1
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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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2
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Ogbonna E, Paul A, Farahat AA, Terrell JR, Mineva E, Ogbonna V, Boykin DW, Wilson WD. X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. ACS BIO & MED CHEM AU 2023; 3:335-348. [PMID: 37599788 PMCID: PMC10436263 DOI: 10.1021/acsbiomedchemau.3c00002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 08/22/2023]
Abstract
The rational design of small molecules that target specific DNA sequences is a promising strategy to modulate gene expression. This report focuses on a diamidinobenzimidazole compound, whose selective binding to the minor groove of AT DNA sequences holds broad significance in the molecular recognition of AT-rich human promoter sequences. The objective of this study is to provide a more detailed and systematized understanding, at an atomic level, of the molecular recognition mechanism of different AT-specific sequences by a rationally designed minor groove binder. The specialized method of X-ray crystallography was utilized to investigate how the sequence-dependent recognition properties in general, A-tract, and alternating AT sequences affect the binding of diamidinobenzimidazole in the DNA minor groove. While general and A-tract AT sequences give a narrower minor groove, the alternating AT sequences intrinsically have a wider minor groove which typically constricts upon binding. A strong and direct hydrogen bond between the N-H of the benzimidazole and an H-bond acceptor atom in the minor groove is essential for DNA recognition in all sequences described. In addition, the diamidine compound specifically utilizes an interfacial water molecule for its DNA binding. DNA complexes of AATT and AAAAAA recognition sites show that the diamidine compound can bind in two possible orientations with a preference for water-assisted hydrogen bonding at either cationic end. The complex structures of AAATTT, ATAT, ATATAT, and AAAA are bound in a singular orientation. Analysis of the helical parameters shows a minor groove expansion of about 1 Å across all the nonalternating DNA complexes. The results from this systematic approach will convey a greater understanding of the specific recognition of a diverse array of AT-rich sequences by small molecules and more insight into the design of small molecules with enhanced specificity to AT and mixed DNA sequences.
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Affiliation(s)
- Edwin
N. Ogbonna
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ananya Paul
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Abdelbasset A. Farahat
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Master
of Pharmaceutical Sciences Program, California
North State University, 9700 W Taron Dr., Elk Grove, California 95757, United States
| | - J. Ross Terrell
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ekaterina Mineva
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Victor Ogbonna
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - David W Boykin
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - W. David Wilson
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
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3
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Ogbonna EN, Paul A, Ross Terrell J, Fang Z, Chen C, Poon GMK, Boykin DW, Wilson WD. Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. Bioorg Med Chem 2022; 68:116861. [PMID: 35661929 DOI: 10.1016/j.bmc.2022.116861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of 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 diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.
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Affiliation(s)
- Edwin N Ogbonna
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - J Ross Terrell
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ziyuan Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Cen Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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4
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Parkinson GN, Berman H. More than forty years of nucleic acid structural science. Bioorg Med Chem 2022; 69:116887. [PMID: 35749839 DOI: 10.1016/j.bmc.2022.116887] [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: 04/15/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022]
Abstract
As scientists who have worked with Stephen Neidle over many years and stages of his career, we present our perspective of his contributions to nucleic acid structural science. We trace some of the highlights of his research on nucleic acid drug interactions and the unique insights about the importance of hydration.
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Affiliation(s)
- Gary N Parkinson
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, UK.
| | - Helen Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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5
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Baron A, Sann CL, Mann J. Symmetric bis-benzimidazoles as DNA minor groove-binding agents with anti-tumour and antibacterial activity, and the evolution of the drug ridinilazole for the treatment of Clostridium difficile infections. Bioorg Med Chem 2022; 58:116656. [PMID: 35183028 DOI: 10.1016/j.bmc.2022.116656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 11/02/2022]
Abstract
We report the synthesis of a range of symmetrical bis-benzimidazoles (BBZ) which possess anticancer and antibacterial activities. One of these BBZs has specific activity against Clostridium difficile and is currently in a phase 3 clinical evaluation as the drug ridinilazole. X-ray and computer modelling studies showed that BBZs typically exhibit high specificity for oligonucleotide sequences that occur in the minor groove of DNA.
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Affiliation(s)
- Anne Baron
- School of Chemistry, Queen's University Belfast, Belfast BT9 5AG, UK
| | - Christine Le Sann
- School of Chemistry, Queen's University Belfast, Belfast BT9 5AG, UK
| | - John Mann
- School of Chemistry, Queen's University Belfast, Belfast BT9 5AG, UK.
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6
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Purohit P, Mittal RK, Khatana K. Quinoline-3-Carboxylic Acids "DNA Minor Groove-Binding Agent. Anticancer Agents Med Chem 2021; 22:344-348. [PMID: 33992065 DOI: 10.2174/1871520621666210513160714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The lead compounds from the series of 2, 4-disubstituted quinoline-3-carboxylic acid derivatives were selected for the in-silico mechanistic study. The compounds were found selective and potent for the cancer cell. Moreover, the relevant ADME in-silico data also support the safety of lead. Objective- The objective of the study is to correlate the interaction of DNA and quinoline derivative, which was reported with the fluorescence microscopy images of cells in-vitro data in the recently published data. METHODS The detailed interaction study with the DNA dodecanucleotide sequenced d(CGCGAATTCGCG) shows the present lead bounds with the A/T minor groove region of a B-DNA duplex through important major and minor hydrogen-bonds. RESULT The present in-silico study supports the interactions of the drug with DNA with sufficient binding interactions and energy. The present study also gives vital information related to the mechanism of drug action, which was initially declared as a DNA targeting molecule through a fluorescence based target study. CONCLUSION The substitution at 2nd position (the carbonyl group) of the lead was revealed as a hydrogen bond donor/acceptor for the adenine and guanine nucleic acid-base pair. The in-silico prediction also confirmed the interaction pattern of the lead with the DNA, which will be further utilized for drug development.
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Affiliation(s)
- Priyank Purohit
- Department of Pharmacy, HIMT, Gautam Budh Nagar, Greater Noida, Uttar Pradesh, 201308, India
| | - Ravi K Mittal
- Department of Natural Product, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, SAS Nagar, Punjab-160062, India
| | - Kavita Khatana
- Department of chemistry, School of basic and applied sciences, SBAS, Galgotias University, Greater Noida. U.P, India
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7
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Kumar S, Kumar P, Nair MS. Exploring the binding of resveratrol to a promoter DNA sequence d(CCAATTGG) 2 through multispectroscopic, nuclear magnetic resonance and molecular dynamics studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 252:119488. [PMID: 33545510 DOI: 10.1016/j.saa.2021.119488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
We report the interaction of resveratrol with an octamer DNA sequence d(CCAATTGG)2, present in the promoter region of many oncogenes, using a combination of absorption, fluorescence, calorimetric and nuclear magnetic resonance techniques to probe the binding. Resveratrol binds to the duplex sequence with a binding constant 2.20 × 106 M-1 in absorption studies. A ligand-duplex stoichiometry of 2.2:1 was obtained with binding constant varying from 103 to 104 M-1 in fluorescence titration measurements. Spectral changes indicated external binding of resveratrol to duplex DNA. Circular dichroism data displayed minimal variation suggesting external binding. Melting temperatures of DNA and its 1:1 complex showed a difference of approximately 2.25 °C, supporting the external binding. Nuclear magnetic resonance data showed resveratrol binds to the minor groove region near the AT base pair from the nuclear Overhauser effect spectroscopic cross peaks. Distance restrained molecular dynamics was employed in explicit solvent condition to obtain the lowest energy structure. The complex was stable and retained the B DNA conformation. Findings in this study identify resveratrol as a minor groove binder to the AT region of DNA and pave the way for exploring resveratrol and its analogues as promising anticancer/antibacterial drug.
