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Cai R, Luo J, Chen C, Ding P, Wang X, Yang K, Zhu X, Guo Y, Chi B, Tuo X. Conformational alterations and functional changes of pepsin induced by a novel food supplement tetrahydrocurcumin: Multispectral techniques and computer simulations. Int J Biol Macromol 2024; 279:135178. [PMID: 39214215 DOI: 10.1016/j.ijbiomac.2024.135178] [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: 05/24/2024] [Revised: 08/15/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Tetrahydrocurcumin (THC), as a novel food supplement, has generated significant interests for its potential impact on health and nutrition. Pepsin serves as the primary enzyme involved in the digestive mechanism. This research investigated the conformational and functional alterations of pepsin induced by THC using multispectral techniques and computer simulations. The results showed that THC enters the cavity of pepsin, in which hydrophobic forces play a major role. The binding constant is 1.044 × 104 M-1 at 310 K. The upregulation or downregulation effect of THC on pepsin activity depends on its concentration. Molecular docking outcomes indicated that THC was encapsulated by various amino acids and established H-bonds with Tyr189 and Ser294, revealing that hydrogen bonds also contribute to maintaining the stability of THC-pepsin complex. In addition, the altered activity of pepsin may be related to the interaction between THC and the amino acids at the active site (Asp32) according to energy contribution results. 3D fluorescence spectroscopy, CD spectra and molecular dynamic simulations show that THC causes conformational changes in pepsin. The existence of THC makes pepsin structure to be less dense, leading to the decrease of energy traps. This suggests that pepsin becomes conformationally more suitable to bind to THC.
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Affiliation(s)
- Ruirui Cai
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Jiaqing Luo
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Chaolan Chen
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Pei Ding
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xiaowei Wang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Kaiyu Yang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xiner Zhu
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Ying Guo
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Baozhu Chi
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China.
| | - Xun Tuo
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China.
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2
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Salahshoori I, Wang Q, Nobre MAL, Mohammadi AH, Dawi EA, Khonakdar HA. Molecular simulation-based insights into dye pollutant adsorption: A perspective review. Adv Colloid Interface Sci 2024; 333:103281. [PMID: 39214024 DOI: 10.1016/j.cis.2024.103281] [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: 10/05/2023] [Revised: 06/20/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Growing concerns about environmental pollution have highlighted the need for efficient and sustainable methods to remove dye contamination from various ecosystems. In this context, computational methods such as molecular dynamics (MD), Monte Carlo (MC) simulations, quantum mechanics (QM) calculations, and machine learning (ML) methods are powerful tools used to study and predict the adsorption processes of dyes on various adsorbents. These methods provide detailed insights into the molecular interactions and mechanisms involved, which can be crucial for designing efficient adsorption systems. MD simulations, detailing molecular arrangements, predict dyes' adsorption behaviour and interaction energies with adsorbents. They simulate the entire adsorption process, including surface diffusion, solvent layer penetration, and physisorption. QM calculations, especially density functional theory (DFT), determine molecular structures and reactivity descriptors, aiding in understanding adsorption mechanisms. They identify stable adsorption configurations and interactions like hydrogen bonding and electrostatic forces. MC simulations predict equilibrium properties and adsorption energies by sampling molecular configurations. ML methods have proven highly effective in predicting and optimizing dye adsorption processes. These models offer significant advantages over traditional methods, including higher accuracy and the ability to handle complex datasets. These methods optimize adsorption conditions, clarify adsorbent functionalization roles, and predict dye removal efficiency under various conditions. This research explores MD, MC, QM, and ML approaches to connect molecular interactions with macroscopic adsorption phenomena. Probing these techniques provides insights into the dynamics and energetics of dye pollutants on adsorption surfaces. The findings will aid in developing and optimizing new materials for dye removal. This review has significant implications for environmental remediation, offering a comprehensive understanding of adsorption at various scales. Merging microscopic data with macroscopic observations enhances knowledge of dye pollutant adsorption, laying the groundwork for efficient, sustainable removal technologies. Addressing the growing challenges of ecosystem protection, this study contributes to a cleaner, more sustainable future.
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Affiliation(s)
- Iman Salahshoori
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran; Department of Polymer Processing, Iran Polymer and Petrochemical Institute, P.O. Box 14965-115, Tehran, Iran.
| | - Qilin Wang
- School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, 2007, Australia
| | - Marcos A L Nobre
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP 19060-900, Brazil
| | - Amir H Mohammadi
- Discipline of Chemical Engineering, School of Engineering, University of KwaZulu-Natal, Howard College Campus, King George V Avenue, Durban 4041, South Africa.
