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Li C, Song Z, Huang M, Zheng Y, Nong C, Jiang T, Li Z, Liu H, Yi Z. The molecular mechanisms of TRβ receptor interaction with polychlorinated biphenyls: A multispectral and computational exploration. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 326:125216. [PMID: 39340948 DOI: 10.1016/j.saa.2024.125216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/14/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024]
Abstract
The thyroid hormone (TH) system is susceptible to the toxic effects of polychlorinated biphenyls (PCBs). Pollutants may disrupt the TH system by binding to serum TH transport proteins or interacting with thyroid hormone receptors (TRs) in target cells. However, the molecular mechanism of interaction with the Thyroid Hormone Receptor Beta (TRβ) is not fully understood. This study employed fluorescence, UV-visible absorption, three-dimensional fluorescence, and Fourier-transform infrared spectroscopy, along with molecular docking and molecular dynamics simulations, to investigate the interaction between TRβ and PCBs. Moreover, molecular docking and fluorescence resonance energy transfer (FRET) findings suggest that TRβ and PCBs underwent resonance energy transfer consistent with Förster's theory. The root mean square deviation (RMSD) and docking outcomes indicate that the TRβ-PCB29 complex exhibited optimal structural stability. Thus, the study concludes that integrating spectroscopic data with molecular docking is essential for a comprehensive analysis. Further analysis of intermolecular interactions using quantum chemistry and reduced density gradient analysis (RDG) analysis revealed that van der Waals forces are the primary drivers of PCBs to TRβ.
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Affiliation(s)
- Cancan Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zeyu Song
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Manting Huang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yanhong Zheng
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Chunke Nong
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Tinghao Jiang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zhanji Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Hongyan Liu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
| | - Zhongsheng Yi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
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Farajzadeh-Dehkordi N, Zahraei Z, Farhadian S, Gholamian-Dehkordi N. The interactions between Reactive Black 5 and human serum albumin: combined spectroscopic and molecular dynamics simulation approaches. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:70114-70124. [PMID: 35583763 DOI: 10.1007/s11356-022-20736-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Azo dyes are made in significant amounts annually and released into the environment after being employed in the industry. There are some reports about the toxic effects of these dyes on several organisms. Thus, the textile dye Reactive Black 5 (RB5) has been examined for its cytotoxic effects on the human serum albumin (HSA) structure. Molecular interaction between RB5 and HSA indicated the combination of docking methods, molecular dynamic simulation, and multi-spectroscopic approaches. HSA's intrinsic fluorescence was well quenched with enhancing RB5 level, confirming complex formation. Molecular dynamics (MD) simulation was done to study the cytotoxic effects of RB5 and HSA conformation. Molecular modeling revealed that the RB5-HSA complex was stabilized by hydrogen bonds and van der Waals interactions. The results of molecular docking revealed that the binding energy of RB5 to HSA was - 27.94 kJ/mol. The change in secondary structure causes the annihilation of hydrogen bonding networks and the reduction of biological activity. This research can indicate a suitable molecular modeling interaction of RB5 and HAS and broaden our knowledge for azo dye toxicity under natural conditions.
