1
|
Saleh AH, Borhan G, Goujon F, Devémy J, Dequidt A, Malfreyt P, Sahihi M. Molecular and Energetic Descriptions of the Plasma Protein Adsorption onto the PVC Surface: Implications for Biocompatibility in Medical Devices. ACS OMEGA 2024; 9:38054-38065. [PMID: 39281894 PMCID: PMC11391563 DOI: 10.1021/acsomega.4c05044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/01/2024] [Accepted: 08/12/2024] [Indexed: 09/18/2024]
Abstract
Protein adsorption on material surfaces plays a key role in the biocompatibility of medical devices. Therefore, understanding the complex interplay of physicochemical factors driving this kind of biofouling is paramount for advancing biomaterial design. In this study, we investigated the interaction of the most prominent plasma proteins with polyvinyl chloride (PVC) as one of the ubiquitous materials in medical devices. Through molecular docking, we identified human serum albumin (HSA) as a plasma protein with the highest affinity for adsorption onto the PVC surface with the binding energy of -25.9 kJ mol-1. Subsequently, utilizing triplicate molecular dynamics (MD) simulations (0.5 μs each), we quantitatively analyzed the interactions between HSA and PVC, probing potential structural changes in the protein upon adsorption. Our findings revealed that water-mediated hydrogen bonds and van der Waals forces are key contributors in stabilizing HSA onto the surface of PVC without significant alteration to its secondary and tertiary structures. The observed distribution of water molecules further highlights the importance of the hydration layer in facilitating and modulating protein-polymer interactions. We further evaluated the thermodynamic properties governing the adsorption process by calculating the potential of mean force (PMF) along the direction normal to the surface. The computed Gibbs free energy of adsorption at 300 K (-507.4 kJ/mol) indicated a thermodynamically favored and spontaneous process. Moreover, our investigations across different temperatures (290 to 310 K) consistently showed an enthalpy-driven adsorption process.
Collapse
Affiliation(s)
- Amr H Saleh
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Ghazal Borhan
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Julien Devémy
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Patrice Malfreyt
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Mehdi Sahihi
- , Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| |
Collapse
|
2
|
Bao J, Ren H, Han J, Yang X, Li Y, Jin J. Levels, tissue distribution and isomer stereoselectivity of Dechlorane Plus in humans: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166156. [PMID: 37572901 DOI: 10.1016/j.scitotenv.2023.166156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Exposure of human tissues to Dechlorane Plus (DP) has raised public concern because of the multiple health threats it may pose to humans. Therefore, it is important to summarize the main findings of previous studies on DP in human tissues and to provide potential guidance for future studies. In this paper, DP levels in different populations and human tissues worldwide since 2009 were systematically reviewed. DP levels in human tissues of workers in e-waste dismantling sites in Guangdong Province, China (median 190 ng·g-1 lw in serum) and DP manufacturing plants in Jiangsu Province, China (mean 857 ng·g-1 lw in whole-blood) are the highest reported worldwide. DP levels in tissues of the general population in recent studies are close to those of residents near e-waste dismantling sites, which should be of concern. DP levels in different human tissues were found to be positively correlated with a pattern of blood > breast milk > adipose tissue. The distribution of DP in different human tissues is mainly lipid-driven and may also be influenced by the interaction of DP with proteins such as human serum albumin. Most of the past studies determined the isomer stereoselectivity of DP in human tissues only by comparing the composition of DP in commercial DP products and human tissues, which lacks evidence of mechanism. Recently, a significantly different affinity of DP isomers for proteins was found, which seems to confirm the isomer selectivity of DP in human tissues. We simulated the binding of DP to human serum albumin and DP to thyroid hormone receptor β by molecular docking and found differences in the binding behavior of syn-DP and anti-DP to the selected proteins. Molecular docking seems to be a feasible approach for future studies to predict and reveal the mechanisms of DP behavior and health effects in human tissues.
Collapse
Affiliation(s)
- Junsong Bao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Haidian District, Beijing 100875, China
| | - Hongmin Ren
- Department of Chemical Engineering, Hebei Petroleum University of Technology, 2 Xueyuanlu Street, Shuangqiao District, Chengde 067000, China
| | - Jiali Han
- College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Xinrui Yang
- Hainan Ecological Environmental Monitoring Center, 98 Baiju Avenue, Haikou 571126, China
| | - Yingxia Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Jun Jin
- College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Street, Haidian District, Beijing 100081, China.