| | - Elmuez A Dawi
- College of Humanities and Sciences, Department of Mathematics, and Science, Ajman University, P.O. Box 346, Ajman, United Arab Emirates
| | - Hossein Ali Khonakdar
- Department of Polymer Processing, Iran Polymer and Petrochemical Institute, P.O. Box 14965-115, Tehran, Iran
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Zhou J, Li J, Cheng C, Yao Y, Li Y, Liu H, Wu L. Unraveling the binding behavior of the antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one with human serum albumin: Multi-spectroscopic, atomic force microscope, computational simulation, and esterase activity. Int J Biol Macromol 2024; 274:133266. [PMID: 38906347 DOI: 10.1016/j.ijbiomac.2024.133266] [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: 04/02/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
As a marine antifouling biocide, 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) exhibited high toxicity to marine organisms. This study investigated the interaction between DCOIT and human serum albumin (HSA) using several spectroscopic techniques combined with computer prediction methods. The UV-vis absorption spectra, Stern-Volmer constant (KSV) and fluorescence resonance energy transfer (FRET) results indicated that DCOIT caused static quenching of HSA fluorescence. The ΔG°, ΔH° and ΔS° values were -31.03 ± 0.17 kJ·mol-1, -133.54 ± 0.88 kJ·mol-1 and -348.46 ± 2.86 J.mol-1·K-1, respectively, suggesting that van der Waals forces and hydrogen bonds governed the spontaneous formation of the complex. Synchronous fluorescence and circular dichroism (CD) spectroscopy observed the burial of Trp residues within HSA and the unfolding of HSA secondary structure induced by DCOIT. Three-dimensional (3D) fluorescence and Atomic Force Microscopy (AFM) further detected DCOIT-induced loosening of HSA peptide chain structure. Site displacement experiments indicated that DCOIT binding at site I of HSA. Computational predictions indicated that hydrophobic interactions were also essential in the complex. The increased RMSD, Rg, SASA, and RMSF confirmed that DCOIT weakened the stability and compactness of HSA, rendering residues more flexible. Lastly, esterase activity assays demonstrated that DCOIT inhibited esterase activity and interfered with the human detoxification process.
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Affiliation(s)
- Junqiao Zhou
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jiayin Li
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Cong Cheng
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - YuJuan Yao
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Yu Li
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Hao Liu
- Liyuan Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430077, PR China
| | - Laiyan Wu
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China.
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Yadollahi E, Shareghi B, Farhadian S, Hashemi Shahraki F. Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation. J Biomol Struct Dyn 2024; 42:3108-3117. [PMID: 37278377 DOI: 10.1080/07391102.2023.2212077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/01/2023] [Indexed: 06/07/2023]
Abstract
Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and β-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Fatemeh Hashemi Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
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Doharey PK, Verma P, Dubey A, Singh SK, Kumar M, Tripathi T, Alonazi M, Siddiqi NJ, Sharma B. Biophysical and in-silico studies on the structure-function relationship of Brugia malayi protein disulfide isomerase. J Biomol Struct Dyn 2024; 42:1533-1543. [PMID: 37079006 DOI: 10.1080/07391102.2023.2201849] [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: 11/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Human Lymphatic filariasis is caused by parasitic nematodes Wuchereria bancrofti, Brugia malayi, and Brugia timori. Protein disulfide isomerase (PDI), a redox-active enzyme, helps to form and isomerize the disulfide bonds, thereby acting as a chaperone. Such activity is essential for activating many essential enzymes and functional proteins. Brugia malayi protein disulfide isomerase (BmPDI) is crucial for parasite survival and an important drug target. Here, we used a combination of spectroscopic and computational analysis to study the structural and functional changes in the BmPDI during unfolding. Tryptophan fluorescence data revealed two well-separated transitions during the unfolding process, suggesting that the unfolding of the BmPDI is non-cooperative. The binding of the fluorescence probe 8-anilino-1-naphthalene sulfonic acid dye (ANS) validated the results obtained by the pH unfolding. The dynamics of molecular simulation performed at different pH conditions revealed the structural basis of BmPDI unfolding. Detailed analysis suggested that under different pH, both the global structure and the conformational dynamics of the active site residues were differentially altered. Our multiparametric study reveals the differential dynamics and collective motions of BmPDI unfolding, providing insights into its structure-function relationship.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pravesh Verma
- Biochemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Amit Dubey
- Computational Chemistry and Drug discovery Division, Quanta calculus Pvt. Ltd, Kushinagar, India
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Sudhir Kumar Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Manish Kumar
- Department of Biochemistry, University of Allahabad, Allahabad, India
| | - Timir Tripathi
- Department of Biochemistry, North-Eastern Hill University, Umshing, India
| | - Mona Alonazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nikhat Jamal Siddiqi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bechan Sharma
- Department of Biochemistry, University of Allahabad, Allahabad, India
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Verma P, Kaur L, Aswal P, Singh A, Pandey R, Ojha H, Pathak M. Binding interactions of Vildagliptin with pepsin: A multi-spectroscopic and in-silico approach and a comparative account with metformin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123368. [PMID: 37748335 DOI: 10.1016/j.saa.2023.123368] [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: 06/23/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Vildagliptin (VDG) and Metformin (Met) belong to a class of dipeptidylpeptidase-4 (DPP-4) inhibitor and biguanide, respectively and used for the management of diabetes mellitus type II (DMTII). Both the drugs are orally available which leads to various side effects due to its oral ingestion. Occurrence of these side effects might be due to some interactions with pepsin at a molecular level. Therefore, in order to investigate these interactions, multi-spectroscopic and in-silico techniques have been extensively studied to identify the binding characteristics of VDG with pepsin. Fluorescence data suggested that the quenching is due to dynamic and static mechanism and static was dominant one. However, fluorescence and UV-Vis spectroscopic measurement analysis suggested that VDG tends to associate with pepsin, via ground-state complex formation. Fluorescence study revealed the binding-constant value which was found to be 0.559 × 103 M-1 at 298.15 K that is non-covalent in nature. VDG-pepsin complex shows exothermic and spontaneous binding as confirmed by the calculated values of ΔH, ΔS, and ΔG, are majorly caused by van der Waals forces and H-bonding interactions. CD spectra of pepsin in presence of VDG confirmed post binding conformational change. Enzyme-activity assay showed that activity of pepsin was decreased by upto 28 %. FRET analysis suggested that energy transfer efficiency is negligible for VDG-pepsin interaction. In-silico analysis reveals that H-bonding and electrostatic negative forces are the significant driving forces involved in the interaction of VDG and pepsin.