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Affiliation(s)
- Nazanin Farajzadeh-Dehkordi
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, 8731751167, Iran
| | - Zohreh Zahraei
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, 8731751167, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P. O. Box 115, Shahrekord, Iran
- Member of Chahar Mahal & Bakhtiari Science and Technology Park, SaNa Zist Pardaz Co, Shahrekord, Iran
| | - Neda Gholamian-Dehkordi
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
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Li W, Zhang X, Tan S, Li X, Gu M, Tang M, Zhao X, Wu Y. Zein enhanced the digestive stability of five citrus flavonoids via different binding interaction. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:4780-4790. [PMID: 35218206 DOI: 10.1002/jsfa.11838] [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: 10/17/2021] [Revised: 01/03/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Zein is commonly used to construct food flavonoid delivery systems. This study investigated the effect and mechanism of zein on the digestive stability of five citrus flavonoids, namely hesperetin (HET), hesperidin (HED), neohesperidin (NHD), naringenin (NEN), and naringin (NIN). RESULTS Zein enhanced the digestive stability of the five citrus flavonoids, especially that of HET and NEN, during digestion in the stomach and small intestine. Fluorescence spectroscopy results suggested that citrus flavonoids spontaneously quenched the endogenous fluorescence of zein in static quenching mode. The binding of HET, HED and NHD to zein was driven respectively by electrostatic, hydrophobic and electrostatic interaction. However, Van der Waals' force and hydrogen (H)-bond interaction represented the primary driving force for binding NEN, and NIN to zein to form complexes. The binding of the five citrus flavonoids to zein also caused a diverse bathochromic shift in ultraviolet absorbance. Analysis using Fourier-transform infrared and Raman spectroscopy revealed that the binding behavior of the five citrus flavonoids had different effects on changes in the secondary structures, disulfide bonds, and tyrosine exposure of zein. The results were also partially verified by molecular dynamic simulation. CONCLUSIONS Zein enhanced the digestive stability of the five citrus flavonoids via different binding interactions that was due to the difference in molecular structure of citrus flavonoids. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Wenfeng Li
- School of Life Science and Biotechnology, Yangtze Normal University, Chongqing, China
| | - Xiaohua Zhang
- School of Life Science and Biotechnology, Yangtze Normal University, Chongqing, China
| | - Si Tan
- School of Life Science and Biotechnology, Yangtze Normal University, Chongqing, China
| | - Xueping Li
- School of Life Science and Biotechnology, Yangtze Normal University, Chongqing, China
| | - Mengyuan Gu
- School of Life Science and Biotechnology, Yangtze Normal University, Chongqing, China
| | - Mengqi Tang
- School of Life Science and Biotechnology, Yangtze Normal University, Chongqing, China
| | - Xin Zhao
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, China
| | - Yingmei Wu
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of the Three Gorges Reservoir Area's Medicinal Herbs, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
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Eslami-Farsani R, Farhadian S, Shareghi B. Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods. J Biomol Struct Dyn 2022; 40:3581-3594. [PMID: 33308044 DOI: 10.1080/07391102.2020.1848633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sadegh Farhadian
- Department of Biology, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
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Mastellone G, Marengo A, Sgorbini B, Scaglia F, Capetti F, Gai F, Peiretti PG, Rubiolo P, Cagliero C. Characterization and Biological Activity of Fiber-Type Cannabis sativa L. Aerial Parts at Different Growth Stages. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030419. [PMID: 35161400 PMCID: PMC8838183 DOI: 10.3390/plants11030419] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 05/19/2023]
Abstract
Currently, there is a renewed interest in cannabis-related products in different fields because of the rich phytocomplex of this plant, together with its fiber and agricultural features. In this context, the current study aims to chemically characterize different samples of fiber-type Cannabis sativa L. grown in Italy as a potential health promoting source. An ultrasound-assisted solid-liquid extraction (UA-SLE) method was first developed and optimized to obtain a fingerprinting of the investigated phytocomplex. Analyses were carried out through an ultra high performance liquid chromatography equipped with a photodiode array detector in series with triple quadrupole system with an electrospray ionization (ESI) interface (UHPLC-UV-ESI-MS/MS) and showed that the phytocomplex mainly includes flavonoids and non-psychotomimetic cannabinoids. The method was then applied to characterize and compare 24 samples of fiber-type Cannabis sativa L. aerial parts (mainly stems and leaves), which differed for the growth stages (from mid-vegetative to early flowering), growth land plots, and methods of drying (forced-draft oven or freeze-drying). The quali-quantitative analysis showed that a freeze-drying method seems to better preserve the chemical composition of the samples, while the location of the land plot and the growth stage of the plant (which did not comprise inflorescences) had minor influences on the chemical pattern. These results were also supported by spectrophotometric in-vitro assays (scavenging of 2,2-diphenyl-1-picrylhydrazyl (DPPH•) and 2,2'-azinobis-3-ethyl-benzthiazoline-6-sulphonate (ABTS+•) radicals and inhibitory activity against tyrosinase and elastase enzymes) to investigate the potential biological activity of these samples and the contribution of non-psychotomimetic cannabinoids.
