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Aggarwal R, Kumar P, Hooda M, Kumar S. Serendipitous N, S-difunctionalization of triazoles with trifluoromethyl-β-diketones: access to regioisomeric 1-trifluoroacetyl-3-aryl-5-(2-oxo-2-arylethylthio)-1,2,4-triazoles as DNA-groove binders. RSC Adv 2024; 14:6738-6751. [PMID: 38405072 PMCID: PMC10884789 DOI: 10.1039/d4ra00083h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024] Open
Abstract
In the present research work, a serendipitous regioselective synthesis of DNA targeting agents, 1-trifluoroacetyl-3-aryl-5-(2-oxo-2-arylethylthio)-1,2,4-triazoles, has been achieved through the one-pot cascade reaction of 3-mercapto[1,2,4]triazoles with trifluoromethyl-β-diktetones in presence of NBS instead of the cyclized thiazolo[3,2-b][1,2,4]triazole. The present protocol offered a unique approach for functionalizing both N-acylation and S-alkylation in a concerted fashion. The structures of the regioisomeric products were thoroughly characterized by heteronuclear 2D NMR experiments. Facile scalability and excellent atom economy through easily available starting reactants are the notable features of the present sustainable protocol. Targeting tumor cell DNA with minor groove-binding small molecules has proven highly effective in the recent past, drawing significant attention for combating tumor-related afflictions. In this context, the synthesized analogs were primarily screened for their ability to bind with the DNA duplex d(CGCGAATTCGCG)2 using molecular modeling tools. Additionally, the most promising compound 14m was deployed as a probe for DNA sensing and interaction mechanisms with calf thymus (ct)DNA through various spectral techniques at a physiologic temperature of 37 °C. It has been found that the compound demonstrated a strong binding affinity (Kb = 1 × 105 M-1) with double-helical DNA, particularly within the minor groove, resulting in the formation of a stable complex through static quenching (Kq = 5.86 ± 0.11 × 1012 M-1 s-1). The fluorescent displacement assay confirmed that the quencher binds to the minor groove of ctDNA, further supported by circular dichroism and viscosity studies.
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Affiliation(s)
- Ranjana Aggarwal
- Department of Chemistry, Kurukshetra University Kurukshetra-136119 Haryana India
- Council of Scientific and Industrial Research-National Institute of Science Communication and Policy Research New Delhi 110012 India +91-9896740740
| | - Prince Kumar
- Department of Chemistry, Kurukshetra University Kurukshetra-136119 Haryana India
| | - Mona Hooda
- Department of Chemistry, Gurugram University Gurugram-122003 Haryana India
| | - Suresh Kumar
- Department of Chemistry, Kurukshetra University Kurukshetra-136119 Haryana India
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Shahabadi N, Ghaffari L, Mardani Z, Shiri F. Interaction studies of water-soluble Zn(II) complex with calf thymus DNA using biophysical and molecular docking methods". NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:493-516. [PMID: 37963106 DOI: 10.1080/15257770.2023.2280001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
The binding between a fluorescent water-soluble Zn(II) complex of {2-[N-(2-hydroxyethylammonioethyl) imino methyl] phenol} and calf thymus DNA (ct-DNA) was investigated using spectroscopic techniques. The complex was prepared and identified by FT-IR, and 1H NMR spectroscopies. The significant changes in the absorption and the circular dichroism spectra of ct-DNA in the presence of the Zn(II) complex implied the interaction between the Zn(II) complex and ct-DNA. Upon addition of ct-DNA, the fluorescence emission intensity of the Zn(II) complex was increased and indicated the interaction between the Zn(II) complex and ct-DNA was occurred. The binding constant values (Kb) resulted from fluorescence spectra clearly showed the Zn(II) complex affinity to ct-DNA. The fluorescence studies also approved the static enhancement mechanism in the Zn(II) complex-DNA complexation process. The thermodynamic profile exhibited the exothermic and spontaneous formation of ct-DNA-Zn(II) complex system via hydrogen bonds and van der Waals forces. The competitive fluorescence investigation by methylene blue (MB), and Hoechst 33258 demonstrated that the Zn(II) complex could replace the DNA-bound Hoechst and bind to the minor groove binding site in ct-DNA. The viscosity changes were negligible, representing the Zn(II) complex binding to DNA via the groove binding mode. Molecular docking simulation affirmed that the Zn(II) complex is located in the minor groove of ct-DNA near the DG12, DA17, DA18, and DG16 nucleobases.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Lida Ghaffari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Aggarwal R, Jain N, Dubey GP, Singh S, Chandra R. Visible Light-Prompted Regioselective Synthesis of Novel 5-Aroyl/hetaroyl-2',4-dimethyl-2,4'-bithiazoles as DNA- and BSA-Targeting Agents. Biomacromolecules 2023; 24:4798-4818. [PMID: 37729507 DOI: 10.1021/acs.biomac.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Organic transformations mediated by visible light have gained popularity in recent years as they are green, renewable, inexpensive, and clean and yield excellent products. The present study describes cyclo-condensation of 2-methylthiazole-4-carbothioamide with differently substituted α-bromo-1,3-diketones achieved by utilizing a white light-emitting diode (LED) (9W) to accomplish the regioselective synthesis of novel 5-aroyl/hetaroyl-2',4-dimethyl-2,4'-bithiazole derivatives as DNA/bovine serum albumin (BSA)-targeting agents. The structure characterization of the exact regioisomer was achieved unequivocally by heteronuclear two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy [1H-13C] HMBC; [1H-13C] HMQC; and [1H-15N] HMBC. In silico toxicity studies indicated that the synthesized compounds exhibit low toxicity risks and adhere to the rules of oral bioavailability without any exception. Computational molecular modeling of the bithiazole derivatives with the dodecamer sequence of the DNA duplex and BSA identified 5-(4-chlorobenzoyl)-2',4-dimethyl-2,4'-bithiazole 7g as the most suitable derivative that can interact effectively with these biomolecules. Furthermore, theoretical results concurred with the ex vivo binding mode of the 7g with calf thymus DNA (ct-DNA) and BSA through a variety of spectroscopic techniques, viz., ultraviolet-visible (UV-visible), circular dichroism (CD), steady-state fluorescence, and competitive displacement assay, along with viscosity measurements.