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Affiliation(s)
- Piyush Verma
- Division of Radiological Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Sciences, Defence R&D Organisation, Brig. S K Mazumdar Road, Timarpur, Delhi 110054, India; School of Pharmaceutical Sciences, Delhi Pharmaceutical Science and Research University (DPSRU), Pushp Vihar, New Delhi 110017, India
| | - Lajpreet Kaur
- Division of Radiological Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Sciences, Defence R&D Organisation, Brig. S K Mazumdar Road, Timarpur, Delhi 110054, India
| | - Priyanka Aswal
- Department of Pharmaceutics, Uttarakhand Technical University, Sudhowala, Dehradun, Uttarakhand 248001, India
| | - Anju Singh
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Rashmi Pandey
- Guru Gobind Singh Indraprastha University, New Delhi 110078, India
| | - Himanshu Ojha
- Division of Radiological Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Sciences, Defence R&D Organisation, Brig. S K Mazumdar Road, Timarpur, Delhi 110054, India
| | - Mallika Pathak
- Department of Chemistry, Miranda House, University of Delhi, Delhi 110007, India.
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7
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Gholizadeh M, Shareghi B, Farhadian S. Elucidating binding mechanisms of naringenin by alpha-chymotrypsin: Insights into non-binding interactions and complex formation. Int J Biol Macromol 2023; 253:126605. [PMID: 37660852 DOI: 10.1016/j.ijbiomac.2023.126605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
As an inevitable parameter in the description of enzyme properties, the investigation of enzyme-ligand interactions has attracted a lot of attention. Alpha-Chymotrypsin (α-Chy) is essential for protein digestion and plays an important role in human health. Naringenin (NAG) as a potent antioxidant has recently been applied in the pharmaceutical industry. Using multispectral methods and computational simulation techniques, the binding strength of NAG to α-Chy was investigated in this research. UV-vis and fluorescence quenching data showed significant spectral changes upon binding of NAG to α-Chy. As demonstrated by fluorescence techniques, NAG could employ a static quenching process to decrease the intrinsic fluorescence of α-Chy. Both circular dichroism (CD) and FTIR spectroscopic analyses revealed that binding of NAG to α-Chy caused more flexible conformation. The slight increases in RMSD (0.06 nm) were observed for the NAG-(α-Chy) compound was supported by the results of thermal stability data. Docking computation confirmed that hydrogen and Van der Waals interactions are the important forces, which is in exact agreement with thermodynamics studies. Kinetic analysis of the enzyme showed an increase in activity, which was consistent, with the MD simulation results. The findings from the in-silico studies were in complete agreement with the experimental results.
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Affiliation(s)
- Mohammad Gholizadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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Zhu S, Wang T, Zheng Y, Shi Q, Guo Q, Zhu J, Mao Y. Spectroscopic and molecular docking study of three kinds of cinnamic acid interaction with pepsin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123169. [PMID: 37517266 DOI: 10.1016/j.saa.2023.123169] [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: 03/06/2023] [Revised: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
In this work, under simulated physiological conditions (pH = 2.2, glycine hydrochloric acid buffer solution), the interactions of cinnamic acid (CA), m-hydroxycinnamic acid (m-CA) and p-hydroxycinnamic acid (p-CA) with pepsin were studied by fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy, circular dichroism (CD) spectroscopy, Fourier transform infrared spectroscopy (FTIR), molecular docking and molecular dynamic simulation (MD). The spectrogram results showed that these three kinds of CA had a strong ability to quench the intrinsic fluorescence of pepsin, and the quenching effects were obvious with the increase of concentration of these three kinds of molecules. The quenching mechanism of CA, m-CA and p-CA on the fluorescence of pepsin was static quenching. In addition, a stable complex was formed between three kinds of CA with pepsin. Thermodynamic data and docking information suggested that three kinds of CA combine with pepsin were mainly driven by electrostatic force and hydrogen bond. The binding constant and the number of binding sites were determined. The interaction of CA, m-CA and p-CA with pepsin was spontaneous, and accompanied by non-radiative energy transfer. The results from CD, FTIR, UV-Vis and synchronous fluorescence spectra measurements manifested that the secondary structure of pepsin was changed by the binding of three kinds of CA. The β-sheet of pepsin increased after the interaction with three kinds of CA. The assay results of pepsin activity showed that three kinds of CA led to a decrease in pepsin activity within the investigated concentrations. Molecular docking investigation revealed the formation of polar hydrogen bonds as well as hydrophobic interactions between three kinds of CA with pepsin, and the ligand within the binding pocket of pepsin. MD results implied the formation of a stable complex between three kinds of CA and pepsin. The research suggested that cinnamic acid and its derivatives could be a potential effect on the structure and properties of digestive enzyme.
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Affiliation(s)
- Sujuan Zhu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
| | - Ting Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Ying Zheng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Qiang Shi
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Qian Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Jing Zhu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Yiyang Mao
- Center for Disease Control and Prevention, Yangzhou, Jiangsu 225009, PR China.