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Affiliation(s)
- Shailendra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Peeyush Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Maya S Nair
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.
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8
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Zhang XX, Brantley SL, Corcelli SA, Tokmakoff A. DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site. Commun Biol 2020; 3:525. [PMID: 32963293 PMCID: PMC7508854 DOI: 10.1038/s42003-020-01241-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the dynamic interactions of ligands to DNA is important in DNA-based nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d(CGCAAATTTGCG)2) complex (H-DNA) with T-jump 2D-IR spectroscopy, the ligand is found to strongly disturb the stability of the three C:G base pairs adjacent to A:T the binding site, with the broken base pairs being more than triple at 100 ns. The strong stabilization effect of the ligand on DNA duplex makes this observation quite striking, which dramatically increases the melting temperature and dissociation time. MD simulations demonstrate an important role of hydration water and counter cations in maintaining the separation of terminal base pairs. The hydrogen bonds between the ligand and thymine carbonyls are crucial in stabilizing H-DNA, whose breaking signal appearing prior to the complete dissociation. Thermodynamic analysis informs us that H-DNA association is a concerted process, where H cooperates with DNA single strands in forming H-DNA.
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Affiliation(s)
- Xin-Xing Zhang
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA.
| | - Shelby L Brantley
- Department of Chemistry and Biochemistry, University of Norte Dame, Notre Dame, IN, 46556, USA
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Norte Dame, Notre Dame, IN, 46556, USA.
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
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9
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Schmitz TC, Dede Eren A, Spierings J, de Boer J, Ito K, Foolen J. Solid-phase silica-based extraction leads to underestimation of residual DNA in decellularized tissues. Xenotransplantation 2020; 28:e12643. [PMID: 32935355 PMCID: PMC9286341 DOI: 10.1111/xen.12643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/05/2020] [Accepted: 08/24/2020] [Indexed: 01/08/2023]
Abstract
Decellularization of animal tissues is a novel route to obtain biomaterials for use in tissue engineering and organ transplantation. Successful decellularization is required as animal DNA causes inflammatory reactions and contains endogenous retroviruses, which could be transmitted to the patient. One of the criteria for successful decellularization is digestion (fragmentation) and elimination (residual quantity) of DNA from the tissue. Quantification of DNA can be done in many ways, but it has recently been shown that silica‐based solid‐phase extraction methods often do not completely purify in particular small DNA fragments. In the context of decellularization, this means that the measured DNA amount is underestimated, which could compromise safety of the processed tissue for in‐patient use. In this article, we review DNA quantification methods used by researchers and assess their influence on the reported DNA contents after decellularization. We find that underestimation of residual DNA amount after silica‐based solid‐phase extraction may be as large as a factor of ten. We therefore recommend a direct assessment of DNA amount in tissue lysate using dsDNA‐specific binding dyes, such as Picogreen, due to their higher accuracy for small fragment detection as well as ease of use and widespread availability.
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Affiliation(s)
- Tara C Schmitz
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Aysegul Dede Eren
- BioInterface Science, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Janne Spierings
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,BioInterface Science, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jan de Boer
- BioInterface Science, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Keita Ito
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jasper Foolen
- Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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10
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Tosolini M, Gianferrara T, Mion G, Dovigo L, Mancin F, Sissi C, Tecilla P. Interaction with plasmid DNA of Hoechst-TACN conjugates. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1699657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Massimo Tosolini
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Teresa Gianferrara
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Giuliana Mion
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Luca Dovigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Paolo Tecilla
- Department of Mathematic and Geosciences, University of Trieste, Trieste, Italy
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11
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Fritzsch R, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Hunt NT. Rapid Screening of DNA–Ligand Complexes via 2D-IR Spectroscopy and ANOVA–PCA. Anal Chem 2018; 90:2732-2740. [DOI: 10.1021/acs.analchem.7b04727] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robby Fritzsch
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, U.K
| | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
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12
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Ranjan N, Kellish P, King A, Arya DP. Impact of Linker Length and Composition on Fragment Binding and Cell Permeation: Story of a Bisbenzimidazole Dye Fragment. Biochemistry 2017; 56:6434-6447. [PMID: 29131946 DOI: 10.1021/acs.biochem.7b00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Small molecules that modulate biological functions are targets of modern day drug discovery efforts. In a common platform fragment-based drug discovery, two fragments that bind to adjacent sites on a target are identified and are then linked together using different linkers to identify the linkage for optimum activity. What are not known from these studies are the effects these linkers, which typically contain C, H, and O atoms, have on the properties of the individual fragment. Herein, we investigate such effects in a bisbenzimidazole fragment whose derivatives have a wide range of therapeutic applications in nucleic acid recognition, sensing, and photodynamic therapy and as cellular probes. We report a dramatic effect of linker length and composition of alkynyl (clickable) Hoechst 33258 derivatives in target binding and cell uptake. We show that the binding of Hoechst 33258-modeled bisbenzimidazoles (1-9) that contain linkers of varying lengths (3-21 atoms) display length- and composition-dependent variation in B-DNA stabilization using a variety of spectroscopic methods. For a dodecamer DNA duplex, the thermal stabilization varied from 0.3 to 9.0 °C as the linker length increased from 3 to 21 atoms, respectively. Compounds with linker lengths of ≤11 atoms (such as compounds 1 and 5) are localized in the nucleus, while compounds with long linkers (such as compounds 8 and 9) are distributed in the extranuclear space, as well, with possible interactions with extranuclear targets. These findings provide insights into future drug design by revealing how linkers can influence the biophysical and cellular properties of individual drug fragments.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Ada King
- NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States.,NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
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13
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Nguyen TQN, Lim KW, Phan AT. A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs. Sci Rep 2017; 7:11969. [PMID: 28931822 PMCID: PMC5607247 DOI: 10.1038/s41598-017-10583-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022] Open
Abstract
Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements. Such a dual-specific targeting strategy would combine the sequence specificity of duplex-binders and the strong binding affinity of quadruplex-binders, potentially allowing the specific targeting of unique quadruplex structures. Future research can be directed towards the development of conjugated compounds targeting specific genomic quadruplex-duplex sites, for which the linker would be highly context-dependent in terms of length and flexibility, as well as the attachment points onto both ligands.
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Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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14
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Issar U, Kumari T, Arora R, Kakkar R. Conformational properties of DNA minor groove binder Hoechst 33258 in gas phase and in aqueous solution. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Ramakers LAI, Hithell G, May JJ, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Hunt NT. 2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model. J Phys Chem B 2017; 121:1295-1303. [PMID: 28102674 DOI: 10.1021/acs.jpcb.7b00345] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.
