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Durga Priyadharshini R, Jeyashree R, Preethi R, Vennila KN, Elango KP. Intercalation of anticancer drug Palbociclib with calf-thymus DNA: new insights from molecular spectroscopic, molecular dynamic simulations and cleavage studies. J Biomol Struct Dyn 2024; 42:1932-1939. [PMID: 37184154 DOI: 10.1080/07391102.2023.2212787] [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: 12/19/2022] [Accepted: 04/08/2023] [Indexed: 05/16/2023]
Abstract
The interaction between the anti-cancer drug Palbociclib (PAL) and calf-thymus DNA (CT-DNA) was investigated using various biophysical techniques in a physiological buffer (pH 7.4). It was found that PAL intercalated into the base pairs of CT-DNA as evidenced from the results of UV-Vis, fluorescence, circular dichroism (CD), competitive binding assay with ethidium bromide (EB) and Hoechst 33258, KI quenching study, the effect of denaturing agent and viscosity measurements. The magnitude of binding constants (106 M-1) at different temperatures suggested strong binding between PAL and CT-DNA during complexation. The observed ΔHo > 0 and ΔSo > 0 indicated that the binding process is primarily driven by hydrophobic interactions. Molecular docking studies indicated partial intercalation of pyridopyrimidine ring between the base pairs of DNA. Free energy surface (FES) analysis derived from metadynamics simulation studies revealed the PAL-induced cleavage of DNA, which was confirmed by gel electrophoresis experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram, India
| | - R Jeyashree
- Centre for Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - R Preethi
- Centre for Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram, India
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2
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Li Y, Liu H, Mu C, Gu J, Li C. Probing the interaction between encapsulated ethoxyquin and its β-cyclodextrin inclusion complex with bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123259. [PMID: 37634329 DOI: 10.1016/j.saa.2023.123259] [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: 05/25/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023]
Abstract
Ethoxyquin (EQ) is a synthetic antioxidant that is derived from quinolines and found in many meat products. EQ is strictly regulated in feed due to its potential health implications. An investigation of the interaction mechanism between EQ and transporter protein before and after β-cyclodextrin (β-CD) encapsulation was conducted with the use of multi-spectroscopy, cyclic voltammetry, and molecular docking. EQ formed complexes with bovine serum albumin (BSA), and affected secondary structure and microenvironment polarity of BSA. However, at 298 K, EQ's fluorescence quenching constants decreased from (9.81 ± 0.05) × 103 L mol-1 to (4.94 ± 0.09) × 103 L mol-1, binding constants decreased from (10.28 ± 0.02) × 103 L mol-1 to (2.08 ± 0.07) × 103 L mol-1, after encapsulation in β-CD as well as the binding distance increased. β-CD contains part of EQ in its hydrophobic cavity, inhibiting its binding to BSA. β-CD inclusion complex prevented adverse effects of EQ on BSA conformation. However, β-CD encapsulation had no effect on EQ's antioxidant activity.
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Affiliation(s)
- Ye Li
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
| | - Hongrui Liu
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
| | - Chunyu Mu
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
| | - Jiali Gu
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China.
| | - Chun Li
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
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3
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Gu J, Liu H, Huang X, Ma Y, Zhang L. Investigation of the separate and simultaneous bindings of warfarin and fenofibrate to bovine serum albumin. Int J Biol Macromol 2023; 236:123978. [PMID: 36906198 DOI: 10.1016/j.ijbiomac.2023.123978] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/12/2023]
Abstract
Lipid-lowering drugs are often taken with anticoagulant drugs in hyperlipidemia patients. Fenofibrate (FNBT) and warfarin (WAR) are common clinical lipid-lowering drugs and anticoagulant drugs, respectively. A study of binding affinity, binding force, binding distance, and binding sites was performed to determine the interaction mechanism between drugs and carrier proteins (bovine serum albumin, BSA), as well as their effects on BSA conformation. Both FNBT and WAR can form complexes with BSA by van der Waals force and hydrogen bonds. WAR had a stronger fluorescence quenching effect on BSA, a stronger binding affinity, and greater effects on BSA conformation than FNBT. According to fluorescence spectroscopy and cyclic voltammetry, co-administration of drugs decreased one drug's binding constant to BSA and increased its binding distance. This suggested that each drug's binding to BSA was disturbed by each other, as well as each drug's binding ability to BSA was altered by the other. It was demonstrated that co-administration of drugs had greater effects on the secondary structure of BSA and microenvironment polarity surrounding amino acid residues, using multiple spectroscopy techniques, such as ultraviolet spectroscopy, Fourier transform infrared spectroscopy, and synchronous fluorescence spectroscopy.