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Ma X, Kuang L, Wang X, Zhang Z, Chen C, Ding P, Chi B, Xu J, Tuo X. Investigation on the interaction of aromatic organophosphate flame retardants with human serum albumin via computer simulations, multispectroscopic techniques and cytotoxicity assay. Int J Biol Macromol 2023; 247:125741. [PMID: 37423437 DOI: 10.1016/j.ijbiomac.2023.125741] [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: 05/28/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Organophosphate flame retardants (OPFRs) are newly emerging estrogenic environmental pollutants, which attracted widespread public interest owing to their potential threats to human. Here, the interaction between two typical aromatic OPFRs, TPHP/EHDPP and HSA was researched by different experiments. Experimental results indicated that TPHP/EHDPP can insert the site I of HSA and be encircled by several amino acid residues, Asp451, Glu292, Lys195, Trp214 and Arg218 played vital roles in this binding process. At 298 K, the Ka value of TPHP-HSA complex was 5.098 × 104 M-1, and the Ka value of EHDPP-HSA was 1.912 × 104 M-1. Except H-bonds and van der Waals forces, the π-electrons on the phenyl ring of aromatic-based OPFRs played a pivotal role in maintaining the stability of the complexes. The content alterations of HSA were observed in the present of TPHP/EHDPP. The IC50 values of TPHP and EHDPP were 157.9 μM and 31.14 μM to GC-2spd cells, respectively. And the existence of HSA has a regulatory effect on the reproductive toxicity of TPHP/EHDPP. In addition, the results of present work implied Ka values of OPFRs and HSA are possible to be a useful parameter for evaluating their relative toxicity.
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Affiliation(s)
- Xiulan Ma
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Lin Kuang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xiaowei Wang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Zihang Zhang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Chaolan Chen
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Pei Ding
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Baozhu Chi
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Junying Xu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xun Tuo
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China.
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10
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Zhang H, Cai R, Chen C, Gao L, Ding P, Dai L, Chi B. Impacts of Halogen Substitutions on Bisphenol A Compounds Interaction with Human Serum Albumin: Exploring from Spectroscopic Techniques and Computer Simulations. Int J Mol Sci 2023; 24:13281. [PMID: 37686087 PMCID: PMC10487517 DOI: 10.3390/ijms241713281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/19/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Bisphenol A (BPA) is an endocrine-disrupting compound, and the binding mechanism of BPA with carrier proteins has drawn widespread attention. Halogen substitutions can significantly impact the properties of BPA, resulting in various effects for human health. Here, we selected tetrabromobisphenol A (TBBPA) and tetrachlorobisphenol A (TCBPA) to investigate the interaction between different halogen-substituted BPAs and human serum albumin (HSA). TBBPA/TCBPA spontaneously occupied site I and formed stable binary complexes with HSA. Compared to TCBPA, TBBPA has higher binding affinity to HSA. The effect of different halogen substituents on the negatively charged surface area of BPA was an important reason for the higher binding affinity of TBBPA to HSA compared to TCBPA. Hydrogen bonds and van der Waals forces were crucial in the TCBPA-HSA complex, while the main driving factor for the formation of the TBBPA-HSA complex was hydrophobic interactions. Moreover, the presence of TBBPA/TCBPA changed the secondary structure of HSA. Amino acid residues such as Lys199, Lys195, Phe211, Arg218, His242, Leu481, and Trp214 were found to play crucial roles in the binding process between BPA compounds and HSA. Furthermore, the presence of halogen substituents facilitated the binding of BPA compounds with HSA.
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Affiliation(s)
- Huan Zhang
- School of Life Sciences, Nanchang University, Nanchang 330031, China;
| | - Ruirui Cai
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China; (R.C.); (C.C.); (L.G.); (L.D.)
| | - Chaolan Chen
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China; (R.C.); (C.C.); (L.G.); (L.D.)
| | - Linna Gao
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China; (R.C.); (C.C.); (L.G.); (L.D.)
| | - Pei Ding
- School of Pharmacy, Nanchang University, Nanchang 330031, China;
| | - Lulu Dai
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China; (R.C.); (C.C.); (L.G.); (L.D.)
| | - Baozhu Chi
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China; (R.C.); (C.C.); (L.G.); (L.D.)
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11
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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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12
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Farajzadeh-Dehkordi M, Mafakher L, Samiee-Rad F, Rahmani B. Computational analysis of missense variant CYP4F2*3 (V433M) in association with human CYP4F2 dysfunction: a functional and structural impact. BMC Mol Cell Biol 2023; 24:17. [PMID: 37161313 PMCID: PMC10170697 DOI: 10.1186/s12860-023-00479-0] [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: 10/11/2022] [Accepted: 05/02/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Cytochrome P450 4F2 (CYP4F2) enzyme is a member of the CYP4 family responsible for the metabolism of fatty acids, therapeutic drugs, and signaling molecules such as arachidonic acid, tocopherols, and vitamin K. Several reports have demonstrated that the missense variant CYP4F2*3 (V433M) causes decreased activity of CYP4F2 and inter-individual variations in warfarin dose in different ethnic groups. However, the molecular pathogenicity mechanism of missense V433M in CYP4F2 at the atomic level has not yet been completely elucidated. METHODS AND RESULTS In the current study, we evaluated the effect of the V433M substitution on CYP4F2 using 14 different bioinformatics tools. Further molecular dynamics (MD) simulations were performed to assess the impact of the V433M mutation on the CYP4F2 protein structure, stability, and dynamics. In addition, molecular docking was used to illustrate the effect of V433M on its interaction with vitamin K1. Based on our results, the CYP4F2*3 variant was a damaging amino acid substitution with a destabilizing nature. The simulation results showed that missense V433M affects the dynamics and stability of CYP4F2 by reducing its compactness and stability, which means that it tends to change the overall structural conformation and flexibility of CYP4F2. The docking results showed that the CYP4F2*3 variant decreased the binding affinity between vitamin K1 and CYP4F2, which reduced the activity of CYP4F2*3 compared to native CYP4F2. CONCLUSIONS This study determined the molecular pathogenicity mechanism of the CYP4F2*3 variant on the human CYP4F2 protein and provided new information for understanding the structure-function relationship of CYP4F2 and other CYP4 enzymes. These findings will aid in the development of effective drugs and treatment options.
