1
|
Verebová V, Bedlovičová Z, Bednáriková Z, Staničová J. Monitoring of DNA structural changes after incorporation of the phenylpyrazole insecticide fipronil. Arch Biochem Biophys 2024; 756:110001. [PMID: 38636692 DOI: 10.1016/j.abb.2024.110001] [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: 01/22/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
The use of insecticides presents a risk to the environment because they can accumulate in the water, soil, air, and organisms, endangering human and animal health. It is therefore essential to investigate the effects of different groups of insecticides on individual biomacromolecules such as DNA. We studied fipronil, which belongs to the group of phenylpyrazole insecticides. The interaction of fipronil with calf thymus DNA was investigated using spectroscopic methods (absorption and fluorescence spectroscopy) complemented with infrared spectroscopy and viscosity measurement. Fluorescence emission spectroscopy showed the formation of a fipronil/DNA complex with a combined static and dynamic type of quenching. The binding constant was 4.15 × 103 L/mol. Viscosity changes were recorded to confirm/disconfirm the intercalation mode of interaction. A slight change in DNA viscosity in the presence of fipronil was observed. The phenylpyrazole insecticide does not cause significant conformational changes in DNA structure or increase of its chain length. We hypothesize that fipronil is incorporated into the minor groove of the DNA macromolecule via hydrogen interactions as indicated by FT-IR and CD measurements.
Collapse
Affiliation(s)
- Valéria Verebová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia
| | - Zdenka Bedlovičová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia
| | - Zuzana Bednáriková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Science, Watsonova 1935/47, 040 01, Košice, Slovakia
| | - Jana Staničová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia; Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, Kateřinská 1, Prague, Czech Republic.
| |
Collapse
|
2
|
Priyadharshini RD, Ponkarpagam S, Vennila KN, Elango KP. Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121363. [PMID: 35580462 DOI: 10.1016/j.saa.2022.121363] [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: 01/31/2022] [Revised: 04/16/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and 31P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 104 M-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG0 < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH0 < 0 and ΔS0 > 0). The up-field shift in the 31P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.
Collapse
Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India.
| |
Collapse
|
3
|
Ezazi-Toroghi S, Salarinejad S, Kamkar-Vatanparast M, Mokaberi P, Amiri-Tehranizadeh Z, Saberi MR, Chamani J. Understanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison. J Biomol Struct Dyn 2022; 41:4180-4193. [PMID: 35437091 DOI: 10.1080/07391102.2022.2064914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The interaction between calf thymus DNA (ctDNA) and Malathion in the absence and presence of Histone 1 has been enquired by the means of spectroscopic, viscometry, molecular modeling, and cell viability assay techniques. Malathion is capable of quenching the fluorescence of ct DNA in the absence and presence of H1. The binding constants of Malathion-ctDNA complex in the absence of H1 have been calculated to be 6.62 × 104, 4.31 × 104 and 1.93 × 104 M-1 at 298, 303, and 308 K, respectively that revealed static quenching in complex formation. The observed negative values of enthalpy and entropy changes indicate that the main binding interaction forces were van der Waals force and hydrogen bonding. The binding constant between Malathion and single-stranded ctDNA (ss ctDNA) seemed to be much weaker than that of Malathion and double-stranded ctDNA (ds ctDNA). Furthermore, Malathion can induce detectable alterations in the CD spectrum of ctDNA, along with changes in its viscosity. In the presence of H1, fluorescence quenching of ctDNA-Malathion complex displays dynamic behavior and binding constants were perceived to be 1.66 × 104, 2.93 × 104 and 5.77 × 104 M-1 at 298, 303, and 308 K, respectively. The different of interaction behavior between ctDNA and Malathion in the absence and presence of H1 clearly revealed H1 role in the complex formation and forces change between ctDNA and Malathion. The positive values of enthalpy and entropy changes have suggested that binding process is primarily driven by hydrophobic interactions. The tendency to interact with ss ctDNA, reduced viscosity have designated that the Malathion bound to ctDNA in the presence of H1 is groove binding. The results of molecular docking and molecular dynamics simulation also confirmed potent interactions between Malathion and the macromolecules in the binary and ternary systems.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sara Ezazi-Toroghi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Shadi Salarinejad