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Affiliation(s)
- Lennart A I Ramakers
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - John J May
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
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16
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Narayanaswamy N, Narra S, Nair RR, Saini DK, Kondaiah P, Govindaraju T. Stimuli-responsive colorimetric and NIR fluorescence combination probe for selective reporting of cellular hydrogen peroxide. Chem Sci 2016; 7:2832-2841. [PMID: 30090277 PMCID: PMC6054040 DOI: 10.1039/c5sc03488d] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/06/2016] [Indexed: 12/13/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a key reactive oxygen species and a messenger in cellular signal transduction apart from playing a vital role in many biological processes in living organisms. In this article, we present phenyl boronic acid-functionalized quinone-cyanine (QCy-BA) in combination with AT-rich DNA (exogenous or endogenous cellular DNA), i.e., QCy-BA⊂DNA as a stimuli-responsive NIR fluorescence probe for measuring in vitro levels of H2O2. In response to cellular H2O2 stimulus, QCy-BA converts into QCy-DT, a one-donor-two-acceptor (D2A) system that exhibits switch-on NIR fluorescence upon binding to the DNA minor groove. Fluorescence studies on the combination probe QCy-BA⊂DNA showed strong NIR fluorescence selectively in the presence of H2O2. Furthermore, glucose oxidase (GOx) assay confirmed the high efficiency of the combination probe QCy-BA⊂DNA for probing H2O2 generated in situ through GOx-mediated glucose oxidation. Quantitative analysis through fluorescence plate reader, flow cytometry and live imaging approaches showed that QCy-BA is a promising probe to detect the normal as well as elevated levels of H2O2 produced by EGF/Nox pathways and post-genotoxic stress in both primary and senescent cells. Overall, QCy-BA, in combination with exogenous or cellular DNA, is a versatile probe to quantify and image H2O2 in normal and disease-associated cells.
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Affiliation(s)
- Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory , New Chemistry Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O. , Bengaluru 560064 , India .
| | - Sivakrishna Narra
- Department of Molecular Reproduction, Development and Genetics , Indian Institute of Science , Bengaluru 560012 , India
| | - Raji R Nair
- Department of Molecular Reproduction, Development and Genetics , Indian Institute of Science , Bengaluru 560012 , India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics , Indian Institute of Science , Bengaluru 560012 , India
| | - Paturu Kondaiah
- Department of Molecular Reproduction, Development and Genetics , Indian Institute of Science , Bengaluru 560012 , India
| | - T Govindaraju
- Bioorganic Chemistry Laboratory , New Chemistry Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O. , Bengaluru 560064 , India .
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17
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Lobachevsky P, Clark GR, Pytel PD, Leung B, Skene C, Andrau L, White JM, Karagiannis T, Cullinane C, Lee BQ, Stuchbery A, Kibedi T, Hicks RJ, Martin RF. Strand breakage by decay of DNA-bound 124I provides a basis for combined PET imaging and Auger endoradiotherapy. Int J Radiat Biol 2016; 92:686-697. [PMID: 26902391 DOI: 10.3109/09553002.2015.1136852] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Purpose DNA ligands labelled with 125I induce cytotoxic DNA double-strand breaks (DSB), suggesting a potential for Auger endoradiotherapy. Since the 60-day half-life of 125I is suboptimal for therapy, we have investigated another Auger-emitter 124I, with shorter half-life (4.18 days), and the additional feature of positron-emission, enabling positron emission tomography (PET) imaging. The purpose of this study was to compare the two radionuclides on the basis of DNA DSB per decay. Materials and methods Using a 124I- (or 125I)-labelled minor groove binding DNA ligand, we investigated DNA breakage using the plasmid DNA assay. Biodistribution of the conjugate of the labelled ligand with transferrin was investigated in nude mice bearing a K562 human lymphoma xenograft. Results The probability of DSB per decay was 0.58 and 0.85 for 124I and 125I, respectively, confirming the therapeutic potential of the former. The crystal structure of the ligand DNA complex shows the iodine atom deep within the minor groove, consistent with the high efficiency of induced damage. Biodistribution studies, including PET imaging, showed distinctive results for the conjugate, compared to the free ligand and transferrin, consistent with receptor-mediated delivery of the ligand. Conclusions Conjugation of 124I-labelled DNA ligands to tumor targeting peptides provides a feasible strategy for Auger endoradiotherapy, with the advantage of monitoring tumor targeting by PET imaging.
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Affiliation(s)
- Pavel Lobachevsky
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre , Melbourne.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia
| | - George R Clark
- c School of Chemical Sciences , The University of Auckland , New Zealand
| | - Patrycja D Pytel
- c School of Chemical Sciences , The University of Auckland , New Zealand
| | - Brenda Leung
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Colin Skene
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Laura Andrau
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Jonathan M White
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Tom Karagiannis
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre , Melbourne
| | - Carleen Cullinane
- b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia.,e Cancer Research Division , Peter MacCallum Cancer Centre , Melbourne
| | - Boon Q Lee
- f Department of Nuclear Physics, Research School of Physics and Engineering , Australian National University , Canberra
| | - Andrew Stuchbery
- f Department of Nuclear Physics, Research School of Physics and Engineering , Australian National University , Canberra
| | - Tibor Kibedi
- f Department of Nuclear Physics, Research School of Physics and Engineering , Australian National University , Canberra
| | - Rodney J Hicks
- b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia.,g Centre for Molecular Imaging, Peter MacCallum Cancer Centre , Melbourne , VIC , Australia
| | - Roger F Martin
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre , Melbourne.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia.,d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
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18
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Narayanaswamy N, Das S, Samanta PK, Banu K, Sharma GP, Mondal N, Dhar SK, Pati SK, Govindaraju T. Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications. Nucleic Acids Res 2015; 43:8651-63. [PMID: 26350219 PMCID: PMC4605319 DOI: 10.1093/nar/gkv875] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/19/2015] [Indexed: 11/30/2022] Open
Abstract
In molecular biology, understanding the functional and structural aspects of DNA requires sequence-specific DNA binding probes. Especially, sequence-specific fluorescence probes offer the advantage of real-time monitoring of the conformational and structural reorganization of DNA in living cells. Herein, we designed a new class of D2A (one-donor-two-acceptor) near-infrared (NIR) fluorescence switch-on probe named quinone cyanine–dithiazole (QCy–DT) based on the distinctive internal charge transfer (ICT) process for minor groove recognition of AT-rich DNA. Interestingly, QCy–DT exhibited strong NIR-fluorescence enhancement in the presence of AT-rich DNA compared to GC-rich and single-stranded DNAs. We show sequence-specific minor groove recognition of QCy–DT for DNA containing 5′-AATT-3′ sequence over other variable (A/T)4 sequences and local nucleobase variation study around the 5′-X(AATT)Y-3′ recognition sequence revealed that X = A and Y = T are the most preferable nucleobases. The live cell imaging studies confirmed mammalian cell permeability, low-toxicity and selective staining capacity of nuclear DNA without requiring RNase treatment. Further, Plasmodium falciparum with an AT-rich genome showed specific uptake with a reasonably low IC50 value (<4 µM). The ease of synthesis, large Stokes shift, sequence-specific DNA minor groove recognition with switch-on NIR-fluorescence, photostability and parasite staining with low IC50 make QCy–DT a potential and commercially viable DNA probe.