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Affiliation(s)
- Mahvash Farajzadeh-Dehkordi
- Department of Molecular Medicine, Faculty of Medical School, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
- Department of Pathology, Faculty of Medical School, Qazvin University of Medical Sciences, Qazvin, Iran.
| | - Fatemeh Samiee-Rad
- Department of Pathology, Faculty of Medical School, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Babak Rahmani
- Department of Molecular Medicine, Faculty of Medical School, Qazvin University of Medical Sciences, Qazvin, Iran.
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13
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Nagar N, Saxena H, Pathak A, Mishra A, Poluri KM. A review on structural mechanisms of protein-persistent organic pollutant (POP) interactions. CHEMOSPHERE 2023; 332:138877. [PMID: 37164191 DOI: 10.1016/j.chemosphere.2023.138877] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/20/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]
Abstract
With the advent of the industrial revolution, the accumulation of persistent organic pollutants (POPs) in the environment has become ubiquitous. POPs are halogen-containing organic molecules that accumulate, and remain in the environment for a long time, thus causing toxic effects in living organisms. POPs exhibit a high affinity towards biological macromolecules such as nucleic acids, proteins and lipids, causing genotoxicity and impairment of homeostasis in living organisms. Proteins are essential members of the biological assembly, as they stipulate all necessary processes for the survival of an organism. Owing to their stereochemical features, POPs and their metabolites form energetically favourable complexes with proteins, as supported by biological and dose-dependent toxicological studies. Although individual studies have reported the biological aspects of protein-POP interactions, no comprehensive study summarizing the structural mechanisms, thermodynamics and kinetics of protein-POP complexes is available. The current review identifies and classifies protein-POP interaction according to the structural and functional basis of proteins into five major protein targets, including digestive and other enzymes, serum proteins, transcription factors, transporters, and G-protein coupled receptors. Further, analysis detailing the molecular interactions and structural mechanism evidenced that H-bonds, van der Waals, and hydrophobic interactions essentially mediate the formation of protein-POP complexes. Moreover, interaction of POPs alters the protein conformation through kinetic and thermodynamic processes like competitive inhibition and allostery to modulate the cellular signalling processes, resulting in various pathological conditions such as cancers and inflammations. In summary, the review provides a comprehensive insight into the critical structural/molecular aspects of protein-POP interactions.
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Affiliation(s)
- Nupur Nagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Harshi Saxena
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Aakanksha Pathak
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, 342011, Rajasthan, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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14
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Habibi A, Farhadian S, Shareghi B, Hashemi-Shahraki F. Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122264. [PMID: 36652806 DOI: 10.1016/j.saa.2022.122264] [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: 10/15/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.
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Affiliation(s)
- Atefeh Habibi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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15
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Hong T, Long L, Sang Y, Jiang Z, Ni H, Zheng M, Li L, Li Q, Zhu Y. Simultaneous enhancement of thermostability and catalytic activity of κ-carrageenase from Pseudoalteromonas tetraodonis by rational design. Enzyme Microb Technol 2023; 167:110241. [PMID: 37060759 DOI: 10.1016/j.enzmictec.2023.110241] [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: 01/08/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023]
Abstract
κ-Carrageenase provides an attractive enzymatic approach to preparation of κ-carrageenan oligosaccharides. Pseudoalteromonas tetraodonis κ-carrageenase is active at the alkaline conditions but displays low thermostability. To further improve its enzymatic performance, two mutants of Q42V and I51H exhibiting both improved thermostability and enzyme activity were screened by the PoPMuSiC algorithm. Compared with the wild-type κ-carrageenase (WT), Q42V and I51H increased the enzyme activity by 20.9% and 25.4%, respectively. After treatment at 50 ℃ for 40 min, Q42V and I51H enhanced the residual activity by 31.1% and 25.9%, respectively. The Tm values of Q42V, I51H, and WT determined by differential scanning calorimetry were 58.2 ℃, 54.8 ℃, and 51.2 ℃, respectively. Compared with untreated and HCl-treated κ-carrageenans, Q42V-treated κ-carrageenan exhibited higher pancreatic lipase inhibitory activity. Molecular docking analysis indicated that the additional pi-sigma force and hydrophobic interaction in the enzyme-substrate complex could account for the increased catalytic activity of Q42V and I51H, respectively. Molecular dynamics analysis indicated that the improved thermostability of mutants Q42V and I51H could be attributed to the less structural deviation and the flexible changes of enzyme conformation at high temperature. This study provides new insight into κ-carrageenase performance improvement and identifies good candidates for their industrial applications.
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Affiliation(s)
- Tao Hong
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Liufei Long
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Yuyan Sang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Mingjing Zheng
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Lijun Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Yanbing Zhu
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China.
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16
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Hashemi-Shahraki F, Shareghi B, Farhadian S, Yadollahi E. A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 289:122240. [PMID: 36527971 DOI: 10.1016/j.saa.2022.122240] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.
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Affiliation(s)
- Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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17
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Dehkordi MF, Farhadian S, Hashemi-Shahraki F, Rahmani B, Darzi S, Dehghan G. The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study. Int J Biol Macromol 2023; 235:123713. [PMID: 36801300 DOI: 10.1016/j.ijbiomac.2023.123713] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.
