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Gaber AA, Sobhy M, Turky A, Eldehna WM, El-Sebaey SA, El-Metwally SA, El-Naggar AM, Ibrahim IM, Elkaeed EB, Metwaly AM, Eissa IH. New [1,2,4]triazolo[4,3-c]quinazolines as intercalative Topo II inhibitors: Design, synthesis, biological evaluation, and in silico studies. PLoS One 2023; 18:e0274081. [PMID: 36716311 PMCID: PMC9886266 DOI: 10.1371/journal.pone.0274081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023] Open
Abstract
Fifteen quinazoline derivatives were designed and synthesized as DNA intercalators. The cytotoxicity of the designed members was assessed against HCT-116 and HepG2 cancer cell lines. In addition, the topoisomerase II (Topo II) inhibitory effect was assessed. Compound 16 was the most cytotoxic and Topo II inhibitor with low cytotoxicity against Vero cells. Compounds 16, 17, and 18 showed significant DNA binding affinities. Compound 16 showed Topo II catalytic inhibitory effect at a concentration of 10 μM. Further mechanistic investigations revealed the capability of compound 16 to induce apoptosis in HCT-116 cells and arrest the growth at the S and G2/M phases. Also, compound 16 showed a significant increase in the level of BAX (2.18-fold) and a marked decrease in the level of Bcl-2 (1.9-fold) compared to the control cells. In silico studies revealed the ability of the synthesized members to bind to the DNA-Topo II complex.
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Affiliation(s)
- Ahmed A. Gaber
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Mohamed Sobhy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Abdallah Turky
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Samiha A. El-Sebaey
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Souad A. El-Metwally
- Department of Basic Science, Higher Technological institute, 10th of Ramadan City, Egypt
| | - Abeer M. El-Naggar
- Department of Chemistry, Faculty of Science, Ain Shams University, Abassia, Cairo, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Riyadh, Saudi Arabia
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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2
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Newton MD, Fairbanks SD, Thomas JA, Rueda DS. A Minimal Load‐and‐Lock Ru
II
Luminescent DNA Probe. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew D. Newton
- Department of Infectious Disease Faculty of Medicine Imperial College London London W12 0NN UK
- Single Molecule Imaging Group, MRC- London Institute of Medical Sciences London W12 0NN UK
| | - Simon D. Fairbanks
- Department of Chemistry University of Sheffield Sheffield S3 7HF UK
- Department of Molecular Biology and Biotechnology University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Jim A. Thomas
- Department of Chemistry University of Sheffield Sheffield S3 7HF UK
| | - David S. Rueda
- Department of Infectious Disease Faculty of Medicine Imperial College London London W12 0NN UK
- Single Molecule Imaging Group, MRC- London Institute of Medical Sciences London W12 0NN UK
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3
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Newton MD, Fairbanks SD, Thomas JA, Rueda DS. A Minimal Load-and-Lock Ru II Luminescent DNA Probe. Angew Chem Int Ed Engl 2021; 60:20952-20959. [PMID: 34378843 PMCID: PMC8518596 DOI: 10.1002/anie.202108077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/26/2022]
Abstract
Threading intercalators bind DNA with high affinities. Here, we describe single-molecule studies on a cell-permeant luminescent dinuclear ruthenium(II) complex that has been previously shown to thread only into short, unstable duplex structures. Using optical tweezers and confocal microscopy, we show that this complex threads and locks into force-extended duplex DNA in a two-step mechanism. Detailed kinetic studies reveal that an individual stereoisomer of the complex exhibits the highest binding affinity reported for such a mono-intercalator. This stereoisomer better preserves the biophysical properties of DNA than the widely used SYTOX Orange. Interestingly, threading into torsionally constrained DNA decreases dramatically, but is rescued on negatively supercoiled DNA. Given the "light-switch" properties of this complex on binding DNA, it can be readily used as a long-lived luminescent label for duplex or negatively supercoiled DNA through a unique "load-and-lock" protocol.
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Affiliation(s)
- Matthew D. Newton
- Department of Infectious DiseaseFaculty of MedicineImperial College LondonLondonW12 0NNUK
- Single Molecule Imaging Group, MRC-London Institute of Medical SciencesLondonW12 0NNUK
| | - Simon D. Fairbanks
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Jim A. Thomas
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
| | - David S. Rueda
- Department of Infectious DiseaseFaculty of MedicineImperial College LondonLondonW12 0NNUK
- Single Molecule Imaging Group, MRC-London Institute of Medical SciencesLondonW12 0NNUK
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4
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Abstract
The behavior of benzoic acid in polyethylene inspired me to reflect on why water is a unique molecule that all living organisms depend upon. From properties of DNA in aqueous solution a seemingly counter-intuitive conjecture emerges: water is needed for the creation of certain dry low-dielectric nm-size environments where hydrogen bonding exerts strong recognition power. Such environments seem to be functionally crucial, and their interactions with other hydrophobic environments, or with hydrophobic agents that modulate the chemical potential of water, can cause structural transformations via ‘hydrophobic catalysis’. Possibly combined with an excluded volume osmosis effect (EVO), hydrophobic catalysis may have important biological roles, e.g., in genetic recombination. Hydrophobic agents are found to strongly accelerate spontaneous DNA strand exchange as well as certain other DNA rearrangement reactions. It is hypothesized that hydrophobic catalysis be involved in gene recognition and gene recombination mediated by bacterial RecA (one of the oldest proteins we know of) as well as in sexual recombination in higher organisms, by Rad51. Hydrophobically catalyzed unstacking fluctuations of DNA bases can favor elongated conformations, such as the recently proposed [Formula: see text]-DNA, with potential regulatory roles. That living cells can survive as dormant spores, with very low water content and in principle as such travel far in space is reflected upon: a random walk model with solar photon pressure as driving force indicates our life on earth could not have originated outside our galaxy but possibly from many solar systems within it — at some place, though, where there was plenty of liquid water.