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| |
Collapse
|
4
|
Zhang Y, Cao Y, Li Y, Zhang X. Interactions between Human Serum Albumin and Sulfadimethoxine Determined Using Spectroscopy and Molecular Docking. Molecules 2022; 27:molecules27051526. [PMID: 35268627 PMCID: PMC8911820 DOI: 10.3390/molecules27051526] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Sulfonamides are widely used antibiotics in agricultural production. However, the potential threat of these drugs to human health has increased global concern. Human serum albumin (HSA) is the main reservoir and transporter of exogenous small molecules in humans. In this study, the interaction between sulfadimethoxine (SMT) and human serum albumin (HSA) was studied using spectroscopy and computer simulation. Our results showed that the hydrogen bonding and van der Waals forces drove SMT to enter the binding site I of HSA spontaneously and resulted in the fluorescence quenching of HSA. The stability of the HSA–SMT complex decreased with an increase in temperature. The binding of SMT to HSA induced alterations in the secondary structure of HSA, where the content of α-helix decreased from 61.0% of the free state to 59.0% of the compound state. The π–π, π–σ, and π–alkyl interactions between HSA and SMT were found to play important roles in maintaining the stability of the complex.
Collapse
Affiliation(s)
- Yuai Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China;
- NanChang Bozekang Pharmaceutical Technology Co., Ltd., Nanchang 330000, China
| | - Yiqing Cao
- Department of Pharmaceutical Analysis, School of Pharmacy, Fudan University, Shanghai 201203, China;
| | - Yan Li
- Department of Pharmaceutical Analysis, School of Pharmacy, Fudan University, Shanghai 201203, China;
- Correspondence: (Y.L.); (X.Z.)
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China;
- Correspondence: (Y.L.); (X.Z.)
| |
Collapse
|
5
|
Sohrabi T, Asadzadeh-Lotfabad M, Shafie Z, Amiri Tehranizadeh Z, Saberi MR, Chamani J. Description of the calf thymus DNA-malathion complex behavior by multi-spectroscopic and molecular modeling techniques: EMF at low and high frequency approaches. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1346-1357. [PMID: 35096292 PMCID: PMC8769509 DOI: 10.22038/ijbms.2021.58083.12907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/07/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Small molecules can bind to DNA via covalent or non-covalent interactions, which results in altering or inhibiting the function of DNA. Thus, understanding the interaction patterns of medicines or other small molecules can be very crucial. In this study, the interaction between malathion and calf thymus DNA (ctDNA), in the absence and presence of electromagnetic field (EMF) at low and high frequencies, was investigated through various spectroscopies and viscosity measurements. MATERIALS AND METHODS The interaction studies were performed by means of absorbance, circular dichroism, fluorescence spectroscopy, viscosity, thermal melting, and molecular modeling techniques. RESULTS The fluorescence intensity of the ctDNA-malathion complex in the presence of EMF, has revealed quenching of fluorescence emission curves. The dynamic interaction and RLS studies have implied the changes in ctDNA-malathion complex throughout the presence of EMF which suggested that hydrophobic forces play the main role in the binding. Studies have revealed that malathion does not have any effect on binding ethidium bromide to ctDNA, which signifies the groove binding. The viscosity of ctDNA increased as the malathion concentration was enlarged. The circular dichroism technique suggested that the ellipticity values of the ctDNA-malathion complex have not increased with enhancing the malathion concentration. Molecular docking and dynamics studies have indicated a potent electrostatic interaction between ctDNA and malathion in the groove binding site. CONCLUSION The results of spectroscopic studies reinforced a potent interaction between malathion and ctDNA in the absence and presence of EMF which can help us for further pharmaceutical drug discoveries.
Collapse
Affiliation(s)
- Tahmineh Sohrabi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Zahra Shafie
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| |
Collapse
|
6
|
van der Westhuizen D, Slabber CA, Fernandes MA, Joubert DF, Kleinhans G, van der Westhuizen CJ, Stander A, Munro OQ, Bezuidenhout DI. A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation. Chemistry 2021; 27:8295-8307. [PMID: 33822431 PMCID: PMC8251726 DOI: 10.1002/chem.202100598] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 12/13/2022]
Abstract
The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.