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Affiliation(s)
- Ranjana Aggarwal
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, Haryana, India
- CSIR-National Institute of Science Communication and Policy Research, New Delhi 110012, India
| | - Naman Jain
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Gyan Prakash Dubey
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Snigdha Singh
- Department of Chemistry, University of Delhi, New Delhi 110007, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, New Delhi 110007, India
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Singh Chauhan S, Mohan Murari B. Fluorescence Spectroscopic Studies to Evaluate Binding Interaction between Hoechst 33258 and Bilirubin. J Fluoresc 2023:10.1007/s10895-023-03440-8. [PMID: 37728846 DOI: 10.1007/s10895-023-03440-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
A detailed spectroscopic study (fluorescence, absorption, and lifetime) was conducted to gain insight into the nature of the binding interaction between fluorophore Hoechst33258 (H258) and jaundice marker Bilirubin (Br). The fluorescence emission of the H258 (Ex/Em = 340-502nm) showed a conc. dependent quenching in the presence of Br (1.25[Formula: see text]M to 10[Formula: see text]M). The Stern-Volmer constant demonstrated an upward curve depicting the occurrence of both static and dynamic quenching with an acquired value of K[Formula: see text] = 3.1x 10[Formula: see text] M[Formula: see text] and biomolecular quenching rate constant K[Formula: see text] = 8.6 x 10[Formula: see text] M[Formula: see text]S[Formula: see text]. The static quenching was evaluated using the sphere of action model and a sphere radius of 0.3nm indicated the presence of a static component in the quenching. The FRET analysis with overlap integral (J) = 1.4x10[Formula: see text] M[Formula: see text]cm[Formula: see text]nm[Formula: see text] and Foster Radius(R[Formula: see text]) = 26.82 Å with 59% efficiency suggested occurrence of dynamic quenching. Further studies with the time-resolved fluorescence also indicated the presence of dynamic quenching. The lifetime values of H258 reduced from 3.9ns to 0.5ns. Molecular docking studies further support both static and dynamic components in quenching. A non-covalent interaction of H258 with Br in the presence of HSA is predominantly characterized by H-bonding with residues Lys, Asn, Glu, Gln, and Br. The H258 and Br interaction was within the distance of 3.04 Å, which is in coherence with the sphere of action model (0.3nm) and Van-der-Waals along with hydrophobic interactions, which suggested both static and dynamic quenching. Thus, H258 can serve as an efficient fluorophore to monitor binding interactions and can be further exploited as a suitable probe for investigating conformational changes and detection of Br in subsequent studies.
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Affiliation(s)
- Srishti Singh Chauhan
- Department of Sensor and Biomedical Technology, School of Electronics Engineering, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Bhaskar Mohan Murari
- Department of Sensor and Biomedical Technology, School of Electronics Engineering, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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Shahabadi N, Zendehcheshm S, Khademi F. Exploring the ct-DNA and plasmid DNA binding affinity of the biogenic synthesized Chloroxine-conjugated silver nanoflowers: Spectroscopic and gel electrophoresis methods. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mallappa M, Savanur MA, Gowda BG, Reddy MBM, Mulla SI. Unravelling the Molecular Interaction of Pentoxifylline with Calf Thymus DNA: A Multitechnique Approach. ChemistrySelect 2022. [DOI: 10.1002/slct.202103781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- M. Mallappa
- Department of Chemistry Maharani's Science College for Women Bangalore 560 001 India
- School of Chemical Science Reva University Bangalore 560 063 India
| | - Mohammed Azharuddin Savanur
- PG Department of Biochemistry Karnatak University Dharwad 580 003 India
- Department of Biochemistry Indian Institute of Science Bangalore 560 012 India
| | - Babu G. Gowda
- Department of Chemistry Maharani's Science College for Women Bangalore 560 001 India
| | | | - Sikandar I Mulla
- Department of Biochemistry School of Applied Sciences REVA University Bangalore 560 064 India
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Binding of α-lipoic acid to human serum albumin: spectroscopic and molecular modeling studies. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02858-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abbas S, Rashid F, Ulker E, Zaib S, Ayub K, Ullah S, Nadeem MA, Yousuf S, Ludwig R, Ali S, Iqbal J. Anticancer evaluation of a manganese complex on HeLa and MCF-7 cancer cells: design, deterministic solvothermal synthesis approach, Hirshfeld analysis, DNA binding, intracellular reactive oxygen species production, electrochemical characterization and density functional theory. J Biomol Struct Dyn 2020; 39:1068-1081. [DOI: 10.1080/07391102.2020.1726818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Saghir Abbas
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
- Department of Chemistry, Quaid-I-Azam University Islamabad, Islamabad, Pakistan
| | - Faisal Rashid
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Emine Ulker
- Department of Chemistry, Faculty of Arts & Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Sumera Zaib
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad, Pakistan
| | - Sana Ullah
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | | | - Sammer Yousuf
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ralf Ludwig
- Leibniz-Institut für Katalyse e. V. an der Universität Rostock, Rostock, Germany
| | - Saqib Ali
- Department of Chemistry, Quaid-I-Azam University Islamabad, Islamabad, Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
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