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Affiliation(s)
- Giulia Mastellone
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
| | - Arianna Marengo
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
| | - Barbara Sgorbini
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
| | - Federica Scaglia
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
| | - Francesca Capetti
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
| | - Francesco Gai
- Institute of Sciences of Food Production, National Research Council, 10095 Grugliasco, Italy; (F.G.); (P.G.P.)
| | - Pier Giorgio Peiretti
- Institute of Sciences of Food Production, National Research Council, 10095 Grugliasco, Italy; (F.G.); (P.G.P.)
| | - Patrizia Rubiolo
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
| | - Cecilia Cagliero
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (G.M.); (A.M.); (B.S.); (F.S.); (F.C.); (P.R.)
- Correspondence: ; Tel.: +39-011-6707133
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Comparative studies on the interaction of ascorbic acid with gastric enzyme using multispectroscopic and docking methods. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Wu J, Li W, Zheng Z, Lu X, Zhang H, Ma Y, Wang R. Design, synthesis, biological evaluation, common feature pharmacophore model and molecular dynamics simulation studies of ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate as Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors. J Biomol Struct Dyn 2020; 39:1174-1188. [PMID: 32036779 DOI: 10.1080/07391102.2020.1726817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SHP2 is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell death pathway (PD-1/PD-L1) and cell growth and differentiation pathway (MAPK). Moreover, mutations in SHP2 have been implicated in Leopard syndrome (LS), Noonan syndrome (NS), juvenile myelomonocytic leukemia (JMML) and several types of cancer and solid tumors. Thus, SHP2 inhibitors are much needed reagents for evaluation of SHP2 as a therapeutic target. A series of novel ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate derivatives were designed and synthesized, and their SHP2 inhibitory activities (IC50) were determined. Among the desired compounds, 1d shares the highest inhibitory activity (IC50 = 0.99 μM) against SHP2. Additionally, a common feature pharmacophore model was established to explain the structure activity relationship of the desired compounds. Finally, molecular dynamics simulation was carried out to explore the most likely binding mode of compound 1d with SHP2. In brief, the findings reported here may at least provide a new strategy or useful insights in discovering novel effective SHP2 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Weiya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhihui Zheng
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug, Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Xinhua Lu
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug, Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Ziaee E, Shareghi B, Farhadian S, Momeni L, Heibati-Goojani F. The effect of putrescine on stability and structural properties of bovine serum albumin. J Biomol Struct Dyn 2020; 39:254-262. [PMID: 31997719 DOI: 10.1080/07391102.2020.1719199] [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: 10/25/2022]
Abstract
Serum albumins are the abounding proteins in plasma. Their most important characteristic is that they act as carriers for a type of compound, for example, different drugs. Bovine Serum Albumin (BSA) is a single-chain polypeptide with 583 amino acids. Polyamines such as putrescine can interact with negatively charged molecules. The effect of putrescine on the structure of bovine serum albumin has been surveyed utilizing the method of UV-Vis spectroscopy, Thermal stability, fluorescence spectroscopy, and molecular docking at temperature 298 K and 308 K at pH 7.4 using Tris-HCl as a buffer. The complex formation between putrescine and bovine serum albumin was discovered as alter in the absorbance at 280 nm. The amount of absorption increases with the addition of putrescine. The adding of putrescine alters the bovine serum albumin and decrements the hydrophobicity of the micro-environment of the Trp residues in the inner hydrophobic zone. The static kind of quenching process was chiefly contained within the quenching of intrinsic emission of the protein. The fluorescence quenching details (Ksv) for complex bovine serum albumin-putrescine revealed one binding site for putrescine. The negative amount of Gibbs free energy change (ΔG°) suggested the binding operation was spontaneous.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Ziaee
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Lida Momeni
- Department of Biology, Faculty of Science, Payam Noor University, Iran
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