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Affiliation(s)
- Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, India
| | - Shubhajit Das
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Khadija Banu
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | | | - Neelima Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suman K Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Swapan K Pati
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - T Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, India
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19
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Mann J, Taylor PW, Dorgan CR, Johnson PD, Wilson FX, Vickers R, Dale AG, Neidle S. The discovery of a novel antibiotic for the treatment of Clostridium difficile infections: a story of an effective academic-industrial partnership. MEDCHEMCOMM 2015; 6:1420-1426. [PMID: 26949507 PMCID: PMC4756575 DOI: 10.1039/c5md00238a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 06/30/2015] [Indexed: 12/13/2022]
Abstract
The story of the discovery of the bis-benzimidazole derivative SMT19969, which is currently in clinical trials against the pathogen Clostridium difficile.
Academic drug discovery is playing an increasingly important role in the identification of new therapies for a wide range of diseases. There is no one model that guarantees success. We describe here a drug discovery story where chance, the ability to capitalise on chance, and the assembling of a range of expertise, have all played important roles in the discovery and subsequent development of an antibiotic chemotype based on the bis-benzimidazole scaffold, with potency against a number of current therapeutically challenging diseases. One compound in this class, SMT19969, has recently entered Phase 2 human clinical trials for the treatment of Clostridium difficile infections.
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Affiliation(s)
- John Mann
- UCL School of Pharmacy , University College London , London WC1N 1AX , UK .
| | - Peter W Taylor
- UCL School of Pharmacy , University College London , London WC1N 1AX , UK .
| | | | | | | | | | - Aaron G Dale
- UCL School of Pharmacy , University College London , London WC1N 1AX , UK .
| | - Stephen Neidle
- UCL School of Pharmacy , University College London , London WC1N 1AX , UK .
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20
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Verma SD, Pal N, Singh MK, Sen S. Sequence-Dependent Solvation Dynamics of Minor-Groove Bound Ligand Inside Duplex-DNA. J Phys Chem B 2015; 119:11019-29. [DOI: 10.1021/acs.jpcb.5b01977] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sachin Dev Verma
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nibedita Pal
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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21
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Nogueira JJ, González L. Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences. Biochemistry 2014; 53:2391-412. [DOI: 10.1021/bi500068z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Juan J. Nogueira
- Institute
of Theoretical
Chemistry, University of Vienna, Währinger Strasse 17 A-1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical
Chemistry, University of Vienna, Währinger Strasse 17 A-1090 Vienna, Austria
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22
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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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23
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Fornander LH, Wu L, Billeter M, Lincoln P, Nordén B. Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule? J Phys Chem B 2013; 117:5820-30. [DOI: 10.1021/jp400418w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Louise H. Fornander
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Lisha Wu
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Martin Billeter
- Department of Chemistry and
Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Bengt Nordén
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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24
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Bialonska D, Song K, Bolton PH. Complexes of mismatched and complementary DNA with minor groove binders. Structures at nucleotide resolution via an improved hydroxyl radical cleavage methodology. Mutat Res 2011; 726:47-53. [PMID: 21893212 DOI: 10.1016/j.mrgentox.2011.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 08/20/2011] [Accepted: 08/23/2011] [Indexed: 11/18/2022]
Abstract
Tumor cell lines can replicate faster than normal cells and many also have defective DNA repair pathways. This has lead to the investigation of the inhibition of DNA repair proteins as a means of therapeutic intervention. An alternative approach is to hide or mask damaged DNA from the repair systems. We have developed a protocol to investigate the structures of the complexes of damaged DNA with drug like molecules. Nucleotide resolution structural information can be obtained using an improved hydroxyl radical cleavage protocol. The use of a dT(n) tail increases the length of the smallest fragments of interest and allows efficient co-precipitation of the fragments with poly(A). The use of a fluorescent label, on the 5' end of the dT(n) tail, in conjunction with modified cleavage reaction conditions, avoids the lifetime and other problems with (32)P labeling. The structures of duplex DNAs containing AC and CC mismatches in the presence and absence of minor groove binders have been investigated as have those of the fully complementary DNA. The results indicate that the structural perturbations of the mismatches are localized, are sequence dependent and that the presence of a mismatch can alter the binding of drug like molecules.
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25
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Zhu Z, Yang C, Zhou X, Qin J. Label-free aptamer-based sensors for L-argininamide by using nucleic acid minor groove binding dyes. Chem Commun (Camb) 2011; 47:3192-4. [PMID: 21270994 DOI: 10.1039/c0cc04844e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The nucleic acid minor groove binding dyes, DAPI and Hoechst 33258, were for the first time used in label-free aptamer-based sensors for L-argininamide. The synergy binding effect results in the enhancement of fluorescence of dyes. The method for detection of L-argininamide is simple, rapid and cost-effective.
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Affiliation(s)
- Zece Zhu
- Department of Chemistry, Hubei Key Lab on Organic and Polymeric Optoelectronic Materials, Wuhan University, Wuhan 430072, P. R. China
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26
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Marathe A, Bansal M. The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level. J Phys Chem B 2010; 114:5534-46. [DOI: 10.1021/jp911055x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arvind Marathe
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 12, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 12, India
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27
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Willis B, Arya DP. Triple recognition of B-DNA by a neomycin-Hoechst 33258-pyrene conjugate. Biochemistry 2010; 49:452-69. [PMID: 20000367 DOI: 10.1021/bi9016796] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Recent developments have indicated that aminoglycoside binding is not limited to RNA, but to nucleic acids that, like RNA, adopt conformations similar to its A-form. We further sought to expand the utility of aminoglycoside binding to B-DNA structures by conjugating neomycin, an aminoglycoside antibiotic, with the B-DNA minor groove binding ligand Hoechst 33258. Envisioning a dual groove binding mode, we have extended the potential recognition process to include a third, intercalative moiety. Similar conjugates, which vary in the number of binding moieties but maintain identical linkages to allow direct comparisons to be made, have also been prepared. We report herein novel neomycin- and Hoechst 33258-based conjugates developed in our laboratories for exploring the recognition potential with B-DNA. Spectroscopic studies such as UV melting, differential scanning calorimetry, isothermal fluorescence titrations, and circular dichroism together illustrate the triple recognition of the novel conjugate containing neomycin, Hoechst 33258, and pyrene. This study represents the first example of DNA molecular recognition capable of minor versus major groove recognition in conjunction with intercalation.
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Affiliation(s)
- Bert Willis
- Laboratories of Medicinal Chemistry, Clemson University, Clemson, South Carolina 29634, USA
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28
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Haynes CA, Sherwood CS, Turner RF. Characterization of an oligonucleotide-binding fluorescent ligand for application in affinity purification of dsDNA. Biotechnol Bioeng 2009; 48:25-35. [PMID: 18623457 DOI: 10.1002/bit.260480106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The fluorescent probe PO-PRO-3 was investigated as a potential ligand for the affinity immobilization and purification of genomic or plasmid DNA fragments. Affinities and mechanisms for PO-PRO-3 binding to superhelical and linearized pUC 18 plasmid DNA were examined through measurement of binding isotherms, continuous-variation analysis, and DNA titrations. In addition, the effects of DNA conformation, protein and RNA contaminants, solvent polarity, and ionic strength are examined with the aim of optimizing binding and elution conditions and of assigning limits to the range of applicability of the affinity purification.
