1
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Kim HS, Park JE, Lee WH, Kwon YB, Seu YB, Kim KS. Novel Amidine Derivative K1586 Sensitizes Colorectal Cancer Cells to Ionizing Radiation by Inducing Chk1 Instability. Int J Mol Sci 2024; 25:4396. [PMID: 38673980 PMCID: PMC11049894 DOI: 10.3390/ijms25084396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Checkpoint kinase 1 (Chk1) is a key mediator of the DNA damage response that regulates cell cycle progression, DNA damage repair, and DNA replication. Small-molecule Chk1 inhibitors sensitize cancer cells to genotoxic agents and have shown preclinical activity as single agents in cancers characterized by high levels of replication stress. However, the underlying genetic determinants of Chk1-inhibitor sensitivity remain unclear. Although treatment options for advanced colorectal cancer are limited, radiotherapy is effective. Here, we report that exposure to a novel amidine derivative, K1586, leads to an initial reduction in the proliferative potential of colorectal cancer cells. Cell cycle analysis revealed that the length of the G2/M phase increased with K1586 exposure as a result of Chk1 instability. Exposure to K1586 enhanced the degradation of Chk1 in a time- and dose-dependent manner, increasing replication stress and sensitizing colorectal cancer cells to radiation. Taken together, the results suggest that a novel amidine derivative may have potential as a radiotherapy-sensitization agent that targets Chk1.
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Affiliation(s)
- Hang Soo Kim
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Ji-Eun Park
- Divisions of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea;
- School of Radiological & Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Won Hyung Lee
- R&D Center, Chemical Business Unit, Pharmicell Co., Ltd., Ulsan 45009, Republic of Korea;
| | - Young Bin Kwon
- Central Research Institute, Kyung Nong Co., Ltd., Gyeongju 38175, Republic of Korea;
| | - Young-Bae Seu
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Kwang Seok Kim
- Divisions of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea;
- School of Radiological & Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Republic of Korea
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2
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Yatsunyk LA, Neidle S. On Water Arrangements in Right- and Left-Handed DNA Structures. Molecules 2024; 29:505. [PMID: 38276583 PMCID: PMC10820154 DOI: 10.3390/molecules29020505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/07/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
DNA requires hydration to maintain its structural integrity. Crystallographic analyses have enabled patterns of water arrangements to be visualized. We survey these water motifs in this review, focusing on left- and right-handed duplex and quadruplex DNAs, together with the i-motif. Common patterns of linear spines of water organization in grooves have been identified and are widely prevalent in right-handed duplexes and quadruplexes. By contrast, a left-handed quadruplex has a distinctive wheel of hydration populating the almost completely circular single groove in this structure.
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Affiliation(s)
- Liliya A. Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA;
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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3
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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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4
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Ali HA, Ismail MA, Fouda AEAS, Ghaith EA. A fruitful century for the scalable synthesis and reactions of biphenyl derivatives: applications and biological aspects. RSC Adv 2023; 13:18262-18305. [PMID: 37333795 PMCID: PMC10274569 DOI: 10.1039/d3ra03531j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/10/2023] [Indexed: 06/20/2023] Open
Abstract
This review provides recent developments in the current status and latest synthetic methodologies of biphenyl derivatives. Furthermore, this review investigates detailed discussions of several metalated chemical reactions related to biphenyl scaffolds such as Wurtz-Fittig, Ullmann, Bennett-Turner, Negishi, Kumada, Stille, Suzuki-Miyaura, Friedel-Crafts, cyanation, amination, and various electrophilic substitution reactions supported by their mechanistic pathways. Furthermore, the preconditions required for the existence of axial chirality in biaryl compounds are discussed. Furthermore, atropisomerism as a type of axial chirality in biphenyl molecules is discussed. Additionally, this review covers a wide range of biological and medicinal applications of the synthesized compounds involving patented approaches in the last decade corresponding to investigating the crucial role of the biphenyl structures in APIs.
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Affiliation(s)
- Hajar A Ali
- Chemistry Department, Faculty of Science, Mansoura University 35516 Mansoura Egypt
| | - Mohamed A Ismail
- Chemistry Department, Faculty of Science, Mansoura University 35516 Mansoura Egypt
| | - Abd El-Aziz S Fouda
- Chemistry Department, Faculty of Science, Mansoura University 35516 Mansoura Egypt
| | - Eslam A Ghaith
- Chemistry Department, Faculty of Science, Mansoura University 35516 Mansoura Egypt
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5
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Myres GJ, Harris JM. Nanomolar Binding of an Antibiotic Peptide to DNA Measured with Raman Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4150-4160. [PMID: 36888905 DOI: 10.1021/acs.langmuir.3c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Immobilization of DNA to surfaces offers a convenient means of screening the binding affinity and selectivity of potential small-molecule therapeutic candidates. Unfortunately, most surface-sensitive methods for detecting these binding interactions are not informative of the molecular structure, information that is valuable for understanding the non-covalent interactions that stabilize binding. In this work, we report a method to meet this challenge by employing confocal Raman microscopy to quantify the association of a minor-groove-binding antimicrobial peptide, netropsin, to duplex DNA hairpin sequences immobilized on the interior surfaces of porous silica particles. To assess binding selectivity, particles functionalized with different sequences of DNA were equilibrated with solutions of 100 nM netropsin, and selective association was detected based on the presence of netropsin Raman scattering in the particles. The selectivity study revealed that netropsin binds to sequences of duplex DNA having AT-rich recognition regions. To quantify binding affinities, these AT-rich DNA sequences were equilibrated with a range of netropsin solution concentrations (1 to 100 nM). Raman scattering intensities of netropsin versus solution concentration were well described by single-binding-site Langmuir isotherms with nanomolar dissociation constants, in agreement with previous isothermal calorimetry and surface plasmon resonance results. Target sequence binding was accompanied with changes in netropsin and DNA vibrational modes consistent with the hydrogen bonding between the amide groups of netropsin and adenine and thymine bases in the DNA minor groove. The binding of netropsin to a control sequence lacking the AT-rich recognition region exhibited an affinity nearly 4 orders of magnitude weaker than found for the target sequences. The Raman spectrum of netropsin interacting with this control sequence showed broad pyrrole and amide mode vibrations at frequencies similar to a free solution, revealing less constrained conformations compared with the specific binding interactions observed with AT-rich sequences.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
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6
