas J. Acid-Base and Electronic Structure-Dependent Properties of Hoechst 33342. J Biomol Struct Dyn 2005; 23:29-36. [PMID: 15918674 DOI: 10.1080/07391102.2005.10507044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
An ab initio quantum mechanical study of the bis-benzimidazole derivative Hoechst 33342 is presented. Specifically, we report on the molecular geometry, proton affinity, gas-phase basicity, hydration, pKa, and molecular interaction potential map of Hoechst 33342 and the forms obtained by its protonation and deprotonation. Results have been compared with those obtained for Hoechst 33258 to analyze the influence of the chemical structure on the properties of this bis-benzimidazole derivative. Finally, the connection of some theoretical predictions with experimental evidences has been examined.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Quimica, E.T.S. d'Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona E-08028, Spain.
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43
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Dolenc J, Borštnik U, Hodošček M, Koller J, Janežič D. An ab initio QM/MM study of the conformational stability of complexes formed by netropsin and DNA. The importance of van der Waals interactions and hydrogen bonding. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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44
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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45
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Wadkins RM, Bearss D, Manikumar G, Wani MC, Wall ME, Von Hoff DD. Hydrophilic camptothecin analogs that form extremely stable cleavable complexes with DNA and topoisomerase I. Cancer Res 2004; 64:6679-83. [PMID: 15374984 DOI: 10.1158/0008-5472.can-04-1885] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Camptothecin (CPT) analogs that form more stable ternary complexes with DNA and topoisomerase I (termed cleavable complexes) show greater activity in their ability to inhibit tumor cell line growth in preclinical studies. Based on our earlier work, we hypothesized that analogs bearing hydrogen bonding moieties at the 7- through 10-position of CPT would result in more stable cleavable complexes. Consequently, we synthesized analogs with 7-mono-, 7-di-, and 7-trihydroxymethylaminomethyl groups. These analogs showed increasing cleavable complex stability as the number of hydroxyl groups was increased. The 7-trihydroxymethylaminomethyl analog of 10,11-methylenedioxycamptothecin (THMAM-MD) showed remarkable ternary complex stability with a half-life of 116 minutes. This is an order of magnitude more stable than any previously examined analog. Our in vitro analysis demonstrated that these analogs were all potent topoisomerase I poisons and could inhibit tumor cell growth in culture. We studied the effects of THMAM-MD in vivo in severe combined immunodeficient mice bearing HT-29 colon cancer and MiaPaCa-2 pancreatic cancer tumors. The THMAM-MD analog showed excellent, persisting activity in inhibiting tumor growth with both lines. Taken together, our results suggest that CPTs with hydrophilic, hydrogen-bonding groups at the 7-position hold the promise of excellent clinical activity.
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Affiliation(s)
- Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA.
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46
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Mallena S, Lee MPH, Bailly C, Neidle S, Kumar A, Boykin DW, Wilson WD. Thiophene-Based Diamidine Forms a “Super” AT Binding Minor Groove Agent. J Am Chem Soc 2004; 126:13659-69. [PMID: 15493923 DOI: 10.1021/ja048175m] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA minor groove is the interaction site for many enzymes and transcription control proteins and as a result, development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of a systematic set of diamidine derivatives with a powerful array of methods including DNase I footprinting, biosensor-SPR methods, and X-ray crystallography. Surprisingly, conversion of the parent phenyl-furan-phenyl diamidine to a phenyl-thiophene-benzimidazole derivative yields a compound with over 10-fold-increased affinity for the minor groove at AT sequences. Single conversion of the furan to a thiophene or a phenyl to benzimidazole does not cause a similar increase in affinity. X-ray results indicate a small bond angle difference between the C-S-C angle of thiophene and the C-O-C angle of furan that, when amplified out to the terminal amidines of the benzimidazole compounds, yields a very significant difference in the positions of the amidines and their DNA interaction strength.
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Affiliation(s)
- Sirish Mallena
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098, USA
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47
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Jacquemard U, Routier S, Tatibouët A, Kluza J, Laine W, Bal C, Bailly C, Mérour JY. Synthesis of diphenylcarbazoles as cytotoxic DNA binding agents. Org Biomol Chem 2004; 2:1476-83. [PMID: 15136803 DOI: 10.1039/b401445f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of a series of novel diphenylcarbazoles designed to interact with DNA. The compounds bearing two or three dimethylaminoalkyloxy side chains were found to bind much more tightly to DNA, preferentially at AT-rich sites, than the corresponding hydroxy compounds. The DNA binding compounds exhibit potent cytotoxic activity toward P388 leukemia cells. The 3,6-diphenylcarbazole thus represent an interesting scaffold to develop antitumor agents interacting with nucleic acids.
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Affiliation(s)
- Ulrich Jacquemard
- Institut de Chimie Organique et Analytique, UMR 6005, Universite d'Orleans, B.P. 6759, 45067 Orleans 2, France
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Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedl KR. Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA. J Biomol Struct Dyn 2004; 21:713-24. [PMID: 14769064 DOI: 10.1080/07391102.2004.10506961] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG)2 in the B-form with two putative intercalation sites at the 5'-CGA-3' step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5'-CGA-3' steps. Thereby--in contrast to X-ray structures--a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5'-CG-3' bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of BI and BII around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.
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Affiliation(s)
- Michael Trieb
- Institute of General Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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49
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Tanious FA, Hamelberg D, Bailly C, Czarny A, Boykin DW, Wilson WD. DNA Sequence Dependent Monomer−Dimer Binding Modulation of Asymmetric Benzimidazole Derivatives. J Am Chem Soc 2004; 126:143-53. [PMID: 14709078 DOI: 10.1021/ja030403+] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A number of studies indicate that DNA sequences such as AATT and TTAA have significantly different physical and interaction properties. To probe these interaction differences in detail and determine the influence of charge, we have synthesized three bisbenzimidazole derivatives, a diamidine, DB185, and monoamidines, DB183 and DB210, that are related to the well-known minor groove agent, Hoechst 33258. Footprinting studies with several natural and designed DNA fragments indicate that the synthetic compounds bind at AT sequences in the minor groove and interact more weakly at sites with TpA steps relative to sites without such steps. Circular dichroism spectroscopy also indicates that the compounds bind in the DNA minor groove. Surprisingly, Tm studies as a function of ratio indicate that the monoamidines bind to TTAA sequences as dimers, whereas the diamidine binds as a monomer. Biosensor-surface plasmon resonance (SPR) studies allowed us to quantitate the interaction differences in more detail. SPR results clearly show that the monoamidine compounds bind to the TTAA sequence in a cooperative 2:1 complex but bind as monomers to AATT. The dication binds to both sequences in monomer complexes but the binding to AATT is significantly stronger than binding to TTAA. Molecular dynamics simulations indicate that the AATT sequence has a narrow time-average minor groove width that is a very good receptor site for the bisbenzimidazole compounds. The groove in TTAA sequences is wider and the width must be reduced to form a favorable monomer complex. The monocations thus form cooperative dimers that stack in an antiparallel orientation and closely fit the structure of the TTAA minor groove. The amidine groups in the dimer are oriented in the 5' direction of the strand to which they are closest. Charge repulsion in the dication apparently keeps it from forming the dimer. It instead reduces the TTAA groove width, in an induced fit process, sufficiently to form a minor groove complex. The dimer-binding mode of DB183 and DB210 is a new DNA recognition motif and offers novel design concepts for selective targeting of DNA sequences with a wider minor groove, including those with TpA steps.
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Affiliation(s)
- Farial A Tanious
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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