Collapse
Affiliation(s)
| | - Cathryn A. Slabber
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Manuel A. Fernandes
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniël F. Joubert
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - George Kleinhans
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
| | - C. Johan van der Westhuizen
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
- Future Production: ChemicalsPharmaceutical Technologies Research GroupCouncil for Scientific and Industrial Research (CSIR)0184PretoriaSouth Africa
| | - André Stander
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - Orde Q. Munro
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniela I. Bezuidenhout
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Laboratory of Inorganic ChemistryEnvironmental and Chemical EngineeringUniversity of Oulu3000OuluFinland
| |
Collapse
|
7
|
Liu Z, Huang X, Jiang Z, Tuo X. Investigation of the binding properties between levamlodipine and HSA based on MCR-ALS and computer modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 245:118929. [PMID: 32961448 DOI: 10.1016/j.saa.2020.118929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/26/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Levamlodipine (LEE) is a drug commonly used for antihypertensive treatment in clinical therapy. The overlapping fluorescence spectra of LEE and human serum albumin (HSA) cause some trouble in analysis of interactions between them by using the classic fluorescence method. Here, the multivariate curve resolution-alternating least squares (MCR-ALS) approach was used to overcome this disadvantage. Meanwhile, the binding properties of LEE-HSA complex were then explored through computer modeling. The MCR-ALS results suggested that LEE-HSA complex was present in the mixture solution of LEE and HSA. This conclusion was then confirmed by the Stern-Volmer equation and time-resolved fluorescence experiment. The binding constant (Ka) was 2.139 × 104 L·mol-1 at 298 K. LEE was located close to the Trp-214 residue of HSA, with van der Waals forces and hydrogen bonding as main driving forces for this interaction. LEE can alter the conformation of HSA, in which the content of α-helix reduced from 57.2% to 52.3%. The Pi-Alkyl interactions contributed to maintaining the stability of the LEE-HSA complex. The results of molecular dynamics simulations showed that LEE-HSA complex was formed within 5 ns, and the particle size (Rg) of HSA was altered by the binding reaction. This study would promote better understanding of the transportation and distribution mechanisms of LEE in the human body.
Collapse
Affiliation(s)
- Zhaoqing Liu
- College of Chemistry, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xiaojian Huang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Zheng Jiang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xun Tuo
- College of Chemistry, Nanchang University, Nanchang 330031, Jiangxi, China.
| |
Collapse
|
8
|
Liu Y, Lu J, Sun J, Lu F, Bie X, Lu Z. Membrane disruption and DNA binding of Fusarium graminearum cell induced by C16-Fengycin A produced by Bacillus amyloliquefaciens. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
9
|
Baltazar C, Mun R, Tajmir-Riahi H, Bariyanga J. Spectroscopic studies on the interaction of mimosine with BSA and DNA. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
10
|
Nasuhoglu D, Westlund P, Isazadeh S, Neamatallah S, Yargeau V. Development of a Facile and High-Throughput Bioluminescence Assay Using Vibrio fischeri to Determine the Chronic Toxicity of Contaminated Samples. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 98:196-203. [PMID: 28028550 DOI: 10.1007/s00128-016-2008-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/09/2016] [Indexed: 06/06/2023]
Abstract
Chronic toxicity testing using the luminescent bacterium, Vibrio fischeri, has recently been demonstrated to be a suitable bioassay for water quality monitoring. The toxicity evaluation is typically based on determining the EC50 at specific time points which may lead to overlooking the dynamic nature of luminescence response and limits information regarding the possible mechanisms of action of target compounds. This study investigated various approaches (standard, integral, and luminescence rate inhibition) to evaluate the chronic toxicity of three target compounds (atrazine, trimethoprim, and acetamiprid) using a 96-well plate based method. The chronic toxicity assay and the methods used for EC50 calculation provided in this work resulted in a high-throughput method of chronic toxicity testing and indicated lower EC50 than the values provided by the standard short term methods, indicating higher toxicity. This study emphasizes the need for additional chronic toxicity testing to further evaluate the toxicity of compounds or unknown samples.