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Affiliation(s)
- Jiali Gu
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China.
| | - Hongrui Liu
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
| | - Xiyao Huang
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
| | - Yanxuan Ma
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
| | - Liang Zhang
- College of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013, PR China
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4
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Rahman Y, Afrin S, Perwez A, Ansari MO, Sarwar T, Ahmed S, Rizvi MA, Shadab GGHA, Tabish M. Nizatidine interacts with ct-DNA causing genotoxicity and cytotoxicity: an assessment by in vitro, in vivo, and in silico studies. J Biomol Struct Dyn 2023; 41:538-549. [PMID: 34856883 DOI: 10.1080/07391102.2021.2008496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
H2 receptor antagonists are the medication given for treating stomach ulcers, but lately, reports have shown their role in healing several malignant ulcers. The present work entails the interaction of H2 blocker nizatidine with calf thymus (ct)-DNA for determining the binding mode and energetics of the interaction. Multi-spectroscopic, calorimetric, viscometric and bioinformatic analysis revealed that nizatidine interacted with ct-DNA via groove-binding mode and is characterised by exothermic reaction. Moreover, assessment of genotoxic potential of nizatidine in vitro was carried out in peripheral human lymphocytes by alkaline comet assay. DNA damage occurred at high concentrations of nizatidine. Genotoxicity of nizatidine was also evaluated in vivo by assessing cytogenetic biomarkers viz. micronuclei formation and chromosomal aberration test. Nizatidine was able to induce micronuclei formation and chromosomal damage at high dose. Additionally, cytotoxic activity of nizatidine was determined in cancer cell lines, namely HeLa and HCT-116 and compared with the normal human cell line HEK-293 employing MTT assay. It was observed that nizatidine was more toxic towards HeLa and HCT-116 than HEK-293. Cell morphology analysis by compound inverted microscopy further strengthens the finding obtained through MTT assay.
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Affiliation(s)
- Yusra Rahman
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, India
| | - Shumaila Afrin
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, India
| | - Ahmad Perwez
- Department of Biosciences, Jamia Millia Islamia, New Delhi
| | - Mohd Owais Ansari
- Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Tarique Sarwar
- Department of Biosciences, Jamia Millia Islamia, New Delhi
| | - Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, India
| | | | - G G Hammad A Shadab
- Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, India
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5
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Exploring Molecular Interaction of Cefpirome with Human Serum Albumin: in vitro and in silico Approaches. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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6
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Facile synthesis of magnetic photo-responsive nanoparticles based on 1,3-diazabicyclo[3.1.0]hex-3-en: An enhanced adsorption of toxic dyes from aqueous solution under sunlight. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Mavis Xhakaza N, Chokkareddy R, Redhi GG. Ionic Liquid Based Electrochemical Sensor for the Detection of Efavirenz. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Muralikrishnan B, Edison LK, Dusthackeer A, Jijimole GR, Ramachandran R, Madhavan A, Kumar RA. Chrysomycin A inhibits the topoisomerase I of Mycobacterium tuberculosis. J Antibiot (Tokyo) 2022; 75:226-235. [PMID: 35136191 DOI: 10.1038/s41429-022-00503-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/09/2022]
Abstract
Novel anti-tuberculosis drugs are essential to manage drug-resistant tuberculosis, caused by Mycobacterium tuberculosis. We recently reported the antimycobacterial activity of chrysomycin A in vitro and in infected macrophages. In this study, we report that it inhibits the growth of drug-resistant clinical strains of M. tuberculosis and acts in synergy with anti-TB drugs such as ethambutol, ciprofloxacin, and novobiocin. In pursuit of its mechanism of action, it was found that chrysomycin A is bactericidal and exerts this activity by interacting with DNA at specific sequences and by inhibiting the topoisomerase I activity of M. tuberculosis. It also exhibits weak inhibition of the DNA gyrase enzyme of the pathogen.
