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Parvin SI, Mandal MK, Gopi P, Singh S, Khan MR, Pandya P, Islam MM, Gazi HAR. A comparative study on DNA and protein binding properties of thymol and thymoquinone. J Biomol Struct Dyn 2023; 41:10944-10956. [PMID: 36841618 DOI: 10.1080/07391102.2023.2180665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 12/10/2022] [Indexed: 02/27/2023]
Abstract
Two phytochemicals, thymol and thymoquinone obtained from thymes (Thymus vulgaris L., Lamiaceae etc.) and Nagila Sativa seed, respectively. Both the phytochemicals show several biochemical activities like anticancer, antimicrobial etc. In this paper, we studied the affinities of thymol and thymoquinone towards calf thymus DNA (CT-DNA) and protein (bovine serum albumin). Spectroscopic and molecular modelling studies revealed that both compounds have a high affinity toward both the receptors; DNA and protein. Both phytochemicals binds to the minor grooves of DNA and suitable pockets of protein. Several free energy function and hydrogen bonding play significant role during the binding phenomenon.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida, India
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida, India
| | | | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida, India
| | - Md Maidul Islam
- Department of Chemistry, Aliah University, New Town, Kolkata, India
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2
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Yaneva Z, Ivanova D, Nikolova N, Toneva M. Organic dyes in contemporary medicinal chemistry and biomedicine. I. From the chromophore to the bioimaging/bioassay agent. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2039077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Zvezdelina Yaneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Donika Ivanova
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Nevena Nikolova
- Ecology Unit, Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Monika Toneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
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Mohammad M, Saha I, Pal K, Karmakar P, Pandya P, Gazi HAR, Islam MM. A comparison on the biochemical activities of Fluorescein disodium, Rose Bengal and Rhodamine 101 in the light of DNA binding, antimicrobial and cytotoxic study. J Biomol Struct Dyn 2022; 40:9848-9859. [PMID: 34121614 DOI: 10.1080/07391102.2021.1936180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biochemical activities of Fluorescein, Rose Bengal and Rhodamine 101 were studied by DNA binding, antibacterial and cytotoxic studies. DNA binding studies were done using spectroscopic, thermodynamic and molecular modeling techniques. Antibacterial activities were investigated against a gram-negative bacteria Escherichia coli and a gram-positive bacteria Staphylococcus aureus. Cytotoxic activities were studied against Wi-38 cell line. We observed these dyes bound to minor groove of DNA and structural diversity of dyes affect the phenomenon. No significant antibacterial and cytotoxic activities of these dyes were found in our observations.
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Affiliation(s)
- Mukti Mohammad
- Department of Chemistry, Aliah University, Kolkata, India
| | - Ishita Saha
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Kunal Pal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, India
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4
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Hybrid perylene-cored poly(amidoamine) dendrimer with coumarin and calcozine red 6G end groups: From photophysical properties to cell imaging. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Rahaman SK, Mohammad M, Laskar RA, Siddiqui MR, Wabaidur SM, Islam MA, Alam SM, Ahmed F, Islam MM, Mir MH. A muconate bridged bipyridyl appended binuclear Cu(II) complex reveals dissimilar affinities to DNA and BSA protein. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Cytotoxic and genotoxic evaluation of dipyridamole and its alternative therapeutic potential in cancer therapy: an in vitro and in vivo approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mohammad M, Al Rasid Gazi H, Pandav K, Pandya P, Islam MM. Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies. ACS OMEGA 2021; 6:2613-2625. [PMID: 33553879 PMCID: PMC7859944 DOI: 10.1021/acsomega.0c04775] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/04/2021] [Indexed: 05/31/2023]
Abstract
Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.