| |
Collapse
|
3
|
Probing the binding interactions between perfluoroalkyl carboxylic acids and adenosine A2A receptors by spectroscopic techniques, molecular simulations and quantum chemistry. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
|
4
|
Xue Q, Liu X, Russell P, Li J, Pan W, Fu J, Zhang A. Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 233:113323. [PMID: 35183811 DOI: 10.1016/j.ecoenv.2022.113323] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Molecular docking is a widely used method to predict the binding modes of small-molecule ligands to the target binding site. However, it remains a challenge to identify the correct binding conformation and the corresponding binding affinity for a series of structurally similar ligands, especially those with weak binding. An understanding of the various relative attributes of popular docking programs is required to ensure a successful docking outcome. In this study, we systematically compared the performance of three popular docking programs, Autodock, Autodock Vina, and Surflex-Dock for a series of structurally similar weekly binding flavonoids (22) binding to the estrogen receptor alpha (ERα). For these flavonoids-ERα interactions, Surflex-Dock showed higher accuracy than Autodock and Autodock Vina. The hydrogen bond overweighting by Autodock and Autodock Vina led to incorrect binding results, while Surflex-Dock effectively balanced both hydrogen bond and hydrophobic interactions. Moreover, the selection of initial receptor structure is critical as it influences the docking conformations of flavonoids-ERα complexes. The flexible docking method failed to further improve the docking accuracy of the semi-flexible docking method for such chemicals. In addition, binding interaction analysis revealed that 8 residues, including Ala350, Glu353, Leu387, Arg394, Phe404, Gly521, His524, and Leu525, are the key residues in ERα-flavonoids complexes. This work provides reference for assessing molecular interactions between ERα and flavonoid-like chemicals and provides instructive information for other environmental chemicals.
Collapse
Affiliation(s)
- Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Paul Russell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China.
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
| |
Collapse
|
5
|
Liu X, Xue Q, Zhang H, Fu J, Zhang A. Structural basis for molecular recognition of G protein-coupled estrogen receptor by selected bisphenols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148558. [PMID: 34328988 DOI: 10.1016/j.scitotenv.2021.148558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Complicated ligand-dependent signaling pathways of bisphenol A (BPA) and its analogues involve not only intranuclear estrogen receptor but also membrane receptor G protein-coupled estrogen receptor (GPER). However, the structural basis for molecular recognition of GPER by the environmental chemicals remains unknown. To reveal the structural dependence of GPER recognition by bisphenols, a systematic molecular dynamics simulation study was performed for selected bisphenols with different electron hybrid orbitals and substituents on their C atoms connecting two phenol rings. BPA was used as a control, bisphenol C(BPC) as an example for a connecting C with sp2 hybrid orbitals to provide more ligand rigidity, bisphenol E(BPE) and bisphenol F(BPF) for decreased steric hindrance and hydrophobicity around the connecting C, and bisphenol B(BPB) and bisphenol AF(BPAF) for increased hydrophobicity and steric hindrance. All the tested bisphenols can bind with GPER at its classic orthosteric site to obtain GPER-ligand complexes, while van der Waals interactions and direct inter-molecular electrostatic energies provide the driving forces for ligand binding. Bulky substituents and structural rigidity of the connecting C dramatically impair hydrogen bonding between GPER and the bisphenols, which results in decreased contribution of both favorable intermolecular hydrogen bonds and unfavorable polar solvation effect to complex stability of BPB and BPC since decreased number of key residues is expected. Increase in substituent lipophilicity enhances the van der Waals interactions and favorable non-polar solvation effect. The six bisphenols of high structural similarity shared two key recognition residues, Leu137TM3 and Trp272TM6, the latter of which was in the highly conserved CWxP motif of TM6 and has been reported as key residue for G protein-coupled receptor activation. Based on the obtained knowledge, GPER affinity and relevant toxicity of BPA alternatives can be easily predicted, and the calculated binding free energies are consistent with the available experimental observations.
Collapse
Affiliation(s)
- Xiuchang Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China
| | - Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Huazhou Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310012, PR China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310012, PR China.
| |
Collapse
|
6
|
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]
|
7
|
Kooravand M, Asadpour S, Haddadi H, Farhadian S. An insight into the interaction between malachite green oxalate with human serum albumin: Molecular dynamic simulation and spectroscopic approaches. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124878. [PMID: 33360194 DOI: 10.1016/j.jhazmat.2020.124878] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/17/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Cationic triarylmethane dyes such as malachite green are aromatic xenobiotic compounds causing environmental pollution. The affinity between hazardous materials and biomolecules makes it important to understand the properties of such compounds. Accordingly, in this study, the possible molecular interaction between this pollutant and the human serum albumin (HSA) was investigated using a combination of molecular docking, molecular dynamic simulation and multi-spectroscopic approaches. The docking results illustrated that malachite green oxalate (MGO) could bind to some of the HSA amino acids with the estimated free energy = -32.93 kJ/mol. Further, the results of the dynamic simulation revealed that MGO had a steady interaction with the protein though increasing flexibility and decreasing the HSA compactness. These results were, therefore, in agreement with those obtained by spectroscopic techniques. The MGO concentration of 0.0005 mM could quench the HSA's intrinsic fluorescence by %16.88. The protein structural changes also revealed that the binding interaction of MGO-HSA was accompanied by an increase in the α-helix and a decrease in the β-sheet of the protein. Overall, this study indicated the suitable molecular modeling interaction of MGO and HSA.