Collapse
Affiliation(s)
- Deniz Nasuhoglu
- Department of Chemical Engineering, McGill University, Montreal, H3A0C5, Canada
| | - Paul Westlund
- Department of Chemical Engineering, McGill University, Montreal, H3A0C5, Canada
| | - Siavash Isazadeh
- Department of Chemical Engineering, McGill University, Montreal, H3A0C5, Canada
| | - Sarah Neamatallah
- Department of Chemical Engineering, McGill University, Montreal, H3A0C5, Canada
| | - Viviane Yargeau
- Department of Chemical Engineering, McGill University, Montreal, H3A0C5, Canada.
| |
Collapse
|
11
|
Wang LH, Zhang ZH, Zeng XA, Gong DM, Wang MS. Combination of microbiological, spectroscopic and molecular docking techniques to study the antibacterial mechanism of thymol against Staphylococcus aureus: membrane damage and genomic DNA binding. Anal Bioanal Chem 2016; 409:1615-1625. [PMID: 27900434 DOI: 10.1007/s00216-016-0102-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/07/2016] [Accepted: 11/15/2016] [Indexed: 12/13/2022]
Abstract
Thymol (2-isopropyl-5-methylphenol) is a natural ingredient used as flavor or preservative agent in food products. The antibacterial mechanism of thymol against Gram-positive, Staphylococcus aureus was investigated in this work. A total of 15 membrane fatty acids were identified in S. aureus cells by gas chromatography-mass spectrometry. Exposure to thymol at low concentrations induced obvious alterations in membrane fatty acid composition, such as decreasing the proportion of branched 12-methyltetradecanoic acid and 14-methylhexadecanoic acid (from 22.4 and 17.3% to 7.9 and 10.3%, respectively). Membrane permeability assay and morphological image showed that thymol at higher concentrations disrupted S. aureus cell membrane integrity, which may decrease cell viability. Moreover, the interaction of thymol with genomic DNA was also investigated using multi-spectroscopic techniques, docking and atomic force microscopy. The results indicated that thymol bound to the minor groove of DNA with binding constant (K a) value of (1.22 ± 0.14) × 104 M-1, and this binding interaction induced a mild destabilization in the DNA secondary structure, and made DNA molecules to be aggregated. Graphical Abstract Thymol exerts its antibacterial effect throught destruction of bacterial cell membrane and binding directly to genomic DNA.
Collapse
Affiliation(s)
- Lang-Hong Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China.,Food Green Processing and Nutrition Regulation Research Center of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, 510641, China
| | - Zhi-Hong Zhang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China.,Food Green Processing and Nutrition Regulation Research Center of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, 510641, China
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China. .,Food Green Processing and Nutrition Regulation Research Center of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, 510641, China.
| | - De-Ming Gong
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Man-Sheng Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348 West Xianjiahu Road, Changsha, Hunan, 410205, China
| |
Collapse
|
12
|
Shahbazy M, Pakravan P, Kompany-Zareh M. Multivariate spectrochemical analysis of interactions of three common Isatin derivatives to calf thymus DNA in vitro. J Biomol Struct Dyn 2016; 35:2539-2556. [DOI: 10.1080/07391102.2016.1225604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mohammad Shahbazy
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Parvaneh Pakravan
- Department of Chemistry, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Mohsen Kompany-Zareh
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| |
Collapse
|
13
|
Esmailzadeh K, Housaindokht MR, Moradi A, Esmaeili AA, Sharifi Z. Synthesis, characterization and biological evaluation of novel α, β unsaturated amides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 161:170-177. [PMID: 26971027 DOI: 10.1016/j.saa.2016.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
Three derivatives of α,β unsaturated amides have been successfully synthesized via Ugi-four component (U-4CR) reaction. The interactions of the amides with calf thymus deoxyribonucleic acid (ct-DNA) have been investigated in the Tris-HCl buffer (pH=7.4) using viscometric, spectroscopic, thermal denaturation studies, and also molecular docking. By UV-Vis absorption spectroscopy studies, adding CT-DNA to the compound solution caused the hypochromism indicates that there are interactions between the compounds and DNA base pairs. In competitive fluorescence with methylene blue as an intercalator probe, adding compounds to DNA-MB solution caused an increase in emission spectra of the complex. This could be because of compound replacing, with similar binding mode of MB, between the DNA base pairs due to release of bonded MB molecules from DNA-MB complex. Thermal denaturation studies and viscometric experiments also indicated that all three investigated compounds bind to CT-DNA by non-classical intercalation mode. Additionally, molecular docking technique predicted partial intercalation binding mode for the compounds. Also, the highest binding energy was obtained for compound 5a. These results are in agreement with results obtained by empirical methods.