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Affiliation(s)
- Mukti Mohammad
- Department
of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, West Bengal 700 160, India
| | - Harun Al Rasid Gazi
- Department
of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, West Bengal 700 160, India
| | - Kumud Pandav
- Department
of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee 247667, India
| | - Prateek Pandya
- Amity
Institute of Forensic Sciences, Amity University, Noida 201313, Uttar Pradesh, India
| | - Md. Maidul Islam
- Department
of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, West Bengal 700 160, India
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Pontillo ARN, Konstanteli E, Bairaktari MM, Detsi A. Encapsulation of the Natural Product Tyrosol in Carbohydrate Nanosystems and Study of Their Binding with ctDNA. Polymers (Basel) 2020; 13:polym13010087. [PMID: 33379388 PMCID: PMC7794917 DOI: 10.3390/polym13010087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 11/16/2022] Open
Abstract
Tyrosol, a natural product present in olive oil and white wine, possesses a wide range of bioactivity. The aim of this study was to optimize the preparation of nanosystems encapsulating tyrosol in carbohydrate matrices and the investigation of their ability to bind with DNA. The first encapsulation matrix of choice was chitosan using the ionic gelation method. The second matrix was β-cyclodextrin (βCD) using the kneading method. Coating of the tyrosol-βCD ICs with chitosan resulted in a third nanosystem with very interesting properties. Optimal preparation parameters of each nanosystem were obtained through two three-factor, three-level Box-Behnken experimental designs and statistical analysis of the results. Thereafter, the nanoparticles were evaluated for their physical and thermal characteristics using several techniques (DLS, NMR, FT-IR, DSC, TGA). The study was completed with the investigation of the impact of the encapsulation on the ability of tyrosol to bind to calf thymus DNA. The results revealed that tyrosol and all the studied systems bind to the minor groove of ctDNA. Tyrosol interacts with ctDNA via hydrogen bond formation, as predicted via molecular modeling studies and corroborated by the experiments. The tyrosol-chitosan nanosystem does not show any binding to ctDNA whereas the βCD inclusion complex shows analogous interaction with that of free tyrosol.
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Affiliation(s)
- Antonella Rozaria Nefeli Pontillo
- Laboratory of Organic Chemistry, Department of Chemical Sciences, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Greece; (A.R.N.P.); (E.K.); (M.M.B.)
| | - Evangelia Konstanteli
- Laboratory of Organic Chemistry, Department of Chemical Sciences, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Greece; (A.R.N.P.); (E.K.); (M.M.B.)
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Maria M. Bairaktari
- Laboratory of Organic Chemistry, Department of Chemical Sciences, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Greece; (A.R.N.P.); (E.K.); (M.M.B.)
| | - Anastasia Detsi
- Laboratory of Organic Chemistry, Department of Chemical Sciences, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Greece; (A.R.N.P.); (E.K.); (M.M.B.)
- Correspondence:
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Akhtaruzzaman, Khan S, Alothman AA, Dutta B, Mohammad Wabaidur S, Mafiz Alam S, Maidul Islam M, Hedayetullah Mir M. Synthesis, crystal structure and DNA binding of a new Ni(II) coordination compound based on 4-(1-naphthylvinyl)pyridine ligand. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Manicardi A, Cadoni E, Madder A. Visible-light triggered templated ligation on surface using furan-modified PNAs. Chem Sci 2020; 11:11729-11739. [PMID: 34094412 PMCID: PMC8162948 DOI: 10.1039/d0sc04875e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.
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Affiliation(s)
- Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
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Khan S, Alothman ZA, Mohammad M, Islam MS, Slawin A, Wabaidur SM, Islam MM, Mir MH. Synthesis and characterization of a hydrogen bonded metal-organic cocrystal: Exploration of its DNA binding study. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Khan S, Ahmad R, Naseem I. Elucidating the interaction of aminophylline with calf thymus DNA using multispectroscopic and molecular docking approach. J Biomol Struct Dyn 2020; 39:970-976. [PMID: 31994973 DOI: 10.1080/07391102.2020.1722240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aminophylline (Am) is a methylxanthine compound clinically applied for chronic lung diseases like asthma, bronchitis or emphysema. Chemically, it comprises theophylline and ethylenediamine in a ratio 2:1. For the widening of the therapeutic window of any class of drug or for the designing of the newer therapeutic compound, an insight into the binding mechanics of available drugs with DNA is quite imperative. In view of that, here in this study we have investigated binding mechanics of aminophylline molecule with calf thymus DNA (Ct-DNA) using various spectroscopic techniques as well as molecular docking approach. Spectral analysis employing UV-visible and fluorescence approach confirmed the formation of aminophylline-Ct-DNA complex. The binding constant was calculated as 3.5 × 104 M-1 with 0.90 as the value of binding site suggestive of minor groove binding mode of aminophylline. The groove binding mode was further confirmed through spectrofluorimetric experiments like competitive displacement assay employing ethidium bromide, hoechst and rhodamine 6 G dyes as well as iodide quenching studies. The circular dichroic spectral evaluation and molecular docking study finally validated the minor groove binding mode of aminophylline with binding energy calculated as -4.5 Kcal/mol.
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Affiliation(s)
- Saniyya Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Rizwan Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Imrana Naseem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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