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Affiliation(s)
- C A Haynes
- Biotechnology Laboratory, The University of British Columbia, British Columbia, Canada
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29
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Banerjee D, Makhal A, Pal SK. Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes. J Fluoresc 2009; 19:1111-8. [PMID: 19565329 DOI: 10.1007/s10895-009-0512-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
Abstract
Understanding the sequence dependent molecular recognition of DNA is crucial for the rational design of many drugs. Femtosecond resolved studies on the hydration dynamics of the dodecamer duplexes having sequences (CGCGAATTCGCG)2 and (CGCAAATTTGCG)2, and their complexes with the nucleic protein histone 1 (H1) reveal significant correlation of the molecular recognition of the DNA and DNA-protein complexes with the dynamics of hydration. The different molecular recognition of DNA and DNA-protein complexes is also borne out by circular dichroism (CD) and fluorescence detected CD measurements.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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30
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Turner KB, Kohlway AS, Hagan NA, Fabris D. Noncovalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: the case of NC-mediated dimerization of genomic RNA in HIV-1. Biopolymers 2009; 91:283-96. [PMID: 18946871 DOI: 10.1002/bip.21107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The nature of specific RNA-RNA and protein-RNA interactions involved in the process of genome dimerization and isomerization in HIV-1, which is mediated in vitro by stemloop 1 (SL1) of the packaging signal and by the nucleocapsid (NC) domain of the viral Gag polyprotein, was investigated by using archetypical nucleic acid ligands as noncovalent probes. Small-molecule ligands make contact with their target substrates through complex combinations of H-bonds, salt bridges, and hydrophobic interactions. Therefore, their binding patterns assessed by electrospray ionization mass spectrometry can provide valuable insights into the factors determining specific recognition between species involved in biopolymer assemblies. In the case of SL1, dimerization and isomerization create unique structural features capable of sustaining stable interactions with classic nucleic acid ligands. The binding modes exhibited by intercalators and minor groove binders were adversely affected by the significant distortion of the duplex formed by palindrome annealing in the kissing-loop (KL) dimer, whereas the modes observed for the corresponding extended duplex (ED) confirmed a more regular helical structure. Consistent with the ability to establish electrostatic interactions with highly negative pockets typical of helix anomalies, polycationic aminoglycosides bound to the stem-bulge motif conserved in all SL1 conformers, to the unpaired nucleotides located at the hinge between kissing hairpins in KL, and to the exposed bases flanking the palindrome duplex in ED. The patterns afforded by intercalators and minor groove binders did not display detectable variations when the corresponding NC-SL1 complexes were submitted to probing. In contrast, aminoglycosides displayed the ability to compete with the protein for overlapping sites, producing opposite effects on the isomerization process. Indeed, displacing NC from the stem-bulges of the KL dimer induced inhibition of stem melting and decreased the efficiency of isomerization. Competition for the hinge region, instead, eliminated the NC stabilization of a grip motif formed by nucleobases of opposite strands, thus facilitating the strand-exchange required for isomerization. These noncovalent probes provided further evidence that the structural context of the actual binding sites has significant influence on the chaperone activities of NC, which should be taken in account when developing potential drug candidates aimed at disrupting genome dimerization and isomerization in HIV-1.
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Affiliation(s)
- Kevin B Turner
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA
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31
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Bielawski K, Bielawska A. Small-Molecule based Delivery Systems for Alkylating Antineoplastic Compounds. ChemMedChem 2008; 3:536-42. [DOI: 10.1002/cmdc.200700229] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Guan Y, Shi R, Li X, Zhao M, Li Y. Multiple Binding Modes for Dicationic Hoechst 33258 to DNA. J Phys Chem B 2007; 111:7336-44. [PMID: 17530793 DOI: 10.1021/jp066344e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of dicationic Hoechst 33258 (ligand) to DNA was characterized by means of the fluorescence spectra, fluorescence intensity titration, time-resolved fluorescence decay, light scattering, circular dichroism, and fluorescence thermal denaturation measurements, and two binding modes were distinguished by the experimental results. Type 1 binding has the stoichiometry of one ligand to more than 12 base pairs, and it is defined as quasi-minor groove binding which has the typical prolonged fluorescence lifetime of about 4.4 ns. In type 1 binding, planar conformation of the ligand is favorable. Type 2 binding with phosphate to ligand ratio (P/L) < 2.5 has the stoichiometry of one ligand to two phosphates. It is defined as a highly dense and orderly stacked binding with DNA backbone as the template. Electrostatic interactions between doubly protonated ligands and negatively charged DNA backbone play a predominant role in the type 2 binding mode. The characteristics of this type of binding result in a twisted conformation of the ligand that has a fluorescence lifetime of less than 1 ns. The results also indicate that the binding is in a cooperative manner primarily by stacking of the aromatic rings of the neighboring ligands. Type 1 binding is only observed for double-stranded DNA (dsDNA) with affinity constant of 1.83 x 10(7) M-1. In the type 2 binding mode, the binding affinity constants are 4.9 x 10(6) and 4.3 x 10(6) M-1 for dsDNA and single-stranded DNA (ssDNA), respectively. The type 2 binding is base pair independent while the type 1 binding is base pair related. The experiments described in this paper revealed that the dication bindings are different from the monocation bindings reported by previous study. The dication binding leads to stronger aggregation at low ligand concentration and results in orderly arrangements of the ligands along DNA chains. Furthermore the dication binding is demonstrated to be beneficial for enhancing the DNA's stability.
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Affiliation(s)
- Yuan Guan
- The Key Laboratory of Bioorganic Chemistry & Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
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33
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Chen Z, Wang X, Zhu Y, Li Y, Guo Z. Selective guanosine binding and cytotoxicity of a benzimidazole derived dinickel complex. J Inorg Biochem 2007; 101:1894-902. [PMID: 17540448 DOI: 10.1016/j.jinorgbio.2007.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 04/10/2007] [Accepted: 04/10/2007] [Indexed: 11/21/2022]
Abstract
A water-soluble dinickel(II) complex of ethylene glycol-bis(beta-aminoethyl ether) N,N,N',N'-tetrakis(2-benzimidazoyl) (EGTB) was synthesized and fully characterized. The complex crystallizes in a monoclinic system with space group P2(1)/c, a=10.125(1)A, b=28.393(3)A, c=11.026(1)A, and beta=98.966(2) degrees. The hexa-coordinated nickel(II) centers in the centrosymmetric complex adopt a distorted octahedron geometry. The complex binds to purine nucleotides covalently and shows a clear preference for guanosine-5'-monophosphate (5'-GMP) over adenosine-5'-monophosphate (5'-AMP). Its binding to calf thymus DNA (CT-DNA) induces a remarkable conformational variation. The cytotoxic activity of the complex was tested against diverse cell lines including human leukemic cell line U937, macrophage cell line Raw 264.7, human cervical cancer cell line Hela, and human hepatocytes cell line L02. The complex shows a significant inhibition against U937 and Raw 264.7 but little inhibition against Hela and L02.