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Myres GJ, Harris JM. Stable Immobilization of DNA to Silica Surfaces by Sequential Michael Addition Reactions Developed with Insights from Confocal Raman Microscopy. Anal Chem 2023; 95:3499-3506. [PMID: 36718639 DOI: 10.1021/acs.analchem.2c05594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The immobilization of DNA to surfaces is required for numerous biosensing applications related to the capture of target DNA sequences, proteins, or small-molecule analytes from solution. For these applications to be successful, the chemistry of DNA immobilization should be efficient, reproducible, and stable and should allow the immobilized DNA to adopt a secondary structure required for association with its respective target molecule. To develop and characterize surface immobilization chemistry to meet this challenge, it is invaluable to have a quantitative, surface-sensitive method that can report the interfacial chemistry at each step, while also being capable of determining the structure, stability, and activity of the tethered DNA product. In this work, we develop a method to immobilize DNA to silica, glass, or other oxide surfaces by carrying out the reactions in porous silica particles. Due to the high specific surface area of porous silica, the local concentrations of surface-immobilized molecules within the particle are sufficiently high that interfacial chemistry can be monitored at each step of the process with confocal Raman microscopy, providing a unique capability to assess the molecular composition, structure, yield, and surface coverage of these reactions. We employ this methodology to investigate the steps for immobilizing thiolated-DNA to thiol-modified silica surfaces through sequential Michael addition reactions with the cross-linker 1,4-phenylene-bismaleimide. A key advantage of employing a phenyl-bismaleimide over a comparable alkyl coupling reagent is the efficient conversion of the initial phenyl-thiosuccinimide to a more stable succinamic acid thioether linkage. This transformation was confirmed by in situ Raman spectroscopy measurements, and the resulting succinamic acid thioether product exhibited greater than 95% retention of surface-immobilized DNA after 12 days at room temperature in aqueous buffer. Confocal Raman microscopy was also used to assess the conformational freedom of surface-immobilized DNA by comparing the structure of a 23-mer DNA hairpin sequence under duplex-forming and unfolding conditions. We find that the immobilized DNA hairpin can undergo reversible intramolecular duplex formation based on the changes in frequencies and intensities of the phosphate backbone and base-specific vibrational modes that are informative of the hybridization state of DNA.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
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7
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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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8
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Li L, Sun W, Tong Z, Bo M, Ken Ostrikov K, Huang Y, Sun CQ. Discriminative ionic polarizability of alkali halide solutions: Hydration cells, bond distortion, surface stress, and viscosity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Shen Y, Wei X, Wang Y, Shen Y, Li L, Huang Y, Ostrikov KK, Sun CQ. Energy absorbancy and freezing-temperature tunability of NaCl solutions during ice formation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Jhan CR, Satange R, Wang SC, Zeng JY, Horng YC, Jin P, Neidle S, Hou MH. Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction. Nucleic Acids Res 2021; 49:9526-9538. [PMID: 33836081 PMCID: PMC8450080 DOI: 10.1093/nar/gkab227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.
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Affiliation(s)
- Cyong-Ru Jhan
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan
| | - Roshan Satange
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.,Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Shun-Ching Wang
- Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Jing-Yi Zeng
- Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Yih-Chern Horng
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, United Kingdom
| | - Ming-Hon Hou
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.,Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
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11
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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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12
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Guo P, Farahat AA, Paul A, Kumar A, Boykin DW, Wilson WD. Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove. Biochemistry 2020; 59:1756-1768. [PMID: 32293884 DOI: 10.1021/acs.biochem.0c00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The majority of current drugs against diseases, such as cancer, can bind to one or more sites in a protein and inhibit its activity. There are, however, well-known limits on the number of druggable proteins, and complementary current drugs with compounds that could selectively target DNA or RNA would greatly enhance the availability of cellular probes and therapeutic progress. We are focusing on the design of sequence-specific DNA minor groove binders that, for example, target the promoter sites of transcription factors involved in a disease. We have started with AT-specific minor groove binders that are known to enter human cells and have entered clinical trials. To broaden the sequence-specific recognition of these compounds, several modules that have H-bond acceptors that strongly and specifically recognize G·C base pairs were identified. A lead module is a thiophene-N-alkyl-benzimidazole σ-hole-based system with terminal phenyl-amidines that have excellent affinity and selectivity for a G·C base pair in the minor groove. Efforts are now focused on optimizing this module. In this work, we are evaluating modifications to the compound aromatic system with the goal of improving GC selectivity and affinity. The lead compounds retain the thiophene-N-alkyl-BI module but have halogen substituents adjacent to an amidine group on the terminal phenyl-amidine. The optimum compounds must have strong affinity and specificity with a residence time of at least 100 s.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States.,Master of Pharmaceutical Sciences Program, California Northstate University, 9700 West Taron Drive, Elk Grove, California 95757, United States
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
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13
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Farahat AA, Guo P, Shoeib H, Paul A, Boykin DW, Wilson WD. Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove. Chemistry 2020; 26:4539-4551. [PMID: 31884714 PMCID: PMC7265973 DOI: 10.1002/chem.201904396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/10/2019] [Indexed: 12/24/2022]
Abstract
A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3 )3 ]2 ) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.
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Affiliation(s)
- Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Hadir Shoeib
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
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14
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A. Ismail M, M. El-Sayed W, Shaaban S, A. Abdelwahab G, S. Hamama W. A Review of Cationic Arylfurans and Their Isosteres: Synthesis and Biological Importance. CURR ORG CHEM 2020. [DOI: 10.2174/1385272823666191029114830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The present study provides an overview of the chemistry and biological importance
of the cationic chalcophene derivatives (furans, thiophenes and selenophenes). The
summarized literature survey includes synthetic methods, reactivity and biological activities
of aryl/hetarylchalcophenes that have been reported mainly from 2001 to 2019 focusing
on monochalcophenes. A discussion demonstrating the proposed mechanisms of some
interesting synthetic routes and linking structure features to biological activities is presented.
These classes of compounds including cationic chalcophenes possess antiproliferative,
antimicrobial and antiprotozoal activities. This review highlights recent advances
for arylchalcophene derivatives and may contribute to the design and structure optimization
of new chalcophene derivatives in the future.
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Affiliation(s)
- Mohamed A. Ismail
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Wael M. El-Sayed
- Department of Zoology, Faculty of Science, University of Ain Shams, Abbassia 11566, Cairo, Egypt
| | - Saad Shaaban
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Ghada A. Abdelwahab
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Wafaa S. Hamama
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
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15
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May L, Daniel S, Müller TJJ. Diversity-oriented approach to functional thiophene dyes by Suzuki coupling-lithiation one-pot sequences. Org Chem Front 2020. [DOI: 10.1039/c9qo01318k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Functional thiophenes, e.g. for organic metal-free dye sensitized solar cells (DSSC), are accessible efficiently via a divergent and diversity-oriented synthetic strategy.