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Affiliation(s)
- Balaji Muralikrishnan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Lekshmi K Edison
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Azger Dusthackeer
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - G R Jijimole
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Ranjit Ramachandran
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Aravind Madhavan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Ramakrishnan Ajay Kumar
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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9
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Shen B, Yang H, Chen J, Liu X, Zhou M. Study the interaction between juglone and calf thymus DNA by spectroscopic and molecular docking techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 261:119998. [PMID: 34091358 DOI: 10.1016/j.saa.2021.119998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 04/25/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Juglone (Jug) is one of the main active substances of Cortex Juglandis Mandshuricae in a folk anti-cancer prescription. Previously, there were few studies on its interaction with DNA and mechanism of action. The present paper studied, the mechanism of action between Jug and calf thymus DNA (ctDNA) by fluorescence spectroscopy, together with ethidium bromide (EB) fluorescence probe, UV-vis absorption spectroscopy, salt effect and ctDNA melting point (Tm) experiment, resonance scattering spectroscopy and molecular docking under the simulated human physiological conditions. The experimental findings indicated that Jug quiescently quenched the fluorescence of EB-ctDNA system, characteristic absorption peak intensity of ctDNA presented a decolorization effect after the interaction of ctDNA and Jug, the interaction with ctDNA enhanced of Jug resonance scattering peak and generated new resonance scattering peak, the salt exerted less effect on the interaction between Jug and ctDNA molecules, and the interaction with Jug increased the Tm value of ctDNA by 5.0 °C The binding constant (KA) between Jug and ctDNA was 2.12 × 105 L/mol (310 K) and the number of binding sites (n) was about 1. The interaction between Jug and ctDNA was an entropically driven spontaneous and endothermic process. The results of molecular docking further showed that the naphthoquinone plane was embedded in the region between the two TA bases in the ctDNA groove, and the 5'-hydroxyl and 4-naphthoquinone groups extended to the outside of the ctDNA double helix.
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Affiliation(s)
- Bingjun Shen
- Department of Bioengineering, School of Life Science and Technology, Changchun University of Science and Technology, NO.7186 Weixing Road, Changchun City, Jilin Province 085238, PR China.
| | - Huiru Yang
- Department of Bioengineering, School of Life Science and Technology, Changchun University of Science and Technology, NO.7186 Weixing Road, Changchun City, Jilin Province 085238, PR China
| | - Jiaqi Chen
- Department of Bioengineering, School of Life Science and Technology, Changchun University of Science and Technology, NO.7186 Weixing Road, Changchun City, Jilin Province 085238, PR China
| | - Xiaoyun Liu
- Department of Bioengineering, School of Life Science and Technology, Changchun University of Science and Technology, NO.7186 Weixing Road, Changchun City, Jilin Province 085238, PR China
| | - Mingyue Zhou
- Department of Bioengineering, School of Life Science and Technology, Changchun University of Science and Technology, NO.7186 Weixing Road, Changchun City, Jilin Province 085238, PR China
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10
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Investigating the anticancer properties of the two new platinum complexes with iso- and tert-pentylglycine by the DFT, molecular docking, and ADMET assessment and experimental confirmations. J Biol Inorg Chem 2021; 26:283-298. [PMID: 33616752 DOI: 10.1007/s00775-021-01851-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
In this study, two new anticancer platinum complexes formulated as [Pt(bpy)(L)]NO3 were synthesized using the iso and tert-pentylglycine ligands, two structural isomer ligands, to investigate side branches effect on the complex-DNA interaction. According to the comparative results of the ADMET assessment, these compounds can be considered as the drug-like molecules and oral medication. Mechanism of tumor inhibition and DNA binding parameters indicated the higher ability of the tert-isomer and also, both complexes acted through the disruption of the base pairs and stacks of helicity by the endothermic process. Fluorescence spectroscopy showed that the quenching mechanism is static for both drugs with large binding constant and high binding affinity towards the DNA. Also, the amount of binding constant of the tert -isomer was about 14 times of another structural isomerous complex. CD spectra indicated the conversion of the B-DNA into A-DNA form via electrostatic interaction for positively charged complexes. The cytotoxic data showed that both compounds have antiproliferative effects against the MCF-7 cell line and the inhibitory effect of the iso-derivative was better than the tert-one. Docking studies showed that the desolvation energy and hydrogen bond are more effective between the other interactions. The torsional free energy for both complexes mainly provided the groove binding along with partially electrostatic and intercalate binding. According to the density-functional theory data and because of positive electron density on the surface of complexes and facilitating of the metal drug to DNA phosphate groups approaching, both complexes may be good candidates for the anticancer drugs. Two new anticancer Pt(II) complexes were synthesized with glycine derivatives. In vitro cytotoxicity effects were tested against the human breast cancer cell line of MCF-7. Moreover, the modes of DNA binding with synthesized compounds were investigated using ADME prediction, DFT, molecular docking and spectroscopic methods.