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Affiliation(s)
- Zhanfen Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
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34
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Chaudhuri P, Ganguly B, Bhattacharya S. An Experimental and Computational Analysis on the Differential Role of the Positional Isomers of Symmetric Bis-2-(pyridyl)-1H-benzimidazoles as DNA Binding Agents. J Org Chem 2007; 72:1912-23. [PMID: 17305396 DOI: 10.1021/jo0619433] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Three symmetrical positional isomers of bis-2-(n-pyridyl)-1H-benzimidazoles (n=2, 3, 4) were synthesized and DNA binding studies were performed with these isomeric derivatives. Like bisbenzimidazole compound Hoechst 33258, these molecules also demonstrate AT-specific DNA binding. The binding affinities of 3-pyridine (m-pyben) and 4-pyridine (p-pyben) derivatized bisbenzimidazoles to double-stranded DNA were significantly higher compared to 2-pyridine derivatized benzimidazole o-pyben. This has been established by combined experimental results of isothermal fluorescence titration, circular dichroism, and thermal denaturation of DNA. To rationalize the origin of their differential binding characteristics with double-stranded DNA, computational structural analyses of the uncomplexed ligands were performed using ab initio/Density Functional Theory. The molecular conformations of the symmetric head-to-head bisbenzimidazoles have been computed. The existence of intramolecular hydrogen bonding was established in o-pyben, which confers a conformational rigidity to the molecule about the bond connecting the pyridine and benzimidazole units. This might cause reduction in its binding affinity to double-stranded DNA compared to its para and meta counterparts. Additionally, the predicted stable conformations for p-, m-, and o-pyben at the B3LYP/6-31G* and RHF/6-31G* levels were further supported by experimental pKa determination. The results provide important information on the molecular recognition process of such symmetric head to head bisbenzimidazoles toward duplex DNA.
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Affiliation(s)
- Padmaparna Chaudhuri
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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35
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Streltsov SA, Gromyko AV, Oleinikov VA, Zhuze AL. The Hoechst 33258 covalent dimer covers a total turn of the double-stranded DNA. J Biomol Struct Dyn 2007; 24:285-302. [PMID: 17054387 DOI: 10.1080/07391102.2006.10507121] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
With the goal to design ligands recognizing extended regions on dsDNA, a covalent dimer of the fluorescent dye Hoechst 33258 [bis-HT(NMe)] composed of two dye molecules linked via the phenol oxygen atoms with a (CH2)3-N+ H(CH3)-(CH2)3 fragment was constructed using computer modeling and then synthesized. Its interactions with the double-stranded DNA (dsDNA) were studied by fluorescent and UV-Vis spectroscopy and circular (CD) and linear dichroism (LD). Based on variations in the affinity to the dsDNA, it was shown that complexes of three types are formed. The first type complexes result from binding of a bis-HT(NMe) monomer in the open conformation; in this case the ligand covers the total dsDNA turn and is located in the minor groove according to the positive value of CD at 370 nm. In addition, the ability to form bis-HT(NMe)-bridges between two dsDNA molecules, i.e., each of the two bis-HT(NMe) ends binds to two different dsDNA molecules, was demonstrated for the first type complexes. Spectral characteristics (maximal absorption at 362 nm, positive sign, and maximal value of CD at 370 nm) of the first type complexes conform to those of the specific Hoechst 33258 complex with poly[d(A-T)] x poly[d(A-T]. The second type complexes correspond to the bis-HT(NMe) sandwich (as an inter- or intramolecular) binding to dsDNA with stoichiometry > or = 5 bp. Thereby, a negative LD at 360 nm and the location of bis-HT(NMe) sandwiches in the minor groove of B form dsDNA seems contradictory. Spectral characteristics (maximal positive CD at 345 nm, a dramatic decrease in fluorescence intensity and the shift of its maximum to 490 nm) of these complexes favor a suggestion that this binding correlates to the formation of nonspecific dimeric Hoechst 33258 complex with dsDNA. The third type complexes are characterized by stoichiometry of one bis-HT(NMe) molecule per approximately 2 bp and the tendency to zero of LD values at 270 and 360 nm. We assume that in these complexes bis-HT(NMe) sandwich dimers are formed on dsDNA. The complexes of this type conform to the aggregation type complex of Hoechst 33258 with dsDNA. The ability of bis-HT(NMe) to cover the whole dsDNA turn or form bridges with two dsDNA upon the formation of the first type complexes essentially distinguishes it from Hoechst 33258, which can only occupy 5 bp and does not form such bridges. This specific property of bis-HT(NMe) may support new biological activities.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia.
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36
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Khan QA, Pilch DS. Topoisomerase I-mediated DNA cleavage induced by the minor groove-directed binding of bibenzimidazoles to a distal site. J Mol Biol 2007; 365:561-9. [PMID: 17095016 PMCID: PMC1849979 DOI: 10.1016/j.jmb.2006.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/13/2006] [Accepted: 10/09/2006] [Indexed: 10/23/2022]
Abstract
Many agents (e.g. camptothecins, indolocarbazoles, indenoisoquinolines, and dibenzonaphthyridines) stimulate topoisomerase I (TOP1)-mediated DNA cleavage (a behavior termed topoisomerase I poisoning) by interacting with both the DNA and the enzyme at the site of cleavage (typically by intercalation between the -1 and +1 base-pairs). The bibenzimidazoles, which include Hoechst 33258 and 33342, are a family of DNA minor groove-directed agents that also stimulate topoisomerase I-mediated DNA cleavage. However, the molecular mechanism by which these ligands poison TOP1 is poorly understood. Toward this goal, we have used a combination of mutational, footprinting, and DNA binding affinity analyses to define the DNA binding site for Hoechst 33258 and a related derivative that results in optimal induction of TOP1-mediated DNA cleavage. We show that this DNA binding site is located downstream from the site of DNA cleavage, encompassing the base-pairs from position +4 to +8. The distal nature of this binding site relative to the site of DNA cleavage suggests that minor groove-directed agents like the bibenzimidazoles poison TOP1 via a mechanism distinct from compounds like the camptothecins, which interact at the site of cleavage.
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Affiliation(s)
- Qasim A. Khan
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635
| | - Daniel S. Pilch
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635
- The Cancer Institute of New Jersey, New Brunswick, NJ 08901
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37
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Turner KB, Hagan NA, Fabris D. Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA. Nucleic Acids Res 2006; 34:1305-16. [PMID: 16522643 PMCID: PMC1390681 DOI: 10.1093/nar/gkl004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 02/10/2006] [Accepted: 02/10/2006] [Indexed: 11/14/2022] Open
Abstract
Disrupting the interactions between human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein and structural elements of the packaging signal (Psi-RNA) could constitute an ideal strategy to inhibit the functions of this region of the genome leader in the virus life cycle. We have employed electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS) to assess the ability of a series of nucleic acid ligands to bind selected structures of Psi-RNA and inhibit their specific interactions with NC in vitro. We found that the majority of the ligands included in the study were able to form stable non-covalent complexes with stem-loop 2, 3 and 4 (SL2-4), consistent with their characteristic nucleic acid binding modes. However, only aminoglycosidic antibiotics were capable of dissociating preformed NC*SL3 and NC*SL4 complexes, but not NC*SL2. The apparent specificity of these inhibitory effects is closely dependent on distinctive structural features of the different NC*RNA complexes. The trends observed for the IC50 values correlate very well with those provided by the ligand binding affinities and the dissociation constants of target NC*RNA complexes. This systematic investigation of archetypical nucleic acid ligands provides a valid framework to support the design of novel ligand inhibitors for HIV-1 treatment.