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Affiliation(s)
- Mahvash Farajzadeh Dehkordi
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Babak Rahmani
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
| | - Sina Darzi
- Health Products Safety Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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18
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Hashemi-Shahraki F, Shareghi B, Farhadian S. Investigation of the interaction behavior between quercetin and pepsin by spectroscopy and MD simulation methods. Int J Biol Macromol 2023; 227:1151-1161. [PMID: 36464189 DOI: 10.1016/j.ijbiomac.2022.11.296] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 10/23/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
The ability of a therapeutic compound to bind to proteins is critical for characterizing its therapeutic impacts. We have selected quercetin (Qu), a most common flavonoid found in plants and vegetables among therapeutic molecules that are known to have anti-inflammatory, antioxidant, anti-genotoxic, and anti-cancer effects. The current study aimed to see how quercetin interacts with pepsin in an aqueous environment under physiological conditions. Absorbance and emission spectroscopy, circular dichroism (CD), and kinetic methods, as well as molecular dynamic (MD) simulation and docking, were applied to study the effects of Qu on the structure, dynamics, and kinetics of pepsin. Stern-Volmer (Ksv) constants were computed for the pepsin-quercetin complex at three temperatures, showing that Qu reduces enzyme emission spectra using a static quenching. With Qu binding, the Vmax and the kcat/Km values decreased. UV-vis absorption spectra, fluorescence emission spectroscopy, and CD result indicated that Qu binding to pepsin leads to microenvironmental changes around the enzyme, which can alter the enzyme's secondary structure. Therefore, quercetin caused alterations in the function and structure of pepsin. Thermodynamic parameters, MD binding, and docking simulation analysis showed that non-covalent reactions, including the hydrophobic forces, played a key role in the interaction of Qu with pepsin. The findings conclude of spectroscopic experiments were supported by molecular dynamics simulations and molecular docking results.
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Affiliation(s)
- Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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19
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Akram M, Osama M, Hashmi MA, Kabir-Ud-Din. Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives. J Biomol Struct Dyn 2023; 41:12276-12291. [PMID: 36695086 DOI: 10.1080/07391102.2023.2168759] [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: 10/01/2022] [Accepted: 01/01/2023] [Indexed: 01/26/2023]
Abstract
The implications of surfactant-enzyme/protein interactions in a variety of fields, including biotechnology, cosmetics, paints and pharmaceuticals, have attracted a lot of attention in contemporary studies. Herein, we have employed several in vitro and in silico techniques such as excitation and absorption spectroscopies, circular dichroism and FT-IR spectroscopies, density functional and molecular dynamics simulations to understand the interaction behavior of oxy-diester-based green cationic Gemini surfactants, N1,N1,N14,N14-tetramethyl-2,13-dioxo-N1,N14-dialkyl-3,6,12-tetraoxateradecane-1,14-diaminiumdichloride (abbreviated as Cm-E2O2-Cm, where 'm' stands for alkyl chain length, m = 12 and 14) with one of the main digestive proteins, pepsin. The spectroscopic techniques confirm the static quenching effect of surfactants on pepsin. The calculated physical parameters (Ksv, Kb and ΔG) and their order reveal the distinguished implications for the surfactants' chain lengths. The spontaneity of interaction was also confirmed by negative Gibbs free energy change values. The extrinsic spectroscopic study with pyrene as fluorescence probe, FT-IR and CD techniques indicated a potential conformational change in pepsin induced by the Gemini surfactants. DFT, docking and MD simulations provided the theoretical understanding regarding the quantum mechanical environment, location of binding and stability of the protein-surfactant complexation in energy terms. We believe this study will be a humble addition to our existing knowledge in the field of protein-surfactant interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Akram
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Mohammad Osama
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Kabir-Ud-Din
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
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20
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Yadollahi E, Shareghi B, Farhadian S. Binding parameters and molecular dynamics of Trypsin-Acid Yellow 17 complexation as a function of concentration. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121589. [PMID: 35872431 DOI: 10.1016/j.saa.2022.121589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Acid Yellow 17 is a kind of azo dye used in food, textile, and cosmetics. Several studies explain the toxicity of azo dye for our body, but one could not find further information about the effects of these dyes on human macromolecules. In the current study, the interaction of AY17 with trypsin is investigated using several techniques. The UV analysis displayed that the absorption of trypsin could be decreased in the presence of this color. The fluorescence investigation indicated that a static form of quenching happens, and a 50% decrease in the fluorescence intensity, also showed the Vander Waals and hydrogen bond are the main forces in the interaction of this color and trypsin. Furthermore, we can observe that the Tm point of trypsin decreases from 46.5 to 42. On the other hand, the CD results were indicated that the interaction of this color with trypsin could decrease the percent of turn, coil and α-helix in trypsin structure. The computational study was undertaken to obtain more information about the interaction between trypsin and AY17. The results were in agreement with the experimental investigation and indicated that the interaction between this color and trypsin leads to less compactness in the trypsin structure.