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11
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Hansda S, Mitra A, Ghosh R. Studies to explore the UVA photosensitizing action of 9-phenylacridine in cells by interaction with DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:393-422. [PMID: 33586599 DOI: 10.1080/15257770.2021.1880011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Acridine and its derivatives are well known for their DNA binding properties. In this report, we present our findings on evaluating different binding parameters of the interaction of 9-phenylacridine (ACPH) with DNA. Absorption spectroscopic studies including standard and reverse titration, the effects of ionic strength and temperature on titration, and Job plot analysis were done to calculate the binding constant and determine the different thermodynamic parameters and stoichiometry of the binding. Spectrofluorimetry and circular dichroism (CD) spectral titration were also utilized to confirm these findings. The results indicated that ACPH binds to DNA reversibly through non-electrostatic interactions by hydrogen bonding and van der Waals interactions. The binding constant and the number of binding sites were of the order 103 M-1 and ≈2, respectively with a binding stoichiometry of 1:4. The binding of ACPH with DNA was spontaneous, exothermic and enthalpy-driven. The extent of uptake of ACPH in B16 melanoma cells was estimated. As this compound absorbs in the UVA region, the effect of treatment with ACPH prior to UVA exposure was assessed to evaluate its phototoxicity in these cells. Our results indicated that the binding to DNA enhanced damage to sensitize cells to killing through apoptosis. Our findings indicated its potential to act as a photosensitizer.
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Affiliation(s)
- Surajit Hansda
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Anindita Mitra
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Rita Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
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12
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Hu M, Zhu M, Xin L, Zhang G, Wu S, Hu X, Gong D. Change of benzo(a)pyrene during frying and its groove binding to calf thymus DNA. Food Chem 2021; 350:129276. [PMID: 33609937 DOI: 10.1016/j.foodchem.2021.129276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/21/2020] [Accepted: 12/20/2020] [Indexed: 01/07/2023]
Abstract
Benzo[a]pyrene (BaP), a prototype of polycyclic aromatic hydrocarbons (PAHs) with potential mutagenicity, toxicity and carcinogenicity, is ubiquitous in deep-fried foods. Herein, the changes in eight specific PAHs (PAH8) concentration in sunflower oil during frying were investigated by gas chromatography-triple quadrupole-mass spectrometry (GC-QqQ-MS). PAH8 concentrations in sunflower oil were 23.92-27.82 μg kg-1 and increased with increasing frying time. The detected BaP levels were 3.64-4.00 μg kg-1, exceeding the upper limit (2 μg kg-1) set by European Union (EU), though below the limiting value (10 μg kg-1) in China. The interaction between BaP and calf thymus DNA (ctDNA) was explored through various spectroscopic methods and molecular docking. Melting studies, denaturation experiments, ionic strength effects and viscosity measurements indicated that BaP interacted with ctDNA primarily via groove binding as evidenced by circular dichroism analysis and molecular docking. Further gel electrophoresis assays suggested that DNA was damaged at high levels of BaP.
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Affiliation(s)
- Mingming Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Miao Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Le Xin
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Bor S. Luh Food Safety Research Centre, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China.