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Affiliation(s)
- Kevin B. Turner
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County1000 Hilltop Circle, Baltimore, MD 21228 USA
| | - Nathan A. Hagan
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County1000 Hilltop Circle, Baltimore, MD 21228 USA
| | - Daniele Fabris
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County1000 Hilltop Circle, Baltimore, MD 21228 USA
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38
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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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39
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Tanada M, Tsujita S, Sasaki S. Design of New Bidentate Ligands Constructed of Two Hoechst 33258 Units for Discrimination of the Length of Two A3T3 Binding Motifs. J Org Chem 2005; 71:125-34. [PMID: 16388627 DOI: 10.1021/jo051836t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
[structure: see text] The aim of this study is to develop bidentate minor-groove binders that bind the double binding motifs cooperatively. The new bidentate ligands (1) have been designed by connecting two Hoechst 33258 units with a polyether linker for cooperative binding with two remote A3T3 sites of DNA. The linker is introduced to the benzimidazole ring so that it is located at the convex side of the Hoechst unit. DNA binding affinity of the ligands was evaluated by measuring surface plasmon resonance (SPR), circular dichroism, and fluorescence spectra. Interestingly, the bidentate ligands (1) did not show affinity to DNA1 with a single A3T3 motif but showed selective affinity to DNA2 with two A3T3 motifs. The Long Bis-H (1L) having a long polyether linker showed specific binding to DNA2(6) with two A3T3 motifs separated by six nonbinding base pairs. The Long Bis-H (1L) has also shown specific binding to the three-way junction DNA4 with two A3T3 motifs. This study has demonstrated that DNA with double binding motifs can be selectively recognized by the newly designed bidentate ligands.
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Affiliation(s)
- Mikimasa Tanada
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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40
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McAteer K, Aceves-Gaona A, Michalczyk R, Buchko GW, Isern NG, Silks LAP, Miller JH, Kennedy MA. Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature. Biopolymers 2005; 75:497-511. [PMID: 15526287 DOI: 10.1002/bip.20168] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In-phase ligated DNA containing T(n)A(n) segments fail to exhibit the retarded polyacrylamide gel electrophoresis (PAGE) migration observed for in-phase ligated A(n)T(n) segments, a behavior thought to be correlated with macroscopic DNA curvature. The lack of macroscopic curvature in ligated T(n)A(n) segments is thought to be due to cancellation of bending in regions flanking the TpA steps. To address this issue, solution-state NMR, including residual dipolar coupling (RDC) restraints, was used to determine a high-resolution structure of [d(CGAGGTTTAAACCTCG)2], a DNA oligomer containing a T3A3 tract. The overall magnitude and direction of bending, including the regions flanking the central TpA step, was measured using a radius of curvature, Rc, analysis. The Rc for the overall molecule indicated a small magnitude of global bending (Rc = 138 +/- 23 nm) towards the major groove, whereas the Rc for the two halves (72 +/- 33 nm and 69 +/- 14 nm) indicated greater localized bending into the minor groove. The direction of bending in the regions flanking the TpA step is in partial opposition (109 degrees), contributing to cancellation of bending. The cancellation of bending did not correlate with a pattern of roll values at the TpA step, or at the 5' and 3' junctions, of the T3A3 segment, suggesting a simple junction/roll model is insufficient to predict cancellation of DNA bending in all T(n)A(n) junction sequence contexts. Importantly, Rc analysis of structures refined without RDC restraints lacked the precision and accuracy needed to reliably measure bending.
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Affiliation(s)
- Kathleen McAteer
- Department of Computer Science and Electrical Engineering, Washington State University Tri-Cities, Richland, WA 99352
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41
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Ladinig M, Leupin W, Meuwly M, Respondek M, Wirz J, Zoete V. Protonation Equilibria ofHoechst 33258 in Aqueous Solution. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200490296] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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42
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Bielawski K, Bielawska A, Anchim T, Wołczyński S. Synthesis, DNA Binding, Topoisomerase Inhibition and Cytotoxic Properties of 2-Chloroethylnitrosourea Derivatives of Hoechst 33258. Biol Pharm Bull 2005; 28:1004-9. [PMID: 15930735 DOI: 10.1248/bpb.28.1004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A number of novel 2-chloroethylnitrosourea derivatives of Hoechst 33258 were synthesized and examined for cytotoxicity in breast cancer cell cultures and for inhibition of topoisomerases I and II. Evaluation of the cytotoxicity of these compounds employing a MTT assay and inhibition of [3H]thymidine incorporation into DNA in both MDA-MB-231 and MCF-7 breast cancer cells demonstrated that these compounds were more active than Hoechst 33258. The DNA-binding ability of these compounds was evaluated by an ultrafiltration method using calf thymus DNA, poly(dA-dT)2 and poly(dG-dC)2, indicated that these compounds as well as Hoechst 33258 well interact with AT base pair compared with GC pair. Binding studies indicate that these compounds bind more tightly to double-stranded DNA than the parent compound Hoechst 33258. The degree to which these compounds inhibited cell growth breast cancer cells was generally consistent with their relative DNA binding affinity. Mechanistic studies revealed that these compounds act as topoisomerase I (topo I) or topoisomerase II (topo II) inhibitors in plasmid relaxation assays.
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Affiliation(s)
- Krzysztof Bielawski
- Department of Medicinal Chemistry and Drug Technology, Medical University of Białystok, Poland.
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43
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Gupta R, Beck JL, Ralph SF, Sheil MM, Aldrich-Wright JR. Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1382-1391. [PMID: 15465350 DOI: 10.1016/j.jasms.2004.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2004] [Revised: 07/12/2004] [Accepted: 07/12/2004] [Indexed: 05/24/2023]
Abstract
Positive and negative ion electrospray ionization (ESI) mass spectra of complexes of positively charged small molecules (distamycin, Hoechst 33258, [Ru(phen)2dpq]Cl2 and [Ru(phen)2dpqC]Cl2) have been compared. [Ru(phen)2dpq]Cl2 and [Ru(phen)2dpqC]Cl2 bind to DNA by intercalation. Negative ion ESI mass spectra of mixtures of [Ru(phen)2dpq]Cl2 or [Ru(phen)2dpqC]Cl2 with DNA showed ions from DNA-ligand complexes consistent with solution studies. In contrast, only ions from free DNA were present in positive ion ESI mass spectra of mixtures of [Ru(phen)2dpq]Cl2 or [Ru(phen)2dpqC]Cl2 with DNA, highlighting the need for obtaining ESI mass spectra of non-covalent complexes under a range of experimental conditions. Negative ion spectra of mixtures of the minor groove binder Hoechst 33258 with DNA containing a known minor groove binding sequence were dominated by ions from a 1:1 complex. In contrast, in positive ion spectra there were also ions present from a 2:1 (Hoechst 33258: DNA) complex, suggesting an alternative binding mode was possible either in solution or in the gas phase. When Hoechst 33258 was mixed with a DNA sequence lacking a high affinity minor groove binding site, the negative ion ESI mass spectra showed that 1:1 and 2:1 complexes were formed, consistent with existence of binding modes other than minor groove binding. The data presented suggest that comparison of positive and negative ion ESI-MS spectra might provide an insight into various binding modes in both solution and the gas phase.
