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Luikham S, Yanthan S, Bhattacharyya J. Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs. Sci Rep 2023; 13:15487. [PMID: 37726357 PMCID: PMC10509242 DOI: 10.1038/s41598-023-40713-5] [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: 02/01/2023] [Accepted: 08/16/2023] [Indexed: 09/21/2023] Open
Abstract
DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.
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Affiliation(s)
- Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, 797103, India
| | - Senchumbeni Yanthan
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, 797103, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, 797103, India.
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Halder S, Aggrawal R, Aswal VK, Ray D, Saha SK. Study of refolding of a denatured protein and microenvironment probed through FRET to a twisted intramolecular charge transfer fluorescent biosensor molecule. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114532] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Paul P, Karar M, Alam MN, Dutta D, Majumdar T, Mallick A. Circumstantial Overdose Management of an Efficient Cancer Cell Photosensitizer with Preclinical Evidence: A Biophysical Study. ACS APPLIED BIO MATERIALS 2020; 3:8049-8060. [PMID: 35019544 DOI: 10.1021/acsabm.0c01121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this article, pharmacological management of circumstantial overdose of an anticancer drug, Harmine (HM), under in vitro and in vivo conditions is described and further validated by employing in silico methods. HM, an efficient cancer cell photosensitizer, interacts extensively with nontoxic β-cyclodextrin (β-CD). Steady-state fluorescence studies and molecular docking analysis established differential nature of molecular inclusion depending on the relative concentrations of β-CD. Presently, β-CD is commonly used as a standard drug-delivery vehicle but its application for controlled drug withdrawal is rarely explored. Flow cytometric results and in vivo investigations on a zebrafish model showed that conditional overdose of preadministered drug molecules can be efficiently removed by encapsulating successfully within nontoxic β-CDs, albeit by controlled application of the same. This is an approach to manage the cytotoxicity of a drug in a safe way that is already administered. We believe that this β-CD-mediated withdrawal of drugs may find possible applications in controlled capturing of excess or unused drug inside living systems and reducing the unwanted toxicity associated with chemotherapeutics.
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Affiliation(s)
- Provakar Paul
- Department of Chemistry, University of Kalyani, Nadia, Kalyani, West Bengal 741235, India
| | - Monaj Karar
- Department of Chemistry, University of Kalyani, Nadia, Kalyani, West Bengal 741235, India
| | - Md Nur Alam
- Department of Life Sciences, Presidency University, Kolkata 700073 West Bengal, India
| | - Debanjan Dutta
- Department of MRDG, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Tapas Majumdar
- Department of Chemistry, University of Kalyani, Nadia, Kalyani, West Bengal 741235, India
| | - Arabinda Mallick
- Department of Chemistry, Kazi Nazrul University, Asansol, West Bengal 713340, India
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Interaction of an anti-cancer photosensitizer with a genomic DNA: From base pair specificity and thermodynamic landscape to tuning the rate of detergent-sequestered dissociation. J Colloid Interface Sci 2016; 470:211-220. [PMID: 26945117 DOI: 10.1016/j.jcis.2016.02.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/23/2022]
Abstract
A detailed characterization of the binding interaction of a potent cancer cell photosensitizer, norharmane (NHM) with a genomic DNA (herring sperm; hsDNA) is undertaken with particular emphasis on deciphering the strength, mode, dynamics, energetics and kinetics of binding. A major focus of the study underlies a successful exploration of the concept of detergent-sequestered dissociation of drug from the drug-DNA complex. Biophysical techniques such as absorption, steady-state and time-resolved fluorescence spectroscopy, circular dichroism, DNA helix melting, stopped-flow fluorescence kinetics and calorimetry have been used. A primarily intercalative mode of binding of NHM with DNA is shown. However, the overall interaction is governed by more than one type of binding forces. We demonstrate that the essential prerequisite of a slower dissociation rate of drug from DNA helix is achieved by tenable choice surfactants. Our results also highlight an effective tunability of the rate of dissociation of the DNA-intercalated drug via detergent-sequestration. A detailed isothermal titration calorimetric study unveils the key role of hydrophobic force underlying NHM-hsDNA association. This is further substantiated by the enthalpy-entropy compensation behavior. The major entropic contribution in detergent-induced dissociation of NHM from NHM-hsDNA complex is also demonstrated. Our results present not only a comprehensive structural and thermodynamic profile, base pair specificity, association kinetics for binding of NHM with DNA but also explore the thermodynamic and kinetic aspects of dissociation of bound drug. Characterization and tuning of the essential prerequisites for a drug to be efficient in anti-cancer functionality bear direct and widespread significance in contemporary global research.
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Kumar H, Chattopadhyay A, Prasath R, Devaraji V, Joshi R, Bhavana P, Saini P, Ghosh SK. Design, Synthesis, Physicochemical Studies, Solvation, and DNA Damage of Quinoline-Appended Chalcone Derivative: Comprehensive Spectroscopic Approach toward Drug Discovery. J Phys Chem B 2014; 118:7257-66. [DOI: 10.1021/jp5025262] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Himank Kumar
- Department
of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Anjan Chattopadhyay
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - R. Prasath
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Vinod Devaraji
- Department
of Pharmaceutical Chemistry, College of Pharmacy, Madras Medical College, Chennai 600003, India
| | - Ritika Joshi
- Department
of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - P. Bhavana
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Praveen Saini
- Department
of Chemistry, BITS-Pilani, K. K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Sujit Kumar Ghosh
- Department
of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
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Kondo M, Li X, Maroncelli M. Characterization of trans-2-[4-[(Dimethylamino)styryl]benzothiazole as an Ultrafast Isomerization Probe and a Modifed Kramers Theory Analysis. J Phys Chem B 2013; 117:12224-33. [DOI: 10.1021/jp407319f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Minako Kondo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiang Li
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mark Maroncelli
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Formation of extended probe–cyclodextrin nanotubular supra structures: Endogenous surfactants triggered on-demand release. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.06.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Atabekyan LS, Vedernikov AI, Avakyan VG, Lobova NA, Gromov SP, Chibisov AK. Photoprocesses in styryl dyes and their pseudorotaxane complexes with cucurbit[7]uril. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2012.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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