Collapse
Affiliation(s)
- K Esmailzadeh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - M R Housaindokht
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research and Technology Center of Biomolecules, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - A Moradi
- Department of Chemistry, Faculty of Science, University of Birjand, Birjand, Iran
| | - A A Esmaeili
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research and Technology Center of Biomolecules, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Z Sharifi
- Research and Technology Center of Biomolecules, Ferdowsi University of Mashhad, Mashhad, Iran
| |
Collapse
|
14
|
Zhou X, Zhang G, Pan J. Groove binding interaction between daphnetin and calf thymus DNA. Int J Biol Macromol 2014; 74:185-94. [PMID: 25541356 DOI: 10.1016/j.ijbiomac.2014.12.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/25/2022]
Abstract
The binding characteristics of daphnetin with calf thymus DNA (ctDNA) were investigated by multispectroscopic and chemometric approaches coupled with DNA viscosity measurements, melting studies and molecular docking technique. The expanded UV-vis spectral data matrix was processed by multivariate curve resolution-alternating least-squares method to obtain the concentration profiles of the components (daphnetin, ctDNA and daphnetin-ctDNA complex) to quantitatively monitor the daphnetin-ctDNA interaction. The groove mode of daphnetin binding to ctDNA was concluded by little change in melting temperature, viscosity of ctDNA and iodide quenching effect as well as increase in single-stranded DNA quenching effect. Moreover, the quantitative data for the competitive binding between daphnetin and Hoechst 33258 for ctDNA obtained by resolving the three-way synchronous fluorescence spectra data using parallel factor analysis modeling further supported the groove binding. The molecular docking visualized the results of the Fourier transform infrared analysis that the adenine and thymine bases in the minor groove of ctDNA were the main binding sites for daphnetin, and the circular dichroism spectra showed that the groove binding of daphnetin to ctDNA led to the conformational change in ctDNA from B-form to A-form. This study revealed the interaction mechanism of daphnetin with ctDNA.
Collapse
Affiliation(s)
- Xiaoyue Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China.
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| |
Collapse
|
15
|
Spectroscopic and Chemometrics Analysis of the Hydrolytic Process of Folpet and Its Interaction with DNA. J SOLUTION CHEM 2014. [DOI: 10.1007/s10953-014-0211-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
16
|
Zhang G, Wang L, Zhou X, Li Y, Gong D. Binding characteristics of sodium saccharin with calf thymus DNA in vitro. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:991-1000. [PMID: 24437661 DOI: 10.1021/jf405085g] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The binding characteristics of sodium saccharin (SSA), an artificial sweetener, with calf thymus DNA (ctDNA) were investigated by multispectroscopic techniques, chemometrics, and molecular simulation. A combined fluorescence and UV-vis spectroscopic data matrix was resolved by the multivariate curve resolution-alternating least-squares (MCR-ALS) chemometrics algorithm. The MCR-ALS analysis extracted simultaneously the concentration profiles and spectra for the three components (SSA, ctDNA, and SSA-ctDNA complex) to quantitatively monitor the SSA-ctDNA interaction, which is difficult to perform by conventional spectroscopic approach. The binding mode of SSA to ctDNA was principally through groove binding as revealed by ctDNA melting temperature studies, viscosity measurements, and iodide and salt quenching effects. Analysis of the Fourier transform infrared and circular dichroism spectra as well as molecular docking indicated that SSA preferentially bound to the guanine base of ctDNA and led to a transformation from B-like DNA structure to A-like conformation. Moreover, gel electrophoresis results suggested that SSA did not induce any significant cleavage in plasmid DNA.
Collapse
Affiliation(s)
- Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | | | | | | | | |
Collapse
|