| | - Shimin Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Bor S. Luh Food Safety Research Centre, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Deming Gong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
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Shahabadi N, Razlansari M. Insight into the binding mechanism of macrolide antibiotic; erythromycin to calf thymus DNA by multispectroscopic and computational approaches. J Biomol Struct Dyn 2021; 40:6171-6182. [PMID: 33525995 DOI: 10.1080/07391102.2021.1877821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In the present study, the interactions between Erythromycin drug and calf thymus deoxyribonucleic acid (ct-DNA) were explored by multi spectroscopic techniques (UV-Visible, fluorescence, circular dichroism spectroscopies), viscosity, molecular docking simulation, and atomic force microscopy (AFM). In addition, the values of binding constant were calculated by the UV-Visible and fluorescence spectroscopy. Competitive fluorescence study with methylene blue (MB), acridine orange (AO), and Hoechst 33258 were indicated that the Erythromycin drug could displace the DNA-bound Hoechst, which displays the strong competition of Erythromycin with Hoechst to interact with the groove binding site of DNA. In addition, the observed complexes in AFM analysis comprise the chains of ct-DNA and Erythromycin with an average size of 314.05 nm. The results of thermodynamic parameter calculations (ΔS° = -332.103 ± 14 J mol-1 K-1 and ΔH° = -115.839 ± 0.02 kJ mol-1) approved the critical role of van der Waals forces and hydrogen bonds in the complexation of Erythromycin-DNA. Fluorescence spectroscopy results demonstrate the existence of a static enhancement mechanism in the interaction of Erythromycin-DNA. According to the obtained results, Erythromycin drug interacts with the major groove of ct-DNA. These consequences were further supported by the molecular docking study, and it could be determined that DNA-Erythromycin docked model was in a rough correlation with our experimental results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mahtab Razlansari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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14
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Ender Biçer, Billy TA, Macit M. Voltammetric and Docking Investigation of the Binding Interaction between (E)-1-[(2-Phenoxyphenylimino)methyl]naphthalen-2-ol and Calf Thymus DNA. RUSS J ELECTROCHEM+ 2021. [DOI: 10.1134/s1023193520120046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Guo H, Xie J, Liao T, Tuo X. Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods. LUMINESCENCE 2020; 36:35-44. [PMID: 32614132 DOI: 10.1002/bio.3911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 01/21/2023]
Abstract
Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady-state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (Kb ) was 0.78 × 104 L·mol-1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP-DNA were 67.92 kJ·mol-1 and 302.96 J·mol-1 ·K-1 , respectively. DNP bound to DNA in a groove-binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi-Sigma force and Pi-Alkyl force were the major hydrophobic force functioning between DNP and DNA.
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Affiliation(s)
- Hui Guo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Jiawen Xie
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Tancong Liao
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Xun Tuo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
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Shahabadi N, Shiri F, Hadidi S, Farshadfar K, Sajadimajd S, Roe SM. Equilibrium and site selective analysis for DNA threading intercalation of a new phosphine copper(I) complex: Insights from X-ray analysis, spectroscopic and molecular modeling studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 235:118280. [PMID: 32248034 DOI: 10.1016/j.saa.2020.118280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
To clarify the interaction of phosphine copper(I) complex with DNA, our study reports the synthesis of a new phosphine copper(I) complex, along with a detailed analysis of the geometry characterization and its interaction with double-stranded DNA. The triclinic phase Cu(PPh3)2(L)(I) with a tetrahedral geometry was identified as the product of the reaction of copper(I) iodide with (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] ligand and triphenylphosphine by single-crystal X-ray analysis. Molecular interaction of the synthesized complex with the calf thymus deoxyribonucleic acid (ct-DNA) was investigated in the physiological buffer (pH 7.4) by multi-spectroscopic approaches associated with a competitive displacement towards Hoechst 33258 and methylene blue (MB) as groove and intercalator probes. The fluorescence and UV/Vis results detected the formation of a complex-DNA adduct in the ground-state with a binding affinity in order of 104 M-1, which is in keeping with both groove binders and intercalators. The thermodynamic parameters, ΔS0 = -200.31 ± 0.08 cal/mol·K and ΔH0 = -63.11 ± 0.24 kcal/mol, confirmed that the van der Waals interaction is the main driving force for the binding process. Moreover, the ionic strength and pH effect experiments demonstrated the electrostatic interactions between the complex and DNA is negligible. Analysis of the molecular docking simulation declared the flat (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] part of the complex was inserted between the sequential A…T/A…T base pairs, while the phosphine substituents were located in the groove, i.e. threading intercalation. Besides, the cytotoxicity of the complex against the MCF-7 human breast cancer cells was detected at IC50 = 10 μg/mL.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Kaveh Farshadfar