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Affiliation(s)
- Bengt Nordén
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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5
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences; Academia Sinica; 128 Sec. 2, Academia Rd. Nankang Taipei Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center; College of Science; National Taiwan University; No.1, Sec. 4, Roosevelt Rd. Taipei Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology; Chi Mei Medical Center; No.901, Zhonghua Rd. Tainan Taiwan
| | - Stephen Neidle
- The School of Pharmacy; University College London; London WC1N 1AX UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
- Institute of Biotechnology; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
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6
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Keane PM, Hall JP, Poynton FE, Poulsen BC, Gurung SP, Clark IP, Sazanovich IV, Towrie M, Gunnlaugsson T, Quinn SJ, Cardin CJ, Kelly JM. Inosine Can Increase DNA′s Susceptibility to Photo‐oxidation by a RuIIComplex due to Structural Change in the Minor Groove. Chemistry 2017; 23:10344-10351. [DOI: 10.1002/chem.201701447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Páraic M. Keane
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
| | - James P. Hall
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
- Diamond Light Source, Harwell Science and Innovation CampusDidcot Oxfordshire OX11 0DE UK
| | - Fergus E. Poynton
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
- Trinity Biomedical Sciences Institute Pearse St. Dublin 2 Ireland
| | - Bjørn C. Poulsen
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
- Trinity Biomedical Sciences Institute Pearse St. Dublin 2 Ireland
| | - Sarah P. Gurung
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
- Diamond Light Source, Harwell Science and Innovation CampusDidcot Oxfordshire OX11 0DE UK
| | - Ian P. Clark
- Central Laser FacilityResearch Complex at Harwell, STFC Rutherford Appleton LaboratoriesDidcot Oxfordshire OX11 0QX UK
| | - Igor V. Sazanovich
- Central Laser FacilityResearch Complex at Harwell, STFC Rutherford Appleton LaboratoriesDidcot Oxfordshire OX11 0QX UK
| | - Michael Towrie
- Central Laser FacilityResearch Complex at Harwell, STFC Rutherford Appleton LaboratoriesDidcot Oxfordshire OX11 0QX UK
| | - Thorfinnur Gunnlaugsson
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
- Trinity Biomedical Sciences Institute Pearse St. Dublin 2 Ireland
| | - Susan J. Quinn
- School of ChemistryUniversity College Dublin, Belfield Dublin 4 Ireland
| | - Christine J. Cardin
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
| | - John M. Kelly
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
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7
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017; 56:8761-8765. [PMID: 28544401 DOI: 10.1002/anie.201703989] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 01/23/2023]
Abstract
Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII (Chro)2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.
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Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Rd. Nankang, Taipei, Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, College of Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology, Chi Mei Medical Center, No.901, Zhonghua Rd., Tainan, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
- Institute of Biotechnology, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
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8
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Saeed HK, Saeed IQ, Buurma NJ, Thomas JA. The Structure of Linkers Affects the DNA Binding Properties of Tethered Dinuclear Ruthenium(II) Metallo-Intercalators. Chemistry 2017; 23:5467-5477. [PMID: 28072487 DOI: 10.1002/chem.201605750] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Indexed: 12/12/2022]
Abstract
With the long-term aim of enhancing the binding properties of dinuclear RuII -based DNA light-switch complexes, a series of eight structurally related mono- and dinuclear systems are reported in which the linker of the bridging ligand has been modulated. These tethered systems have been designed to explore issues of steric demand at the binding site and the thermodynamic cost of entropy loss upon binding. Detailed spectroscopic and isothermal titration calorimetry (ITC) studies on the new complexes reveal that one of the linkers produces a dinuclear system that binds to duplex DNA with an affinity (Kb >107 m-1 ) that is higher than its corresponding monometallic complex and is the highest affinity for a non-threading bis-intercalating metal complex. These studies confirm that the tether has a major effect on the binding properties of dinuclear complexes containing intercalating units and establishes key design rules for the construction of dinuclear complexes with enhanced DNA binding characteristics.
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Affiliation(s)
- Hiwa K Saeed
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Ibrahim Q Saeed
- Physical Organic Chemistry Centre, School of Chemistry, Cardiff University, Main Building Park Place, Cardiff, CF10 3AT, UK
| | - Niklaas J Buurma
- Physical Organic Chemistry Centre, School of Chemistry, Cardiff University, Main Building Park Place, Cardiff, CF10 3AT, UK
| | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
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