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Fatima S, Hussain I, Ahmed S, Afaq MA, Tabish M. Insight into the interaction of isochroman with bovine serum albumin: extensive experimental and computational investigations. J Biomol Struct Dyn 2024:1-15. [PMID: 38319026 DOI: 10.1080/07391102.2024.2310203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
The way therapeutic compounds interact with serum protein provides valuable information on their pharmacokinetics, toxicity, effectiveness, and even their structural-related information. Isochroman (IC) is a phytochemical compound obtained from the leaves of Olea europea plant. The derivatives of IC have various pharmacological properties including antidepressants, antihistamines, antiinflammation, anticonvulsants, appetite depressants, etc. The binding of small molecules to bovine serum albumin (BSA) is useful to ensure their efficacy. Thus, in this study, we have found out the binding mode of IC with BSA using several spectroscopic and in silico studies. UV and fluorescence spectroscopy suggested the complex formation between IC and BSA with a binding constant of 103 M-1. IC resulted in fluorescence quenching in BSA through static mechanism. The microenvironmental and conformational changes in BSA were confirmed using synchronous and three-dimensional studies. Site marker experiment revealed the IC binding in site-III of BSA. The influence of vitamins, metals and β-cyclodextrin (β-CD) on binding constant of IC-BSA complex was also examined. Circular dichroism spectra showed that α-helical of BSA decreased upon interaction with IC. Computational and experimental results were complimentary with one another and assisted in determining the binding sites, nature of bonds and amino acids included in the IC-BSA complex formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sana Fatima
- Department of Biochemistry, Faculty of Life Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Irfan Hussain
- Department of Biochemistry, Faculty of Life Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Abuzar Afaq
- Department of Biochemistry, Faculty of Life Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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2
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Bag S, Bhowmik S. Fluorescence Spectroscopy: A Useful Method to Explore the Interactions of Small Molecule Ligands with DNA Structures. Methods Mol Biol 2024; 2719:33-49. [PMID: 37803111 DOI: 10.1007/978-1-0716-3461-5_3] [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] [Indexed: 10/08/2023]
Abstract
Small molecule ligands-DNA interactions have recently received a lot of attention in the fields of life sciences, medicine, and chemical sciences. To decode these interactions, many strategies have been developed. DNA is the primary target for a wide range of drugs that may interact with DNA in particular or non-specific ways and impact its activities. Fluorescence spectroscopy is a highly advanced and non-invasive technology for measuring the concentrations of substrates and products or identifying characteristic processing states. Small molecule ligands-DNA interaction studies are beneficial not only in comprehending the method of interaction, but also in synthesizing DNA-targeted particular drugs. Several small compounds that bind to DNA are clinically established therapeutic medicines, while their specific mechanism of action is unknown. Figuring out their molecular recognizing patterns is the only way to construct innovative compounds that can target specific DNA sequences with strong affinities. This book chapter will mostly explore several fluorescence spectroscopic methodologies used to investigate interactions between small molecule ligands and DNA. In addition, we provide many approaches for determining a drug's binding mode with DNA. These strategies produce data that is both trustworthy and easy to comprehend. All of the knowledge gained by studying these fluorescence spectroscopies are supposed to lead to the development of more efficient new pharmaceuticals that might aid in the treatment of diseases.
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Affiliation(s)
- Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry, India.