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Affiliation(s)
- Lars May
- Heinrich-Heine-Universität Düsseldorf
- Institut für Organische Chemie und Makromolekulare Chemie
- D-40225 Düsseldorf
- Germany
| | - Sven Daniel
- Heinrich-Heine-Universität Düsseldorf
- Institut für Organische Chemie und Makromolekulare Chemie
- D-40225 Düsseldorf
- Germany
| | - Thomas J. J. Müller
- Heinrich-Heine-Universität Düsseldorf
- Institut für Organische Chemie und Makromolekulare Chemie
- D-40225 Düsseldorf
- Germany
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16
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Das AK, Ihmels H, Kölsch S. Diphenylaminostyryl-substituted quinolizinium derivatives as fluorescent light-up probes for duplex and quadruplex DNA. Photochem Photobiol Sci 2019; 18:1373-1381. [PMID: 30916703 DOI: 10.1039/c9pp00096h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
(E)-2-[1'-((Diphenylamino)styryl)quinolizinium (3a) and 2,2'-{(phenylimino)-bis[(E)-1'',1'''-styryl]}-bis[quinolizinium] (3b) were synthesized, and their interactions with duplex DNA and quadruplex DNA were investigated with a particular focus on their ability to operate as DNA-sensitive fluorescent probes. Due to the significantly different size and steric demand of these quinolizinium derivatives they exhibit different binding modes. Thus, 3a intercalates into duplex DNA and binds through π stacking to quadruplex DNA, whereas 3b favours groove binding to both DNA forms. The emission intensity of these compounds is very low in aqueous solution, but it increases drastically upon association with duplex DNA by a factor of 11 (3a) and >100 (3b) and with quadruplex DNA by a factor of >100 (3a) and 10 (3b), with emission bands between 600 and 750 nm.
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Affiliation(s)
- Avijit Kumar Das
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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17
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Sun CQ, Huang Y, Zhang X. Hydration of Hofmeister ions. Adv Colloid Interface Sci 2019; 268:1-24. [PMID: 30921543 DOI: 10.1016/j.cis.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 01/08/2023]
Abstract
Water dissolves salt into ions and then hydrates the ions to form an aqueous solution. Hydration of ions deforms the hydrogen bonding network and triggers the solution with what the pure water never shows such as conductivity, molecular diffusivity, thermal stability, surface stress, solubility, and viscosity, having enormous impact to many branches in biochemistry, chemistry, physics, and energy and environmental industry sectors. However, regulations for the solute-solute-solvent interactions are still open for exploration. From the perspective of the screened ionic polarization and O:H-O bond relaxation, this treatise features the recent progress and a perspective in understanding the hydration dynamics of Hofmeister ions in the typical YI, NaX, ZX2, and NaT salt solutions (Y = Li, Na, K, Rb, Cs; X = F, Cl, Br, I; Z = Mg, Ca, Ba, Sr; T = ClO4, NO3, HSO4, SCN). Phonon spectrometric analysis turned out the f(C) number fraction of bonds transition from the mode of deionized water to the hydrating. The linear f(C) ∝ C form features the invariant hydration volume of small cations that are fully-screened by their hydration H2O dipoles. The nonlinear f(C) ∝ 1 - exp.(-C/C0) form describes that the number insufficiency of the ordered hydrating H2O dipoles partially screens the anions. Molecular anions show stronger yet shorter electric field of dipoles. The screened ionic polarization, inter-solute interaction, and O:H-O bond transition unify the solution conductivity, surface stress, viscosity, and critical energies for phase transition.
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18
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Depauw S, Lambert M, Jambon S, Paul A, Peixoto P, Nhili R, Marongiu L, Figeac M, Dassi C, Paul-Constant C, Billoré B, Kumar A, Farahat AA, Ismail MA, Mineva E, Sweat DP, Stephens CE, Boykin DW, Wilson WD, David-Cordonnier MH. Heterocyclic Diamidine DNA Ligands as HOXA9 Transcription Factor Inhibitors: Design, Molecular Evaluation, and Cellular Consequences in a HOXA9-Dependant Leukemia Cell Model. J Med Chem 2019; 62:1306-1329. [PMID: 30645099 DOI: 10.1021/acs.jmedchem.8b01448] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most transcription factors were for a long time considered as undruggable targets because of the absence of binding pockets for direct targeting. HOXA9, implicated in acute myeloid leukemia, is one of them. To date, only indirect targeting of HOXA9 expression or multitarget HOX/PBX protein/protein interaction inhibitors has been developed. As an attractive alternative by inhibiting the DNA binding, we selected a series of heterocyclic diamidines as efficient competitors for the HOXA9/DNA interaction through binding as minor groove DNA ligands on the HOXA9 cognate sequence. Selected DB818 and DB1055 compounds altered HOXA9-mediated transcription in luciferase assays, cell survival, and cell cycle, but increased cell death and granulocyte/monocyte differentiation, two main HOXA9 functions also highlighted using transcriptomic analysis of DB818-treated murine Hoxa9-transformed hematopoietic cells. Altogether, these data demonstrate for the first time the propensity of sequence-selective DNA ligands to inhibit HOXA9/DNA binding both in vitro and in a murine Hoxa9-dependent leukemic cell model.
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Affiliation(s)
- Sabine Depauw
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Mélanie Lambert
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Samy Jambon
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Ananya Paul
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Paul Peixoto
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Raja Nhili
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Laura Marongiu
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Martin Figeac
- Functional and Structural Genomic Platform , Lille University , F-59000 Lille , France
| | - Christelle Dassi
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Charles Paul-Constant
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Benjamin Billoré
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Arvind Kumar
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Abdelbasset A Farahat
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Mohamed A Ismail
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Ekaterina Mineva
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Daniel P Sweat
- Department of Chemistry and Physics , Augusta University , Augusta , Georgia 30904 , United States
| | - Chad E Stephens
- Department of Chemistry and Physics , Augusta University , Augusta , Georgia 30904 , United States
| | - David W Boykin
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
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19
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DNA recognition by linear indole-biphenyl DNA minor groove ligands. Biophys Chem 2018; 245:6-16. [PMID: 30513446 DOI: 10.1016/j.bpc.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 11/21/2022]
Abstract
Linear heterocyclic cations are interesting DNA minor groove ligands due to their lack of isohelical curvature classically associated with groove-binding compounds. We determined the DNA binding properties of four related dications harboring a linear indole-biphenyl core: the diamidine DB1883, a ditetrahydropyrimidine derivative (DB1804), and their monocationic counterparts (DB1944 and DB2627). These compounds exhibit heterogeneity in binding in accordance with their structures. Whereas the monocations exhibit salt-sensitive 1:1 binding to the duplex 5'-CGCGAATTCGCG-3' (A2T2), the dications show a marked preference for a salt-insensitive 2:1 complex. The two binding modes are differentially modulated by salt and specific non-ionic co-solutes. For both dications, 2-methyl-2,4-pentanediol enforces 1:1 binding as observed crystallographically. Fluorescence quenching studies show self-association without DNA in a relative order that is correlated with preference for the 2:1 complex. The data support a structure-binding relationship in which favorable cation-π interactions drive dimer formation via antiparallel stacking of the linear indole-biphenyl cation motif.