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Affiliation(s)
- Rajesh Gupta
- Department of Chemistry and Vice-Chancellors Unit, University of Wollongong, Northfields Avenue, 2522, Wollongong, New South Wales, Australia
| | - Jennifer L Beck
- Department of Chemistry and Vice-Chancellors Unit, University of Wollongong, Northfields Avenue, 2522, Wollongong, New South Wales, Australia
| | - Stephen F Ralph
- Department of Chemistry and Vice-Chancellors Unit, University of Wollongong, Northfields Avenue, 2522, Wollongong, New South Wales, Australia
| | - Margaret M Sheil
- Department of Chemistry and Vice-Chancellors Unit, University of Wollongong, Northfields Avenue, 2522, Wollongong, New South Wales, Australia.
| | - Janice R Aldrich-Wright
- School of Science, Food and Horticulture, Campbelltown Campus, University of Western Sydney, New South Wales, Australia
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44
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Imoto S, Haruta Y, Watanabe K, Sasaki S. New DNA binding ligands as a model of chromomycin A3. Bioorg Med Chem Lett 2004; 14:4855-9. [PMID: 15341939 DOI: 10.1016/j.bmcl.2004.07.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 07/20/2004] [Accepted: 07/21/2004] [Indexed: 11/20/2022]
Abstract
Small molecules with DNA-binding affinity within the minor groove have become of great interest. In this study, new DNA-binding ligands were designed to mimic Chromomycin A(3) (CRA(3)), which contains a hydroxylated tetrahydroanthracene chromophore substituted with di and trisaccharides. The trisaccharide part of CRA(3) that is supposed to contribute to form the Mg(2+)-coordinated dimer was expected to be mimicked by a simple alkyl group attached to the chromophore part as new model compounds. The present study has successfully demonstrated that the new ligands form Mg(2+)-coordinated dimer complexes to exhibit DNA-binding affinity.
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Affiliation(s)
- Shuhei Imoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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45
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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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46
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Madhumalar A, Bansal M. Structural insights into the effect of hydration and ions on A-tract DNA: a molecular dynamics study. Biophys J 2003; 85:1805-16. [PMID: 12944294 PMCID: PMC1303353 DOI: 10.1016/s0006-3495(03)74609-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
DNA structure is known to be sensitive to hydration and ionic environment. To explore the dynamics, hydration, and ion binding features of A-tract sequences, a 7-ns Molecular dynamics (MD) study has been performed on the dodecamer d(CGCAAATTTGCG)(2). The results suggest that the intrusion of Na(+) ion into the minor groove is a rare event and the structure of this dodecamer is not very sensitive to the location of the sodium ions. The prolonged MD simulation successfully leads to the formation of sequence dependent hydration patterns in the minor groove, often called spine of hydration near the A-rich region and ribbon of hydration near the GC regions. Such sequence dependent differences in the hydration patterns have been seen earlier in the high resolution crystal structure of the Drew-Dickerson sequence, but not reported for the medium resolution structures (2.0 approximately 3.0 A). Several water molecules are also seen in the major groove of the MD simulated structure, though they are not highly ordered over the extended MD. The characteristic narrowing of the minor groove in the A-tract region is seen to precede the formation of the spine of hydration. Finally, the occurrence of cross-strand C2-H2.O2 hydrogen bonds in the minor groove of A-tract sequences is confirmed. These are found to occur even before the narrowing of the minor groove, indicating that such interactions are an intrinsic feature of A-tract sequences.
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Affiliation(s)
- A Madhumalar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Adhikary A, Buschmann V, Müller C, Sauer M. Ensemble and single-molecule fluorescence spectroscopic study of the binding modes of the bis-benzimidazole derivative Hoechst 33258 with DNA. Nucleic Acids Res 2003; 31:2178-86. [PMID: 12682368 PMCID: PMC153736 DOI: 10.1093/nar/gkg308] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ensemble and single-molecule fluorescence measurements of 2'-(4-hydroxyphenyl)-5-[5-(4-methylpiperazine-1-yl) benzimidazo-2-yl]-benzimidazole (H-258)- calf thymus (CT) DNA complexes at various [H-258]/[DNA bp] ratios were performed to elucidate the binding of H-258 with DNA. Upon binding to double-stranded CT DNA (CT ds DNA) at a [H-258]/[DNA bp] ratio of 0.05 the relative fluorescence quantum yield, Phi(f), of H-258 increases from 0.02 to 0.58. The fluorescence decay can be fitted almost by a mono-exponential model with a lifetime of approximately 3.6 ns. This indicates that H-258 binds almost quantitatively in the minor groove of DNA at low [H-258]/[DNA bp] ratios. With increasing [H-258]/[DNA bp] ratios, e.g. 0.15 and 0.20, the fluorescence quantum yield of H-258 decreases to 0.28 and 0.19, respectively. Fitting of the fluorescence decays measured for higher [H-258]/[DNA bp] ratios reveals the presence of additional shorter fluorescence lifetime components in the range of 0.5-2.0 ns. Our results suggest that H-258 partially intercalates in G:C sequences at higher [H-258]/[DNA bp] ratios reflected by a lifetime component of 1.5-2 ns. In addition, stacking or adsorption of H-258 molecules on DNA occurs at higher [H-258]/[DNA bp] ratios. These molecules exhibit a short fluorescence lifetime of approximately 500 ps and are more exposed to the aqueous environment. Fluorescence transients of the intensity and lifetime of single H-258 CT ds DNA demonstrate that weakly (unspecific) bound H-258 molecules exhibit a shorter fluorescence lifetime and a strongly reduced photostability.
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Affiliation(s)
- Amitava Adhikary
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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Bailly C, Chessari G, Carrasco C, Joubert A, Mann J, Wilson WD, Neidle S. Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition. Nucleic Acids Res 2003; 31:1514-24. [PMID: 12595560 PMCID: PMC149830 DOI: 10.1093/nar/gkg237] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in explicit solvent. The footprinting and SPR methods find that the former compound has enhanced affinity and selectivity for AT sequences in DNA. The molecular modeling studies have suggested that, due to the presence of the oxygen atom in each side chain of the former compound, a water molecule is immobilized and effectively bridges between side chain and DNA base edges via hydrogen bonding interactions. This additional contribution to ligand-DNA interactions would be expected to result in enhanced DNA affinity, as is observed.
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Affiliation(s)
- Christian Bailly
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France
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Bielawski K, Bielawska A, Wołczyński S. Synthesis, DNA-binding activity and cytotoxicity of carbamate derivatives of Hoechst 33258 in breast cancer MCF-7 cells. Biol Pharm Bull 2002; 25:916-9. [PMID: 12132669 DOI: 10.1248/bpb.25.916] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of carbamate derivatives of Hoechst 33258 was prepared as potential anticancer agents. These new compounds (1-4) were readily prepared in good yields by addition of chloroethyl, bromoethyl, chloropropyl or 4-(chloromethyl)phenyl isocyanates to Hoechst 33258. Their cytotoxic activity was evaluated on human breast cancer MCF-7. Compounds 1-4 were more cytotoxic than Hoechst 33258. In particular derivative 4, the most active of the series, is up to 3 times more potent than Hoechst 33258. The DNA-binding ability of these compounds was evaluated by an ultrafiltration method using calf thymus DNA. These data show that in broad terms the cytotoxic potency of 1-4 in cultured breast cancer MCF-7 cells increases, in accord with their increases in DNA affinity, as shown by the binding constant values.
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Affiliation(s)
- Krzysztof Bielawski
- Department of Medicinal Chemistry and Drug Technology, Medical Academy of Białystok, Poland.
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50
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