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3
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Qin C, Xiang L, Wang YZ, Yu PF, Meng C, Li YW, Zhao HM, Hu X, Gao Y, Mo CH. Binding interaction of environmental DNA with typical emerging perfluoroalkyl acids and its impact on bioavailability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167392. [PMID: 37758138 DOI: 10.1016/j.scitotenv.2023.167392] [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: 03/08/2023] [Revised: 08/17/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
As the replacement compounds of perfluoroalkyl acids (PFAAs), emerging PFAAs generally exhibit equal or more hazardous toxicity than legacy PFAAs. Numerous DNA as environmental organic matters coexists with emerging PFAAs, but their interactions and the resulting interaction impacts on the bioavailability of emerging PFAAs remain insufficiently understood. Here, we studied the binding strength and mechanism between DNA and emerging PFAAs (perfluorobutyric acid, perfluorobutylsulfonic acid, and hexafluoropropylene oxide dimer acid) using perfluorooctanoic acid as the control, and further investigated the impacts of DNA binding on the bioavailability of the emerging PFAAs. Isothermal titration calorimetry and quantum chemical calculation found that the emerging PFAAs could bind with DNA bases (main thymine) by van der Waals force and halogen-bond, showing the binding affinities in the range of 7.87 × 104 to L/mol to 6.54 × 106 L/mol. The PFAAs-DNA binding significantly decreased the bioavailability of the PFAAs in both seedlings and plants of pakchoi (Brassica chinensis L.), with little differences in bioavailability change extent among PFAAs. The findings highlight the universality and similarity of the DNA binding effects on PFAAs bioavailability, which can be the natural detoxification mechanism for response to the PFAAs pollution.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yi-Ze Wang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Peng-Fei Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Can Meng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Fatima S, Hussain I, Ahmed S, Tabish M. In vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques. J Biomol Struct Dyn 2023; 41:8795-8809. [PMID: 36281697 DOI: 10.1080/07391102.2022.2137243] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022]
Abstract
A wide range of therapeutic molecules uses deoxyribonucleic acid (DNA) as an intracellular target. The interaction of small molecules to DNA is a key feature in pharmacology and plays a vital role in the development of novel and more efficient drugs with increased selective activity and enhanced therapeutic effectiveness. Isochroman (IC) is a constituent of Olea europea plant, which has been shown to exhibit several beneficial pharmacological activities. At present, its interaction studies using calf thymus DNA (ct-DNA) have not been explained. A set of multi-spectroscopic techniques has been performed to determine the interaction mechanism of isochroman with ct-DNA. Absorption spectra and quenching in fluorescence studies show that isochroman and ct-DNA form a complex. The static mode of quenching was determined by the Stern-Volmer plot. The value of binding constant, Kb = 4.0 × 103 M-1 revealed moderate type of binding. Effects of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and ionic strength were studied to examine the isochroman binding to ct-DNA. Potassium iodide (KI) quenching effects and competitive binding studies clearly showed that isochroman binds in the minor groove of ct-DNA. Circular dichroic and DNA melting experiments also confirmed these results. The experimental outputs were further corroborated via in silico computational modelling studies. Lipinski's rule of 5 and SwissADME showed drug-likeness and oral bioavailability scores. Protox ІІ online software predicts oral and organ toxicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sana Fatima
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, Uttar Pradesh, India
| | - Irfan Hussain
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, Uttar Pradesh, India
| | - Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, Uttar Pradesh, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, Uttar Pradesh, India
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Tavakoli Hafshajani K, Sohrabi N, Eslami Moghadam M, Oftadeh M. Spectroscopy and molecular dynamic study of the interaction of calf thymus DNA by anticancer Pt complex with butyl glycine ligand. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 299:122826. [PMID: 37216815 DOI: 10.1016/j.saa.2023.122826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Despite the past few decades since the discovery of anticancer drugs, there is still no definitive treatment for its treatment. Cisplatin is a chemotherapy medication used to treat some cancers. In this research, the DNA binding affinity of Pt complex with butyl glycine ligand was studied by various spectroscopy methods and simulation studies. Fluorescence and UV-Vis spectroscopic data showed groove binding in ct-DNA-[Pt(NH3)2(butylgly)]NO3 complex formation by the spontaneous process. The results were also confirmed by small changes in CD spectra and thermal study (Tm), as well as the quenching emission of [Pt(NH3)2(butylgly)]NO3 complex on DNA. Finally, thermodynamic and binding parameters displayed that hydrophobic forces are the main forces. Based on docking simulation, [Pt(NH3)2(butylgly)]NO3 could bind to DNA and via minor groove binding on C-G center on DNA, formed a stable DNA complex.