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Affiliation(s)
- Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box 115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box 115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box 115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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21
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Yue Y, Wang Y, Tu Q, Xu Y, Zhang Y, Tang Q, Liu J. A comprehensive insight into the effects of punicalagin on pepsin: Multispectroscopy and simulations methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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22
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Yadollahi E, Shareghi B, Farhadian S. Noncovalent interactions between Quinoline yellow and trypsin: In vitro and in silico methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Ashrafi N, Shareghi B, Farhadian S, Hosseini-Koupaei M. A comparative study of the interaction of naringenin with lysozyme by multi-spectroscopic methods, activity comparisons, and molecular modeling procedures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120931. [PMID: 35085994 DOI: 10.1016/j.saa.2022.120931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/31/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
The present study applied steady-state fluorescence, UV-Vis spectrophotometry, molecular docking studies, and circular dichroism (CD) to investigate the interaction of naringenin with lysozyme in an aqueous medium. The UV-Vis measurement indicated the changes in lysozyme secondary and tertiary structure change as a function of the concentration of naringenin. Naringenin could be used to turn the static quenching mechanism into the intrinsic fluorescence of lysozyme. The negative amount of Gibbs free energy (ΔG°) suggested that the binding operation was spontaneous. Fluorescence studies also demonstrated the changes occurring in the Trp microenvironment upon the concatenation into lysozyme. Analysis of thermodynamic parameters also revealed that hydrophobic forces played a fundamental role in determining the complex stability; this was consistent with the previous modeling studies. Circular dichroism also suggested that the alpha-helicity of lysozyme was enhanced as ligand was bound. Naringenin inhibited lysozyme enzymatic activity, displaying its affinity with the lysozyme active site. Further, molecular docking studies demonstrated that naringenin could bind to both residues essential for catalytic activity in the proximity of Trp 62 and Trp 63.
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Affiliation(s)
- Narges Ashrafi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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Mavani A, Ovung A, Luikham S, Suresh Kumar G, Das A, Ray D, Aswal VK, Bhattacharyya J. Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin. J Biomol Struct Dyn 2022; 41:3779-3790. [PMID: 35380096 DOI: 10.1080/07391102.2022.2057358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×104, M-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A. Mavani
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Aben Ovung
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhi Das
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Vinod K. Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
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Huang X, Huang M, Yong L, Jia D, Miao W, Yi Z, Liu H. Study on Spectral Method and Computational Simulation of Chlorinated Bisphenol Compound and Thyroxine‐Binding Globulin. ChemistrySelect 2022. [DOI: 10.1002/slct.202104376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaomei Huang
- College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Muwei Huang
- College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Li Yong
- College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Dan Jia
- College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Wangli Miao
- 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
| | - Hongyan Liu
- College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
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26
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Yazdani F, Shareghi B, Farhadian S, Momeni L. Structural insights into the binding behavior of flavonoids naringenin with Human Serum Albumin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Eslami-Farsani R, Farhadian S, Shareghi B, Momeni L. Structural insights into the binding behavior of NiO with myoglobin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Mohammadi M, Shareghi B, Farhadian S, Momeni L, Saboury AA. The interaction of xylitol with carboxypeptidase A: The influence of xylitol on enzyme structure and activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Farhadian S, Hashemi-Shahraki F, Amirifar S, Asadpour S, Shareghi B, Heidari E, Shakerian B, Rafatifard M, Firooz AR. Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer. Int J Biol Macromol 2022; 194:790-799. [PMID: 34838577 DOI: 10.1016/j.ijbiomac.2021.11.126] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/08/2023]
Abstract
Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.
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Affiliation(s)
- Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sogand Amirifar
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Saeid Asadpour
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Ehsan Heidari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Behnam Shakerian
- Cardiovascular Diseases Research Department, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Rafatifard
- Exercise Science/Physiology, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ali Reza Firooz
- Department of Chemistry, University of Isfahan, Isfahan, Iran
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Moradi S, Shareghi B, Saboury AA, Farhadian S. Molecular aspects of the interaction of acid phosphatase with TiO2 nanoparticles: Kinetic and multispectroscopic studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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Investigation on the interaction behavior between safranal and pepsin by spectral and MD simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Peng L, Wang Z, Zhu H, Zeng T, Zhou W, Yao S, Song H. Synthesis, physico-chemical properties of novel tropine-amino acid based ionic liquids and their effects on the lipase activity. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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33
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Hashemi-Shahraki F, Shareghi B, Farhadian S. Characterizing the binding affinity and molecular interplay between quinoline yellow and pepsin. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117317] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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34
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Li Y, Li N, Chen F, Yang X, Lei Y, Liu Y, Tuo X. Evaluation of binding properties of human serum albumin and mono-benzyl phthalate (MBZP): Multi-spectroscopic analysis and computer simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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35
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Evaluation of interactions between food colorant, tartrazine, and Apo-transferrin using spectroscopic analysis and docking simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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36
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Heibati-Goojani F, Farhadian S, Shareghi B, Shahraki FH, Ziaee E. Insights into the binding mechanism of Putrescine on α-amylase by multiple spectroscopic techniques and molecular docking. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Li X, Liu H, Wu X, Xu R, Ma X, Zhang C, Song Z, Peng Y, Ni T, Xu Y. Exploring the interactions of naringenin and naringin with trypsin and pepsin: Experimental and computational modeling approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119859. [PMID: 33957444 DOI: 10.1016/j.saa.2021.119859] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/11/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Naringenin and naringin are two natural compounds with important health benefits, whether as food or drug. It is necessary to study the interactions between naringenin/naringin and digestive proteases, such as trypsin and pepsin. In this study, the bindings of naringenin and naringin to trypsin and pepsin were investigated using multi-spectroscopy analysis and computational modeling approaches. Fluorescence experiments indicate that both naringenin and naringin can quench the intrinsic fluorescence of trypsin/pepsin via static quenching mechanism. Naringin binds trypsin/pepsin in a more firmly way than naringenin. Thermodynamic analysis reveals that the interactions of naringenin/naringin and trypsin/pepsin are synergistically driven by enthalpy and entropy, and the major driving forces are hydrophobic, electrostatic interactions and hydrogen bonding. Synchronous fluorescence spectroscopy, circular dichroism spectroscopy and FT-IR show that naringenin/naringin may induce microenvironmental and conformational changes of trypsin and pepsin. Molecular docking reveals that naringenin binds in the close vicinity of the active site (Ser-195) of trypsin and Asp-32 (the catalytic activity of pepsin) appears in naringin-pepsin system. The direct interactions between naringenin or naringin and catalytic amino acid residues will inhibit the catalytic activity of trypsin and pepsin, respectively. The results of molecular dynamic simulation validate the reliability of the docking results.