- Department of Chemistry, Islamic Azad University, Central Tehran Branch, Poonak, Tehran 1469669191, Iran
| | | | - S Mark Roe
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
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Wani TA, Alsaif N, Bakheit AH, Zargar S, Al-Mehizia AA, Khan AA. Interaction of an abiraterone with calf thymus DNA: Investigation with spectroscopic technique and modelling studies. Bioorg Chem 2020; 100:103957. [DOI: 10.1016/j.bioorg.2020.103957] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/11/2023]
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18
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Varela-Garcia A, Concheiro A, Alvarez-Lorenzo C. Cytosine-functionalized bioinspired hydrogels for ocular delivery of antioxidant transferulic acid. Biomater Sci 2020; 8:1171-1180. [PMID: 31995040 DOI: 10.1039/c9bm01582e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Contact lenses (CLs) are being pointed out as feasible platforms for controlled delivery of ophthalmic drugs. Bioinspired strategies may endow CLs with affinity for a given drug by mimicking its physiological receptor using adequate functional monomers and tuning their conformation in the space through the molecular imprinting technology. However, there are some active substances, such as efficient antioxidant agents, that cannot be used as templates because they degrade during polymerization or even hinder the polymerization itself. Therefore, the development of CLs able to sustain the release of antioxidants for the prevention and/or treatment of several age-related and light-induced eye diseases has not been explored yet. Searching for an alternative bioinspired strategy, the present work relies on the fact that some drugs owe their therapeutic action to their ability to interact with nucleotides that build up DNA and RNA. Thus, the aim of this work was to design hydrogels functionalized with the nitrogenous base cytosine for the controlled uptake and release of transferulic acid (TA) having a complementary chemical structure in terms of hydrogen bonding and π-π stacking ability. Hydrogels were prepared from mixtures of 2-hydroxyethyl methacrylate (HEMA), glycidyl methacrylate (GMA) and ethyleneglycolphenylether methacrylate (EGPEM). GMA was used as a bridge to immobilize cytosine after hydrogel synthesis, while EGPEM was added to reinforce hydrophobic interactions with TA. The hydrogels were characterized in terms of suitability to be used as CLs (swelling, light transmission, mechanical properties, biocompatibility) and capability to host TA and sustain its release in lachrymal fluid while maintaining the antioxidant activity. Relevantly, the bioinspired CLs favored TA accumulation in cornea and sclera tissues.
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Affiliation(s)
- Angela Varela-Garcia
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma, Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Angel Concheiro
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma, Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma, Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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19
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Talebpour Z, Haghighi F, Taheri M, Hosseinzadeh M, Gharavi S, Habibi F, Aliahmadi A, Sadr AS, Azad J. Binding interaction of spherical silver nanoparticles and calf thymus DNA: Comprehensive multispectroscopic, molecular docking, and RAPD PCR studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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20
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De la Cruz Morales K, Alarcón‐Angeles G, Merkoçi A. Nanomaterial‐based Sensors for the Study of DNA Interaction with Drugs. ELECTROANAL 2019. [DOI: 10.1002/elan.201900286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- K. De la Cruz Morales
- Universidad Autónoma Metropolitana-XochimilcoDepartamento de Sistemas Biológicos C.P. 04960 México City
| | - G. Alarcón‐Angeles
- Universidad Autónoma Metropolitana-XochimilcoDepartamento de Sistemas Biológicos C.P. 04960 México City
| | - A. Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST Campus UAB, Bellaterra 08193 Barcelona Spain
- ICREA – Catalan Institution for Research and Advanced Studies Barcelona 08010 Spain
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21