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Affiliation(s)
| | - Nasrin Sohrabi
- Department of Chemistry, Payame Noor University (PNU), P.O.Box 19395-4697, Tehran, Iran.
| | | | - Mohsen Oftadeh
- Department of Chemistry, Payame Noor University (PNU), P.O.Box 19395-4697, Tehran, Iran
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Hu AH, Duan QX, Xiong XY, Kang Z, Bai AM, Yin MM, Hu YJ. Revealing the effects of ligands of silver nanoclusters on the interactions between them and ctDNA: Abstraction to visualization. Int J Biol Macromol 2023; 236:123965. [PMID: 36906202 DOI: 10.1016/j.ijbiomac.2023.123965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
Silver nanoclusters (AgNCs) have been widely applied in the field of biology, drug therapy and cell imaging in the last decade. In order to study the biosafety of AgNCs, GSH-AgNCs and DHLA-AgNCs were synthesized using glutathione (GSH) and dihydrolipoic acid (DHLA) as ligands, and their interactions with calf thymus DNA (ctDNA) from abstraction to visualization were studied. The results of spectroscopy, viscometry and molecular docking demonstrated that GSH-AgNCs mainly bound to ctDNA in a groove mode, while DHLA-AgNCs were both groove and intercalation binding. Fluorescence experiments suggested that the quenching mechanism of both AgNCs to the emission of ctDNA-probe were both in static mode, and thermodynamic parameters demonstrated that the main forces between GSH-AgNCs and ctDNA were hydrogen bonds and van der Waals forces, while hydrogen bonds and hydrophobic forces contributed to the binding of DHLA-AgNCs to ctDNA. The binding strength demonstrated that DHLA-AgNCs bound to ctDNA more strongly than that of GSH-AgNCs. The results of circular dichroism (CD) spectroscopy reflected small effects of both AgNCs on the structure of ctDNA. This study will support the theoretical foundation for the biosafety of AgNCs and have a guiding significance for the preparation and application of AgNCs.
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Affiliation(s)
- Ao-Hong Hu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Qi-Xuan Duan
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Xin-Yuan Xiong
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Zhuo Kang
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Ai-Min Bai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Miao-Miao Yin
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Yan-Jun Hu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
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Naik R, Seetharamappa J. In Vitro and Computational Approaches to Untangle the Binding Mechanism of Galangin with Calf Thymus DNA. J Fluoresc 2023; 33:13-24. [PMID: 36209269 DOI: 10.1007/s10895-022-03033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/20/2022] [Indexed: 02/04/2023]
Abstract
Flavonoids have potential applications in the nutraceutical, medicinal, pharmaceutical and cosmetic fields. The binding of flavonoids with DNA could unravel essential information required for the design of novel and effective chemical agents. The present paper describes the interaction of a flavonoid and a potent anticancer drug, galangin (GAL) with calf thymus DNA (ct-DNA) by fluorescence, UV absorption, melting studies, viscosity measurements and molecular docking studies. A hyperchromic effect was noticed in the absorption spectra of ct-DNA in the presence of the GAL system, indicating the presence of a groove mode of binding. Furthermore, GAL persuaded the minor changes in ct-DNA viscosity, indicating a non-intercalative mode of binding. Fluorescence studies revealed that the GAL quenched the fluorescence intensity of ct-DNA-Hoechst, thereby indicating the interaction between GAL and ct-DNA. Fluorescence results obtained at 298, 308 and 318 K revealed that the fluorescence quenching of ct-DNA-Hoechst-GAL occurred through the static quenching mechanism. Thermodynamic parameters for ct-DNA-Hoechst-GAL were computed and suitable conclusions were drawn. The changes noticed in the conformation of ct-DNA upon interaction with GAL were evaluated in terms of molar ellipticity. It indicated a plausible interaction between ct-DNA and GAL. The molecular docking studies also confirmed the groove mode of binding in the ct-DNA-GAL system. Thus, this work helped to unravel the binding mechanism between GAL and ct-DNA.
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Affiliation(s)
- Roopa Naik
- Department of Chemistry, Karnatak University, Dharwad, 580003, Karnataka, India
| | - J Seetharamappa
- Department of Chemistry, Karnatak University, Dharwad, 580003, Karnataka, India.