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Affiliation(s)
- Xiangrong Li
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Hongyi Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Xinzhe Wu
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Ruonan Xu
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Xiaoyi Ma
- Grade 2018, Pharmaceutics, School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Congxiao Zhang
- Grade 2018, Pharmaceutics, School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Zhizhi Song
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Yanru Peng
- Grade 2017, Clinical Pharmacy, School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Tianjun Ni
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.
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Yanti S, Wu ZW, Agrawal DC, Chien WJ. Interaction between phloretin and insulin: a spectroscopic study. J Anal Sci Technol 2021. [DOI: 10.1186/s40543-021-00284-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AbstractDiabetes is among the top ten deadly diseases in the world. It occurs either when the pancreas does not produce enough insulin (INS) or when the body cannot effectively use the insulin it produces. Phloretin (PHL) has a biological effect that can treat diabetes. A spectroscopic study was carried out to explore the interaction between phloretin and insulin. UV/Vis spectroscopy, fluorescence spectroscopy, and circular dichroism spectropolarimeter were used in the study. UV/Vis spectra showed that the interaction between PHL and INS produced strong absorption at a wavelength of 282 nm. The fluorescence analysis results showed that the excitation and emission occurred at 280-nm and 305-nm wavelengths, respectively. Temperature changes did not affect INS emissions. However, the interaction of PHL–INS caused a redshift at 305 to 317 nm. Temperature affected the binding constant (Ka) and the binding site (n). Ka decreased with increasing temperature and increased the binding site. The thermodynamic parameters such as enthalpy (ΔH0) and entropy (ΔS0) each had a value of − 16,514 kJ/mol and 22.65 J/mol·K. PHL and INS interaction formed hydrogen bonds and hydrophobic interaction. The free energy (ΔG0) recorded was negative. PHL and INS interactions took place spontaneously. The quenching effect was dynamic and static. KD values were greater than KS. The higher the temperature, the less was KD and KS. The appearance of two negative signals on circular dichroism (CD) spectropolarimeter implies that phloretin could induce regional configuration changes in insulin. The addition of PHL has revealed that the proportion of α-helix in the insulin stabilizes its structure. Phloretin’s stabilization and enhancement of the α-helix structural configuration in insulin indicate that phloretin can improve insulin resistance.
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Insights on the interaction mechanism of exemestane to three digestive enzymes by multi-spectroscopy and molecular docking. Int J Biol Macromol 2021; 187:54-65. [PMID: 34274402 DOI: 10.1016/j.ijbiomac.2021.07.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 01/27/2023]
Abstract
Exemestane is an irreversible steroidal aromatase inhibitor, typically used to treat breast cancer. As an anti-tumor drug, exemestane has more obvious side effects on the gastrointestinal tract. The purpose of this work is to investigate the combination of exemestane with three important digestive enzymes including pepsin (Pep), trypsin (Try) and α-Chymotrypsin (α-ChT) so as to analyze the mechanism of the gastrointestinal adverse effects causing by exemestane binding. Enzyme activity experiment showed that the enzyme activity of Pep was decreased in the presence of exemestane. Fluorescence spectra revealed that exemestane formed stable complexes with digestive enzymes, and the quenching mechanism of drug-digestive enzymes interaction were all static quenching. The binding constants of Pep, Try and α-ChT at 298 K were 2.34 × 105, 1.45 × 105, and 2.05 × 105 M-1, respectively. Synchronous fluorescence and 3D fluorescence spectroscopy showed that the conformation of exemestane was slightly changed after combining with digestive enzymes, and non-radiative energy transfer occurred. Circular dichroism results indicated that exemestane could change the secondary structure of digestive enzymes via increase the α-helix content and decrease in the β-sheet content. Thermodynamic parameters (ΔH0, ΔS0, and ΔG0) revealed that exemestane interacted with α-ChT through electrostatic force, and the binding force with Pep and Try was van der Waals interactions and hydrogen, which was basically consistent with the molecular docking results.
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40
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A comparative study of structural and dynamical properties of bovine serum albumin in the presence of spermine. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Huang M, Yong L, Xu J, Zuo Y, Yi Z, Liu H. Determinants of Adenosine A
2A
Receptors‐Perfluoroalkyl Sulfonates Complex: Multi‐Spectroscopic and Molecular Dynamics Simulation Study. ChemistrySelect 2021. [DOI: 10.1002/slct.202100863] [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)
- Manting Huang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Li Yong
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Jie Xu
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Yanqiu Zuo
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Zhongsheng Yi
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
| | - Hongyan Liu
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection College of Chemistry and Bioengineering Guilin University of Technology Guilin 541004 China
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Chu S, He F, Yu H, Liu G, Wan J, Jing M, Li Y, Cui Z, Liu R. Evaluation of the binding of UFCB and Pb-UFCB to pepsin: Spectroscopic analysis and enzyme activity assay. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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44
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Raeessi-babaheydari E, Farhadian S, Shareghi B. The interaction of the green tea polyphenol (catechin) with pepsin: Insights from spectroscopic to molecular dynamics studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115196] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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