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20
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Sun CQ. Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1544446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chang Q. Sun
- EBEAM, Yangtze Normal University, Chongqing, People's Republic of China
- NOVITAS, EEE, Nanyang Technological University, Singapore, Singapore
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21
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Mizuta R, Devos JM, Webster J, Ling WL, Narayanan T, Round A, Munnur D, Mossou E, Farahat AA, Boykin DW, Wilson WD, Neidle S, Schweins R, Rannou P, Haertlein M, Forsyth VT, Mitchell EP. Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide. NANOSCALE 2018; 10:5550-5558. [PMID: 29517086 PMCID: PMC5885265 DOI: 10.1039/c7nr03875e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
We describe a novel self-assembling supramolecular nanotube system formed by a heterocyclic cationic molecule which was originally designed for its potential as an antiparasitic and DNA sequence recognition agent. Our structural characterisation work indicates that the nanotubes form via a hierarchical assembly mechanism that can be triggered and tuned by well-defined concentrations of simple alkali halide salts in water. The nanotubes assembled in NaCl have inner and outer diameters of ca. 22 nm and 26 nm respectively, with lengths that reach into several microns. Our results suggest the tubes consist of DB921 molecules stacked along the direction of the nanotube long axis. The tubes are stabilised by face-to-face π-π stacking and ionic interactions between the charged amidinium groups of the ligand and the negative halide ions. The assembly process of the nanotubes was followed using small-angle X-ray and neutron scattering, transmission electron microscopy and ultraviolet/visible spectroscopy. Our data demonstrate that assembly occurs through the formation of intermediate ribbon-like structures that in turn form helices that tighten and compact to form the final stable filament. This assembly process was tested using different alkali-metal salts, showing a strong preference for chloride or bromide anions and with little dependency on the type of cation. Our data further demonstrates the existence of a critical anion concentration above which the rate of self-assembly is greatly enhanced.
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Affiliation(s)
- R Mizuta
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France and European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - J M Devos
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J Webster
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France and European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - W L Ling
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - T Narayanan
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - A Round
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France and Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - D Munnur
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France and European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France. and School of Pharmacy, University College London, Brunswick Square, London, WC1N 1AX, UK
| | - E Mossou
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France and Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - A A Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA and Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - D W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - W D Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - S Neidle
- School of Pharmacy, University College London, Brunswick Square, London, WC1N 1AX, UK
| | - R Schweins
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - P Rannou
- Univ. Grenoble Alpes, CNRS, CEA, INAC-SyMMES, 38000 Grenoble, France
| | - M Haertlein
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V T Forsyth
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France and Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - E P Mitchell
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France. and Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
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22
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Liu Y, Hu X, Wu Y, Zhang W, Chen X, You X, Hu L. Synthesis and structure-activity relationship of novel bisindole amidines active against MDR Gram-positive and Gram-negative bacteria. Eur J Med Chem 2018; 150:771-782. [PMID: 29604581 DOI: 10.1016/j.ejmech.2018.03.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 03/08/2018] [Accepted: 03/09/2018] [Indexed: 11/17/2022]
Abstract
A series of novel diamidines with N-substituents on an amidine N-atom were synthesized and evaluated for their cytotoxicity and in vitro antibacterial activity against a range of Gram-positive and Gram-negative bacterial strains. Based on structure-activity relationship, N-substituents with a branched chain and a shorter carbon chain on the amidine N-atom exhibited more promising activity against Gram-negative and MDR-Gram-positive bacteria; compounds 5c and 5i were the most powerful candidate compounds. Compound 5c showed greater efficacy than levofloxacin against most drug-resistant Gram-positive bacteria and exhibited broad-spectrum antibacterial activity against Gram-negative bacteria, with MIC values in the range of 2-16 μg/mL. Slightly more potent antibacterial activity against Klebsiella pneumoniae, Acinetobacter calcoaceticus, Enterobacter cloacae, and Proteus mirabilis was observed for 5i in comparison with 5c. Compound 5i also showed remarkable antibacterial activity against NDM-1-producing Gram-negative bacteria, with MIC values in the range of 2-4 μg/mL, and was superior to the reference drugs meropenem and levofloxacin. Effective antibacterial activity of 5i was also shown in vivo in a mouse model of Staphylococcus aureus MRSA strain, with an ED50values of 2.62 mg/kg.
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Affiliation(s)
- Yonghua Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China.
| | - Xinxin Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China
| | - Yanbin Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China
| | - Weixing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China
| | - Xiaofang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China
| | - Xuefu You
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China.
| | - Laixing Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tian Tan Xi Li 1#, Beijing, 100050, China.