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Çeşme M, Özaltay A. DNA‐Binding Studies of Ofloxacin Using a Series of Spectroscopic, Electrochemical Techniques and in Silico Approaches. ChemistrySelect 2022. [DOI: 10.1002/slct.202202278] [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)
- Mustafa Çeşme
- Department of Chemistry Faculty of Sciences Kahramanmaras Sütçü İmam University 46040 Kahramanmaras TURKEY
| | - Ayşe Özaltay
- Department of Chemistry Faculty of Sciences Kahramanmaras Sütçü İmam University 46040 Kahramanmaras TURKEY
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Oguzcan E, Koksal Z, Taskin-Tok T, Uzgoren-Baran A, Akbay N. Spectroscopic and molecular modeling methods to investigate the interaction between psycho-stimulant modafinil and calf thymus DNA using ethidium bromide as a fluorescence probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 270:120787. [PMID: 34990918 DOI: 10.1016/j.saa.2021.120787] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/02/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Interaction type of modafinil with calf thymus DNA (ct-DNA) was examined systematically using ethidium bromide (EB) as a fluorescence probe by fluorescence spectroscopy, UV-Vis spectroscopy, viscosity and molecular docking method. The fluorescence quenching mechanism of ct-DNA-EB by modafinil can be combination of static and dynamic quenching. Results of UV-Vis absorption, competitive binding with Hoechst 33258, ionic strength effect studies, viscosity measurements were confirmed that the interaction type of modafinil with ct-DNA was intercalation. According to docking studies R-modafinil showed better interaction with ct-DNA which is consistent with known pharmacological properties of modafinil. The calculated thermodynamic parameters, enthalpy and entropy change, suggested that the driven forces are hydrogen bonding or van der Walls forces. Results of the docking studies were compatible with the experimental results and confirmed the hydrogen bond formation between modafinil and ct-DNA.
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Affiliation(s)
- Esra Oguzcan
- Department of Chemistry, Istanbul Medeniyet University, 34700 Istanbul, Turkey
| | - Zeynep Koksal
- Department of Chemistry, Istanbul Medeniyet University, 34700 Istanbul, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Gaziantep University, 27310 Gaziantep, Turkey; Department of Bioinformatics and Computational Biology, Gaziantep University, 27310 Gaziantep, Turkey
| | - Ayse Uzgoren-Baran
- Department of Chemistry, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Nuriye Akbay
- Department of Chemistry, Istanbul Medeniyet University, 34700 Istanbul, Turkey.
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Isolation, Identification, Spectral Studies and X-ray Crystal Structures of Two Compounds from Bixa orellana, DFT Calculations and DNA Binding Studies. CRYSTALS 2022. [DOI: 10.3390/cryst12030380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
4,6-Diacetylresorcinol (1) and 3-O-methylellagic acid dihydrate (2), both biologically significant compounds, were extracted from Bixa orellana and studied using IR, 1H, and 13C NMR, and UV-vis spectroscopic techniques. X-ray crystallographic techniques were also used to establish the molecular structure of the isolated compounds 1 and 2. Geometric parameters, vibrational frequencies, and gauge including atomic orbital (GIAO) 1H and 13C NMR of 1 and 2 in the ground state were computed by the density functional theory (DFT) using B3LYP/6-311G(d,p) basis set backing up experimental studies and established the correct structure of isolated compounds. The parameters obtained from the combined DFT, and X-ray diffraction studies are mutually agreed to establish correct structures of 1 and 2. In addition, an electrostatic potential map and HOMO−LUMO energy gap were made using the DFT calculation to determine the distribution of energy and the chemical reactivity region of the isolated compounds. The current study also provides further insights into the interaction of compound 2 with ct-DNA using numerous biophysical and in silico techniques. Moreover, in silico studies indicate that compound 2 binds to the DNA in the minor groove. Lipinski’s rule of five revealed a higher tendency of compound 2 towards drug-likeness. The bioavailability and synthetic accessibility score for compound 2 was found to be 0.55 and 3.21, suggesting that compound 2 could serve as an effective therapeutic candidate.
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Zhang D, Pan J, Gong D, Zhang G. Groove binding of indole-3-butyric acid to calf thymus DNA: Spectroscopic and in silico approaches. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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