Collapse
Affiliation(s)
- Masoumeh Kooravand
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran
| | - Saeid Asadpour
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran.
| | - Hedayat Haddadi
- Department of Chemistry, Faculty of Sciences, Shahrekord University, P. O. Box 115, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Sciences, Shahrekord University, P. O. Box.115, Shahrekord, Iran
| |
Collapse
|
8
|
Rui Y, Zuo Y, Yang L, Xu J, Wei Y, Yi Z. Molecular dynamics and spectral analysis for the binding of methoxylated polybrominated diphenyl ethers to lysozyme. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
Yong L, Huang M, Wei Y, Xu J, Yi Z. Investigating the interaction between three perfluorinated carboxylic acids and the G protein-coupled estrogen receptor: spectroscopic analyses and computational simulations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3944-3953. [PMID: 32743632 DOI: 10.1039/d0ay01052a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this paper, perfluorinated compounds (PFCs), such as perfluorobutyric acid (PFBA), perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), were selected as typical representatives of perfluorinated carboxylic acids (PFCAs) to study the effects of PFCAs on the G protein-coupled estrogen receptor (GPER). The interaction mechanism of the three types of PFCAs with the GPER was investigated using steady-state fluorescence spectroscopy, ultraviolet-visible spectroscopy, three-dimensional fluorescence spectroscopy, and Fourier transform infrared spectroscopy combined with molecular docking and molecular dynamics simulations. Among these techniques, steady-state fluorescence and ultraviolet-visible spectroscopic analyses showed that PFBA, PFOA and PFDoA quenched the endogenous GPER fluorescence by combined dynamic and static quenching and non-radiative energy transfer. The binding constants (Ka) of PFCAs on the GPER were all larger than 105 L mol-1, indicating that their affinity for the GPER was strong. Fourier transform infrared spectroscopy and three-dimensional fluorescence showed that the secondary structure of the GPER changed after binding to PFCAs. Thermodynamic analysis showed ΔG < 0, which indicated that the interaction between the GPER and PFCAs was spontaneous. For the binding of PFBA and PFOA to the GPER, ΔH > 0 and ΔS > 0, indicating that the interaction was mainly driven by hydrophobic forces; for the binding of PFDoA to the GPER, ΔH < 0 and ΔS < 0, suggesting that van der Waals force and hydrogen bonding were the main interaction forces. Molecular dynamics simulations suggested that the stability of the GPER-PFCA complexes was higher than that of the free GPER, and also that the structure and hydrophobicity of the GPER changed after binding to PFCAs. Molecular docking analysis showed that all three PFCAs could form hydrogen bonds with the GPER, which improved the stability of the complex.
Collapse
Affiliation(s)
- 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.
| | | | | | | | | |
Collapse
|
10
|
Gan R, Zhao L, Sun Q, Tang P, Zhang S, Yang H, He J, Li H. Binding behavior of trelagliptin and human serum albumin: Molecular docking, dynamical simulation, and multi-spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 202:187-195. [PMID: 29787915 DOI: 10.1016/j.saa.2018.05.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/11/2018] [Accepted: 05/13/2018] [Indexed: 06/08/2023]
Abstract
This study aims to investigate the interaction mechanism of a hypoglycemic agent, trelagliptin (TLP), and human serum albumin (HSA) through computer simulation and assisted spectroscopy methods. Computer simulation including molecular docking and molecular dynamics analysis was conducted under physiological conditions. Molecular docking results indicate that TLP bound to HSA at site I, and the binding behavior was mainly governed by hydrophobic force. Competitive experiments further verified the theoretical conclusion from molecular docking. Molecular dynamics simulation revealed that TLP indeed stably bound to site I of HSA in the hydrophobic subdomain IIA. Moreover, TLP presented a certain effect on the structural compactness of HSA. In molecular dynamics simulation, hydrogen bonds appeared, which suggested the reliability and stability of the combination. The binding energy of the stable phase is around -250 kJ/mol. Fluorescence quenching studies and time-resolved fluorescence analysis indicated that the evident fluorescence quenching phenomenon of HSA could be due to TLP binding initiated by static quenching mechanism. The binding constants (Ka) of the complex were found to be around 104 via fluorescence data, and the calculated thermodynamic parameters indicated that hydrophobic force played major role in the binding of TLP to HSA. Synchronous fluorescence and three-dimensional fluorescence results demonstrated that TLP slightly disturbed the microenvironment of amino residues. Circular dichroism spectra showed that TLP affected the secondary structure of HSA. The theoretical and experimental results showed excellent agreement.
Collapse
Affiliation(s)
- Ruixue Gan
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Ludan Zhao
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Qiaomei Sun
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Peixiao Tang
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China.
| | - Shuangshuang Zhang
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Hongqin Yang
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Jiawei He
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Hui Li
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China.
| |
Collapse
|