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23
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Pramanik A, Abbasi M, Maji K, Nandi SK, Datta R, Haldar D. Selective Sensing of Ammonium Ion Over Other Biologically Important Ammonia Derivatives by a Coumarin-Based ϵ-Amino Ester. ChemistrySelect 2018. [DOI: 10.1002/slct.201702068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Apurba Pramanik
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Mazharul Abbasi
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Krishnendu Maji
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Sujay Kumar Nandi
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Rupak Datta
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Debasish Haldar
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
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24
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Harika NK, Germann MW, Wilson WD. First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences. Chemistry 2017; 23:17612-17620. [PMID: 29044822 DOI: 10.1002/chem.201704563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 12/24/2022]
Abstract
The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both A⋅T and G⋅C bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the G⋅C base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA
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25
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Maity D, Matković M, Li S, Ehlers M, Wu J, Piantanida I, Schmuck C. Peptide-Based Probes with an Artificial Anion-Binding Motif for Direct Fluorescence "Switch-On" Detection of Nucleic Acid in Cells. Chemistry 2017; 23:17356-17362. [PMID: 28967979 DOI: 10.1002/chem.201703813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 01/08/2023]
Abstract
This work reports two new peptide-based fluorescence probes (1 and 2) for the detection of ds-DNA at physiological pH. Probes 1 and 2 contain a fluorophore, either amino-naphthalimide or diethyl-aminocoumarin, respectively, and two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) anion-binding motif. These probes show "switch-on" fluorescence response upon binding to ds-DNA, whereby they can differentiate between various types of polynucleotides. For instance, they exhibit more pronounced fluorescence response for AT-rich polynucleotides than GC-rich polynucleotides, and both give only negligible response to ds-RNA. The fluorimetric response of 1 is proportional to the AT-basepair content in DNA, whereas the fluorescence of 2 is sensitive to the secondary structure of the polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies suggest that 1 interacts with ds-DNA in a combined intercalation and minor groove binding, whereas 2 interacts mainly with the outer surface of DNA/RNA. As 1 and 2 have a very low cytotoxicity, 1 can be applied for the imaging of nuclear DNA in cells.
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Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | | | - Shang Li
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Martin Ehlers
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Junchen Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
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26
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Guo P, Paul A, Kumar A, Harika NK, Wang S, Farahat AA, Boykin DW, Wilson WD. A modular design for minor groove binding and recognition of mixed base pair sequences of DNA. Chem Commun (Camb) 2017; 53:10406-10409. [PMID: 28880316 PMCID: PMC5616130 DOI: 10.1039/c7cc06246j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design and synthesis of compounds that target mixed, AT/GC, DNA sequences is described. The design concept connects two N-methyl-benzimidazole-thiophene single GC recognition units with a flexible linker that lets the compound fit the shape and twist of the DNA minor groove while covering a full turn of the double helix.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
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27
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Cindrić M, Jambon S, Harej A, Depauw S, David-Cordonnier MH, Kraljević Pavelić S, Karminski-Zamola G, Hranjec M. Novel amidino substituted benzimidazole and benzothiazole benzo[ b ]thieno-2-carboxamides exert strong antiproliferative and DNA binding properties. Eur J Med Chem 2017; 136:468-479. [DOI: 10.1016/j.ejmech.2017.05.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/02/2017] [Accepted: 05/03/2017] [Indexed: 01/05/2023]
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28
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Grotkopp O, Müller TJJ. Synthesis of bi- and terthiophenes initiated by microwave-assisted coupling-isomerization reaction. Chem Heterocycl Compd (N Y) 2017. [DOI: 10.1007/s10593-017-2022-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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de Camargo MS, da Silva MM, Correa RS, Vieira SD, Castelli S, D'Anessa I, De Grandis R, Varanda E, Deflon VM, Desideri A, Batista AA. Inhibition of human DNA topoisomerase IB by nonmutagenic ruthenium(II)-based compounds with antitumoral activity. Metallomics 2016; 8:179-92. [PMID: 26758075 DOI: 10.1039/c5mt00227c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein we synthesized two new ruthenium(II) compounds [Ru(pySH)(bipy)(dppb)]PF6 (1) and [Ru(HSpym)(bipy)(dppb)]PF6 (2) that are analogs to an antitumor agent recently described, [Ru(SpymMe2)(bipy)(dppb)]PF6 (3), where [(Spy) = 2-mercaptopyridine anion; (Spym) = 2-mercaptopyrimidine anion and (SpymMe2) = 4,6-dimethyl-2-mercaptopyrimidine anion]. In vitro cell culture experiments revealed significant anti-proliferative activity for 1-3 against HepG2 and MDA-MB-231 tumor cells, higher than the standard anti-cancer drugs doxorubicin and cisplatin. No mutagenicity is detected when compounds are evaluated by cytokinesis-blocked micronucleus cytome and Ames test in the presence and absence of S9 metabolic activation from rat liver. Interaction studies show that compounds 1-3 can bind to DNA through electrostatic interactions and to albumin through hydrophobic interactions. The three compounds are able to inhibit the DNA supercoiled relaxation mediated by human topoisomerase IB (Top1). Compound 3 is the most efficient Top1 inhibitor and the inhibitory effect is enhanced upon pre-incubation with the enzyme. Analysis of different steps of Top1 catalytic cycle indicates that 3 inhibits the cleavage reaction impeding the binding of the enzyme to DNA and slows down the religation reaction. Molecular docking shows that 3 preferentially binds closer to the residues of the active site when Top1 is free and lies on the DNA groove downstream of the cleavage site in the Top1-DNA complex. Thus, 3 can be considered in further studies for a possible use as an anticancer agent.
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Affiliation(s)
- Mariana S de Camargo
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905, São Carlos, SP, Brazil.
| | - Monize M da Silva
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905, São Carlos, SP, Brazil.
| | - Rodrigo S Correa
- Departamento de Química, ICEB, Universidade Federal de Ouro Preto, CEP 35400-000, Ouro Preto, MG, Brazil
| | - Sara D Vieira
- Dipartimento di Biologia, Università Tor Vergata di Roma, 00133 Rome, Italy
| | - Silvia Castelli
- Dipartimento di Biologia, Università Tor Vergata di Roma, 00133 Rome, Italy
| | - Ilda D'Anessa
- Dipartimento di Biologia, Università Tor Vergata di Roma, 00133 Rome, Italy
| | - Rone De Grandis
- Departamento de Ciências Biológicas, Faculdade de Ciências Farmacêuticas, UNESP, CEP 14800-900, Araraquara, SP, Brazil
| | - Eliana Varanda
- Departamento de Ciências Biológicas, Faculdade de Ciências Farmacêuticas, UNESP, CEP 14800-900, Araraquara, SP, Brazil
| | - Victor M Deflon
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | | | - Alzir A Batista
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905, São Carlos, SP, Brazil.
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30
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Guo P, Paul A, Kumar A, Farahat AA, Kumar D, Wang S, Boykin DW, Wilson WD. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove. Chemistry 2016; 22:15404-15412. [PMID: 27624927 PMCID: PMC5214980 DOI: 10.1002/chem.201603422] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/10/2022]
Abstract
In spite of its importance in cell function, targeting DNA is under-represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G⋅C base pairs (bp) in DNA sequences. To overcome this barrier, an entirely new design concept for modules that can bind to mixed G⋅C and A⋅T sequences of DNA is reported herein. Because of their successes in biological applications, minor-groove-binding heterocyclic cations were selected as the platform for design. Binding to A⋅T sequences requires hydrogen-bond donors whereas recognition of the G-NH2 requires an acceptor. The concept that we report herein uses pre-organized N-methylbenzimidazole (N-MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma hole (positive electrostatic potential) and the electron-donor nitrogen of N-MeBI preorganizes the conformation for accepting an hydrogen bond from G-NH2 . The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N-MeBI-thiophene monomer compounds can strongly and selectively recognize single G⋅C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma-holes, can lead to new approaches for small molecules in biomolecular interactions.