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Mansouri-Torshizi H, Khosravi F, Abdi K, Zareian-Jahromi S. Ordering selected Zn(II), Cu(II), Pd(II) and Co(III) complex compounds: their separately and combinedly antibacterial therapy and DNA-binding studies. J Biomol Struct Dyn 2019; 37:4419-4432. [PMID: 30526379 DOI: 10.1080/07391102.2018.1554509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In this study, four Co(III)-, Cu(II)-, Zn(II)- and Pd(II)-based potent antibacterial complexes of formula K3[Co(ox)3]·3H2O (I), [Cu(phen)2Cl]Cl·6.5H2O (II), [Zn(phen)3]Cl2 (III) and [Pd(phen)2](NO3)2 (IV) (where ox is oxalato and phen is 1,10-phenanthroline) were synthesized. They were characterized by elemental analysis, molar conductivity measurements, UV-vis, Fourier transform infrared (FT-IR) and proton nuclear magnetic resonance (1H-NMR) techniques. These metal complexes were ordered in three combination series of I+II, I+II+III and I+II+III+IV. Antibacterial screening for each metal complex and their combinations against Gram-positive and Gram-negative bacteria revealed that all compounds were more potent antibacterial agents against the Gram-negative than those of the Gram-positive bacteria. The four metal complexes showed antibacterial activity in the order I > II > III > IV, and the activity of their combinations followed the order of I+II+III+IV > I+II+III > I+II. The DNA-binding properties of complex (I) and its three combinations were studied using electronic absorption and fluorescence (ethidium bromide displacement assay) spectroscopy. The results obtained indicated that all series interact effectively with calf thymus DNA (CT-DNA). The binding constant (Kb), the number of binding sites (n) and the Stern-Volmer constant (Ksv) were obtained based on the results of fluorescence measurements. The calculated thermodynamic parameters supported that hydrogen bonding and van der Waals forces play a major role in the association of each series of metal complexes with CT-DNA and follow the above-binding affinity order for the series. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hassan Mansouri-Torshizi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan , Zahedan , Iran
| | - Fatemeh Khosravi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan , Zahedan , Iran.,Department of Chemistry, University of Zabol , Zabol , Iran
| | - Khatereh Abdi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan , Zahedan , Iran
| | - Sareh Zareian-Jahromi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan , Zahedan , Iran
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22
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Feng J, Qi H, Sun X, Feng S, Liu Z, Song Y, Qiao X. Synthesis of Novel Pyrazole Derivatives as Promising DNA-Binding Agents and Evaluation of Antitumor and Antitopoisomerases I/II Activities. Chem Pharm Bull (Tokyo) 2018; 66:1065-1071. [DOI: 10.1248/cpb.c18-00546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Jiajia Feng
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University
| | - Hui Qi
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University
| | - Xiaoyang Sun
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University
| | - Siran Feng
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University
| | - Zhenming Liu
- Drug Design Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University
| | - Yali Song
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University
| | - Xiaoqiang Qiao
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University
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23
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Tian Z, Wang Z, Han X, Wang N, Wang R. Study on the interaction between cannabinol and DNA using acridine orange as a fluorescence probe. J Mol Recognit 2017; 31. [DOI: 10.1002/jmr.2682] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/01/2017] [Accepted: 09/28/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Zhengshan Tian
- School of Chemistry and Environmental Engineering; Pingdingshan University; Pingdingshan China
| | - Zechun Wang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou China
| | - Xinxin Han
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou China
| | - Ning Wang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou China
| | - Ruiyong Wang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou China
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Li S, Pan J, Zhang G, Xu J, Gong D. Characterization of the groove binding between di-(2-ethylhexyl) phthalate and calf thymus DNA. Int J Biol Macromol 2017; 101:736-746. [DOI: 10.1016/j.ijbiomac.2017.03.136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/03/2023]
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25
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Yang H, Tang P, Tang B, Huang Y, He J, Li S, Li H. Studies of DNA-binding properties of lafutidine as adjuvant anticancer agent to calf thymus DNA using multi-spectroscopic approaches, NMR relaxation data, molecular docking and dynamical simulation. Int J Biol Macromol 2017; 99:79-87. [DOI: 10.1016/j.ijbiomac.2017.02.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 02/01/2023]
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26
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Raj M, Gupta P, Thapliyal N, Goyal RN. A Novel Hybrid Nano-composite Grafted Electrochemically Reduced Graphene Oxide Based Sensor for Sensitive Determination of Efavirenz. ELECTROANAL 2016. [DOI: 10.1002/elan.201600397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mamta Raj
- Department of Chemistry; Indian Institute of Technology Roorkee; Roorkee - 247667 India
| | - Pankaj Gupta
- Department of Chemistry; Indian Institute of Technology Roorkee; Roorkee - 247667 India
| | - Neeta Thapliyal
- Department of Pharmaceutical Chemistry, College of Health Sciences; University of KwaZulu-Natal; Durban 4000 South Africa
| | - Rajendra N. Goyal
- Department of Chemistry; Indian Institute of Technology Roorkee; Roorkee - 247667 India
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