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Affiliation(s)
- Pu Guo
- 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
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dhiraj Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Siming Wang
- 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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31
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Abou-Elkhair RAI, Hassan AEA, Boykin DW, Wilson WD. Lithium Hexamethyldisilazane Transformation of Transiently Protected 4-Aza/Benzimidazole Nitriles to Amidines and their Dimethyl Sulfoxide Mediated Imidazole Ring Formation. Org Lett 2016; 18:4714-7. [PMID: 27607538 DOI: 10.1021/acs.orglett.6b02359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Trimethylsilyl-transient protection successfully allowed the use of lithium hexamethyldisilazane to prepare benzimidazole (BI) and 4-azabenzimidazole (azaBI) amidines from nitriles in 58-88% yields. This strategy offers a much better choice to prepare BI/azaBI amidines than the lengthy, low-yielding Pinner reaction. Synthesis of aza/benzimidazole rings from aromatic diamines and aldehydes was affected in dimethyl sulfoxide in 10-15 min, while known procedures require long time and purification. These methods are important for the BI/azaBI-based drug industry and for developing specific DNA binders for expanded therapeutic applications.
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Affiliation(s)
- Reham A I Abou-Elkhair
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States.,Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Sciences, Zagazig University , Zagazig 44519, Egypt
| | - Abdalla E A Hassan
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Sciences, Zagazig University , Zagazig 44519, Egypt
| | - David W Boykin
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
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32
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Zhou Y, Huang Y, Ma Z, Gong Y, Zhang X, Sun Y, Sun CQ. Water molecular structure-order in the NaX hydration shells(X=F, Cl, Br, I). J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.06.066] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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33
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Maity D, Jiang J, Ehlers M, Wu J, Schmuck C. A FRET-enabled molecular peptide beacon with a significant red shift for the ratiometric detection of nucleic acids. Chem Commun (Camb) 2016; 52:6134-7. [PMID: 27071707 DOI: 10.1039/c6cc02138g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A cationic molecular peptide beacon NAP1 functionalized with a fluorescence resonance energy transfer-pair at its ends allows the ratiometric detection of ds-DNA with a preference for AT rich sequences. NAP1 most likely binds in a folded form into the minor groove of ds-DNA, which results in a remarkable change in its fluorescence properties. As NAP1 exhibits quite low cytotoxicity, it can also be used for imaging of nuclear DNA in cells.
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Affiliation(s)
- Debabrata Maity
- Institute for Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany.
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34
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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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35
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Neidle S. A Personal History of Quadruplex-Small Molecule Targeting. CHEM REC 2015; 15:691-710. [DOI: 10.1002/tcr.201500011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Stephen Neidle
- UCL School of Pharmacy; University College London; 29-39 Brunswick Square London WC1N 1AX UK
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36
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Mo GZ, Wu YC, Hao ZF, Luo QF, Liang XY, Guan LT, Wang ZY. Synthesis and characterization of a novel drug-loaded polymer, poly(lactic acid-co-aminomethyl benzimidazole). Des Monomers Polym 2015. [DOI: 10.1080/15685551.2015.1041085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Guang-Zhen Mo
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, P.R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou 510006, P.R. China
| | - Yan-Cheng Wu
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, P.R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou 510006, P.R. China
| | - Zhi-Feng Hao
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, P.R. China
| | - Qiao-Fang Luo
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, P.R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou 510006, P.R. China
| | - Xin-Yu Liang
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, P.R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou 510006, P.R. China
| | - Li-Tao Guan
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Zhao-Yang Wang
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, P.R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou 510006, P.R. China
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37
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Buceta D, Busto N, Barone G, Leal JM, Domínguez F, Giovanetti LJ, Requejo FG, García B, López-Quintela MA. Ag2and Ag3Clusters: Synthesis, Characterization, and Interaction with DNA. Angew Chem Int Ed Engl 2015; 54:7612-6. [DOI: 10.1002/anie.201502917] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 01/07/2023]
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38
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Buceta D, Busto N, Barone G, Leal JM, Domínguez F, Giovanetti LJ, Requejo FG, García B, López-Quintela MA. Ag2and Ag3Clusters: Synthesis, Characterization, and Interaction with DNA. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Ismail MA, Arafa RK, Youssef MM, El-Sayed WM. Anticancer, antioxidant activities, and DNA affinity of novel monocationic bithiophenes and analogues. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:1659-72. [PMID: 25302019 PMCID: PMC4189708 DOI: 10.2147/dddt.s68016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A series of 15 monocationic bithiophenes and isosteres were prepared and subjected to in vitro antiproliferative screening using the full National Cancer Institute (NCI)-60 cell line panel, representing nine types of cancer. Among the nine types of cancer involved in a five-dose screen, non-small cell lung and breast cancer cell lines were the most responsive to the antiproliferative effect of the tested compounds, especially cell lines A549/ATCC, NCI-H322M, and NCI-H460, whereas compounds 1a, 1c, 1d, and 7 exhibited potent activity, with GI50 values (drug concentration that causes 50% inhibition of cell growth) from less than 10 nM to 102 nM. In addition, compounds 1c and 1d gave GI50 values of 73 nM and 79 nM, respectively, against the MDA-MB-468 breast cancer cell line. Structure-activity relationship findings indicated that the mononitriles were far less active than their corresponding monoamidines and, within the amidines series, the bioisosteric replacement of a thiophene ring by a furan led to a reduction in antiproliferative activity. Also, molecular manipulations, involving substitution on the phenyl ring, or its replacement by a pyridyl, or alteration of the position of the amidine group, led to significant alteration in antiproliferative activity. On the other hand, DNA studies demonstrated that these monoamidine bichalcophenes have promising ability to cleave the genomic DNA. These monoamidines show a wide range of DNA affinities, as judged from their DNA cleavage effect, which are remarkably sensitive to all kinds of structural modifications. Finally, the novel bichalcophenes were tested for their antioxidant property by the ABTS (2,2'-azino- bis(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt) assay, as well as lipid and nitric oxide scavenging techniques, and were found to exhibit good-to-potent antioxidant abilities.
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Affiliation(s)
- Mohamed A Ismail
- Departments of Chemistry and Biological Sciences, College of Science, King Faisal University, Hofuf, Saudi Arabia ; Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Reem K Arafa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Magdy M Youssef
- Departments of Chemistry and Biological Sciences, College of Science, King Faisal University, Hofuf, Saudi Arabia ; Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Wael M El-Sayed
- Departments of Chemistry and Biological Sciences, College of Science, King Faisal University, Hofuf, Saudi Arabia ; Department of Zoology, Faculty of Science, University of Ain Shams, Abbassia, Cairo, Egypt
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40
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Nagle PS, McKeever C, Rodriguez F, Nguyen B, Wilson WD, Rozas I. Unexpected DNA affinity and sequence selectivity through core rigidity in guanidinium-based minor groove binders. J Med Chem 2014; 57:7663-72. [PMID: 25158031 DOI: 10.1021/jm5008006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this paper we report the design and biophysical evaluation of novel rigid-core symmetric and asymmetric dicationic DNA binders containing 9H-fluorene and 9,10-dihydroanthracene cores as well as the synthesis of one of these fluorene derivatives. First, the affinity toward particular DNA sequences of these compounds and flexible core derivatives was evaluated by means of surface plasmon resonance and thermal denaturation experiments finding that the position of the cations significantly influence the binding strength. Then their affinity and mode of binding were further studied by performing circular dichroism and UV studies and the results obtained were rationalized by means of DFT calculations. We found that the fluorene derivatives prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to others, whereas the dihydroanthracene compounds bind via intercalation to all the DNA sequences studied here.
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Affiliation(s)
- Padraic S Nagle
- School of Chemistry, Trinity College Dublin , Dublin 2, Ireland
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41
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O'Sullivan P, Rozas I. Understanding the guanidine-like cationic moiety for optimal binding into the DNA minor groove. ChemMedChem 2014; 9:2065-73. [PMID: 25087855 DOI: 10.1002/cmdc.201402264] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 01/01/2023]
Abstract
Based on our previous positive results with bis-guanidine-like diaromatic compounds as DNA minor groove binders, we propose a new family: bis-2-amino-1,4,5,6-tetrahydropyrimidines. According to calculated parameters, these dicationic systems would have a more suitable size and lipophilicity for binding into the minor groove than previous series. Moreover, their DFT-optimised structures and docking into an AT oligomer model show that they would bind in the minor groove with good strength and without energy penalty. Hence, we prepared compounds 4 a-c and evaluated their binding to ssDNA and poly(dA-dT)2 by thermal denaturation experiments. The results showed that 4 a (CO) and 4 d (NH) were the best DNA binders. Compared to the previous series, 4 a-d are better binders than bis-guanidiniums but poorer than bis-2-aminoimidazolinium derivatives. Moreover, circular dichroism experiments using ssDNA and poly(dA-dT)2 confirmed binding into the minor groove. Based on our computational design as well as biophysical studies, we have been able to determine that the optimal interaction of guanidine-like dications in the minor grove occurs with bis-2-aminoimidazolinium systems.
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Affiliation(s)
- Patrick O'Sullivan
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College, University of Dublin, 152-160 Pearse St., Dublin 2 (Ireland)
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42
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Chai Y, Munde M, Kumar A, Mickelson L, Lin S, Campbell NH, Banerjee M, Akay S, Liu Z, Farahat AA, Nhili R, Depauw S, David-Cordonnier MH, Neidle S, Wilson WD, Boykin DW. Structure-dependent binding of arylimidamides to the DNA minor groove. Chembiochem 2013; 15:68-79. [PMID: 24323836 DOI: 10.1002/cbic.201300622] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Indexed: 12/12/2022]
Abstract
Heterocyclic diamidines are strong DNA minor-groove binders and have excellent antiparasitic activity. To extend the biological activity of these compounds, a series of arylimidamides (AIAs) analogues, which have better uptake properties in Leishmania and Trypanosoma cruizi than diamidines, was prepared. The binding of the AIAs to DNA was investigated by Tm , fluorescence displacement titration, circular dichroism, DNase I footprinting, biosensor surface plasmon resonance, X-ray crystallography and molecular modeling. These compounds form 1:1 complexes with AT sequences in the DNA minor groove, and the binding strength varies with substituent size, charge and polarity. These substituent-dependent structure and properties provide a SAR that can be used to estimate K values for binding to DNA in this series. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for AIAs.
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Affiliation(s)
- Yun Chai
- Department of Chemistry, Georgia State University, 50 Decatur St. SE., Atlanta, GA 30303 (USA)
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43
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Dumat B, Bordeau G, Faurel-Paul E, Mahuteau-Betzer F, Saettel N, Metge G, Fiorini-Debuisschert C, Charra F, Teulade-Fichou MP. DNA Switches on the Two-Photon Efficiency of an Ultrabright Triphenylamine Fluorescent Probe Specific of AT Regions. J Am Chem Soc 2013; 135:12697-706. [DOI: 10.1021/ja404422z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Blaise Dumat
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Guillaume Bordeau
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Elodie Faurel-Paul
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | | | - Nicolas Saettel
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Germain Metge
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
| | | | - Fabrice Charra
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
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44
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Imaizumi Y, Kasahara Y, Fujita H, Kitadume S, Ozaki H, Endoh T, Kuwahara M, Sugimoto N. Efficacy of base-modification on target binding of small molecule DNA aptamers. J Am Chem Soc 2013; 135:9412-9. [PMID: 23734784 DOI: 10.1021/ja4012222] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nucleic acid aptamers are receptors of single-stranded oligonucleotides that specifically bind to their targets. Significant interest is currently focused on development of small molecule aptamers owing to their applications in biosensing, diagnostics, and therapeutics involving low molecular weight biomarkers and drugs. Despite great potential for their diverse applications, relatively few aptamers that bind to small molecules have been reported, and methodologies to enhance and broaden their functions by expanding chemical repertories have barely been examined. Here we describe construction of a modified DNA library that includes (E)-5-(2-(N-(2-(N(6)-adeninyl)ethyl))carbamylvinyl)-uracil bases and discovery of high-affinity camptothecin-binding DNA aptamers using a systematic evolution of ligands by the exponential enrichment method. Our results are the first to demonstrate the superior efficacy of base modification on affinity enhancement and the usefulness of unnatural nucleic acid libraries for development of small molecule aptamers.
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Affiliation(s)
- Yuri Imaizumi
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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45
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El-Sayed WM, Hussin WA, Al-Faiyz YS, Ismail MA. The position of imidazopyridine and metabolic activation are pivotal factors in the antimutagenic activity of novel imidazo[1,2-a]pyridine derivatives. Eur J Pharmacol 2013; 715:212-8. [PMID: 23747653 DOI: 10.1016/j.ejphar.2013.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/13/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The antimutagenic activity of eight novel imidazo[1,2-a]pyridine derivatives (I-VIII) against sodium azide (NaN3) and benzo[a]pyrene (B[a]P) was evaluated using the Salmonella reverse mutation assay. At non-toxic concentrations (12.5-50 µM), imidazopyridines I, II, III, and V with a terminal imidazopyridine group were mutagenic, while derivatives VII and VIII with a central imidazopyridine group were not mutagenic. Compounds IV, VII, and VIII exerted a moderate antimutagenic activity against NaN3 under pre-exposure conditions, and a strong activity (>40%) against B[a]P in the presence of S9 under both pre- and co-exposure conditions and mostly independent on the dose. Imidazopyridines possibly inhibited the microsomal-dependent activation of B[a]P. The demethylated derivative VII was the most active antimutagen. All imidazopyridines had a low to moderate antioxidant activity. The antibacterial activity of imidazopyridines was sporadic and moderate probably due to the failure of bacteria to convert imidazopyridines into active metabolites. The position of imidazopyridine was a pivotal factor in the mutagenic/antimutagenic activity. The strong antimutagenic compounds were dicationic planar compounds with a centered imidazo[1,2-a]pyridine spacer. With LD50 of 60 mg/kg in mice for both derivatives VII and VIII, it is safe to investigate the anticancer activity of these derivatives in animal models.
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Affiliation(s)
- Wael M El-Sayed
- King Faisal University, Faculty of Science, Departments of Biological Sciences and Chemistry, Al-Hufof 31982, Ahsaa, KSA.
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Nanjunda R, Wilson WD. Binding to the DNA minor groove by heterocyclic dications: from AT-specific monomers to GC recognition with dimers. ACTA ACUST UNITED AC 2013; Chapter 8:Unit8.8. [PMID: 23255206 DOI: 10.1002/0471142700.nc0808s51] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, have found extensive uses in biotechnology, and are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences.
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Affiliation(s)
- Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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Wei D, Wilson WD, Neidle S. Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster. J Am Chem Soc 2013; 135:1369-77. [PMID: 23276263 DOI: 10.1021/ja308952y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
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Affiliation(s)
- DengGuo Wei
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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49
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Nhili R, Peixoto P, Depauw S, Flajollet S, Dezitter X, Munde MM, Ismail MA, Kumar A, Farahat AA, Stephens CE, Duterque-Coquillaud M, David Wilson W, Boykin DW, David-Cordonnier MH. Targeting the DNA-binding activity of the human ERG transcription factor using new heterocyclic dithiophene diamidines. Nucleic Acids Res 2013; 41:125-38. [PMID: 23093599 PMCID: PMC3592449 DOI: 10.1093/nar/gks971] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 12/04/2022] Open
Abstract
Direct modulation of gene expression by targeting oncogenic transcription factors is a new area of research for cancer treatment. ERG, an ETS-family transcription factor, is commonly over-expressed or translocated in leukaemia and prostate carcinoma. In this work, we selected the di-(thiophene-phenyl-amidine) compound DB1255 as an ERG/DNA binding inhibitor using a screening test of synthetic inhibitors of the ERG/DNA interaction followed by electrophoretic mobility shift assays (EMSA) validation. Spectrometry, footprint and biosensor-surface plasmon resonance analyses of the DB1255/DNA interaction evidenced sequence selectivity and groove binding as dimer. Additional EMSA evidenced the precise DNA-binding sequence required for optimal DB1255/DNA binding and thus for an efficient ERG/DNA complex inhibition. We further highlighted the structure activity relationships from comparison with derivatives. In cellulo luciferase assay confirmed this modulation both with the constructed optimal sequences and the Osteopontin promoter known to be regulated by ERG and which ERG-binding site was protected from DNaseI digestion on binding of DB1255. These data showed for the first time the ERG/DNA complex modulation, both in vitro and in cells, by a heterocyclic diamidine that specifically targets a portion of the ERG DNA recognition site.
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Affiliation(s)
- Raja Nhili
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Paul Peixoto
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Sabine Depauw
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Sébastien Flajollet
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Xavier Dezitter
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Manoj M. Munde
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Mohamed A. Ismail
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Arvind Kumar
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Abdelbasset A. Farahat
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Chad E. Stephens
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Martine Duterque-Coquillaud
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W. David Wilson
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W. Boykin
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Marie-Hélène David-Cordonnier
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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50
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Wang S, Nanjunda R, Aston K, Bashkin JK, Wilson WD. Correlation of local effects of DNA sequence and position of β-alanine inserts with polyamide-DNA complex binding affinities and kinetics. Biochemistry 2012; 51:9796-806. [PMID: 23167504 DOI: 10.1021/bi301327v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
To improve our understanding of the effects of β-alanine (β) substitution and the number of heterocycles on DNA binding affinity and selectivity, we investigated the interactions of an eight-ring hairpin polyamide (PA) and two β derivatives as well as a six-heterocycle analogue with their cognate DNA sequence, 5'-TGGCTT-3'. Binding selectivity and the effects of β have been investigated with the cognate and five mutant DNAs. A set of powerful and complementary methods have been employed for both energetic and structural evaluations: UV melting, biosensor surface plasmon resonance, isothermal titration calorimetry, circular dichroism, and a DNA ligation ladder global structure assay. The reduced number of heterocycles in the six-ring PA weakens the binding affinity; however, the smaller PA aggregates significantly less than the larger PAs and allows us to obtain the binding thermodynamics. The PA-DNA binding enthalpy is large and negative with a large negative ΔC(p) and is the primary driving component of the Gibbs free energy. The complete SPR binding results clearly show that β substitutions can substantially weaken the binding affinity of hairpin PAs in a position-dependent manner. More importantly, the changes in the binding of PA to the mutant DNAs further confirm the position-dependent effects on the PA-DNA interaction affinity. Comparison of mutant DNA sequences also shows a different effect in recognition of T·A versus A·T base pairs. The effects of DNA mutations on binding of a single PA as well as the effects of the position of β substitution on binding tell a clear and very important story about sequence-dependent binding of PAs to DNA.
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Affiliation(s)
- Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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