1
|
Wang Y, Zhou H, Fu Y, Wang Z, Gao Q, Yang D, Kang J, Chen L, An Z, Hammock BD, Zhang J, Huo J. Establishment of an indirect competitive immunoassay for the detection of dicamba based on a highly specific nanobody. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170567. [PMID: 38296098 PMCID: PMC10936929 DOI: 10.1016/j.scitotenv.2024.170567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/28/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
Dicamba, a traditional highly effective and low toxicity herbicide, has gained new life with the development of dicamba-tolerant transgenic crops in recent years. However, dicamba is highly volatile and therefore easy to cause drift damage to sensitive crops. The development of efficient and sensitive detection methods is essential for monitoring of trace dicamba in the environment. Nanobody-based immunoassay plays an important role in on-site detection of pesticides. However, now rapid and sensitive immunoassay methods based on nanobody for dicamba detection were lacking. In this study, the nanobodies specifically recognizing dicamba were successfully obtained by immunising camels and phage display library construction, and then an indirect competitive immunoassay based on Nb-242 was constructed with IC50 of 0.93 μg/mL and a linear range of 0.11-8.01 μg/mL. Nb-242 had good specificity with no cross-reactivities against the dicamba analogs other than 2,3,6-trichlorobenzoic acid and the developed immnoassay had a good correlation with the standard HPLC in the spike-recovery studies. Finally, the key amino acid Ala 123, Tyr 55, Tyr 59 and Arg 72 of Nb-242 that specifically recognizing and binding with dicamba were identified by homologous modeling and molecular docking, laying an important foundation for further structural modification of Nb-242. This study has important guiding significance for constructing immunoassay method of dicamba based on nanobody and provides a sensitive, specific, and reliable detection method that is suitable for the detection of dicamba in the environment.
Collapse
Affiliation(s)
- Yasen Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Hui Zhou
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Yining Fu
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Zhengzhong Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Qingqing Gao
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Dongchen Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Jia Kang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Lai Chen
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Zexiu An
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Bruce D Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States of America
| | - Jinlin Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China.
| | - Jingqian Huo
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China.
| |
Collapse
|
2
|
Zhu T, Yu Y, Tao T. A comprehensive evaluation of liposome/water partition coefficient prediction models based on the Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) method: Challenges from different descriptor dimension reduction methods and machine learning algorithms. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130181. [PMID: 36257111 DOI: 10.1016/j.jhazmat.2022.130181] [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: 07/31/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The liposome/water partition coefficient (Klip/w) is a key parameter to evaluate the bioaccumulation potential of pollutants. Considering that it is difficult to determine the Klip/w values of all pollutants through experiments, researchers gradually developed models to predict it. However, there is currently no research on how to comprehensively evaluate prediction models and recommend a compelling optimal modeling method. To remedy the defect of single parameters in a traditional model comparison, the TOPSIS evaluation method, based on entropy weight, was first proposed. We use this method to comprehensively evaluate models from multiple angles in this study. Thirty QSPR models, including 3 descriptor dimension reduction methods and 10 algorithms (belonging to 4 tribes), were used to predict Klip/w and verify the effectiveness of the comprehensive assessment method. The results showed that RF (descriptor dimension reduction method), symbolism (tribes) and RF (algorithm) exhibited significant advantages in establishing the Klip/w value prediction model. At present, the application of TOPSIS in environmental model evaluations is almost absent. We hope that the proposed TOPSIS evaluation method can be applied to more chemical datasets and provide a more systematic and comprehensive basis for the application of the QSPR model in environmental studies and other fields.
Collapse
Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China.
| | - Yan Yu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Tianyun Tao
- College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| |
Collapse
|
3
|
Zhu T, Chen Y, Tao C. Multiple machine learning algorithms assisted QSPR models for aqueous solubility: Comprehensive assessment with CRITIC-TOPSIS. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159448. [PMID: 36252662 DOI: 10.1016/j.scitotenv.2022.159448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
As an essential environmental property, the aqueous solubility quantifies the hydrophobicity of a compound. It could be further utilized to evaluate the ecological risk and toxicity of organic pollutants. Concerned about the proliferation of organic contaminants in water and the associated technical burden, researchers have developed QSPR models to predict aqueous solubility. However, there are no standard procedures or best practices on how to comprehensively evaluate models. Hence, the CRITIC-TOPSIS comprehensive assessment method was first-ever proposed according to a variety of statistical parameters in the environmental model research field. 39 models based on 13 ML algorithms (belonged to 4 tribes) and 3 descriptor screening methods, were developed to calculate aqueous solubility values (log Kws) for organic chemicals reliably and verify the effectiveness of the comprehensive assessment method. The evaluations were carried out for exhibiting better predictive accuracy and external competitiveness of the MLR-1, XGB-1, DNN-1, and kNN-1 models in contrast to other prediction models in each tribe. Further, XGB model based on SRM (XGB-1, C = 0.599) was selected as an optimal pathway for prediction of aqueous solubility. We hope that the proposed comprehensive evaluation approach could act as a promising tool for selecting the optimum environmental property prediction methods.
Collapse
Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China.
| | - Ying Chen
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Cuicui Tao
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| |
Collapse
|
4
|
Zhou J, Liu J, Song S, Liu L, Xu C, Kuang H, Ma W. Development of monoclonal antibodies for the detection of diuron in water and sugarcane and their application in immunochromatographic strips. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4202-4208. [PMID: 36255350 DOI: 10.1039/d2ay01006b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Diuron (DR) as a chemical herbicide persists in soil and water for a long time and causes extensive harm to humans. We have produced an excellent monoclonal antibody (mAb) with the ability to sensitively and specifically recognize DR in water and sugarcane samples. The semi-inhibitory concentration (IC50) of this mAb was 0.28 ng mL-1, and the limit of detection (LOD) was 0.07 ng mL-1. Based on the mAb, an immunochromatographic assay (ICA) strip was developed. The visual detection limits of the strip assay were estimated, and the critical values of DR in water and sugarcane samples were determined to be 5 and 10 ng mL-1, respectively, when assessed by the naked eye. The ICA strip was validated by HPLC-MS for water and sugarcane samples which had been spiked with DR. This ICA strip could be a useful tool for in-site and rapid detection of DR in water and sugarcane samples.
Collapse
Affiliation(s)
- Jian Zhou
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Jie Liu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shanshan Song
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Liqiang Liu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Wei Ma
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
| |
Collapse
|
5
|
Yang J, Wang Y, Zhang Y, Zeng X, Liu J, Tian Y, Wang H, Xu Z, Shen Y. Reverse Distal Similarity of Hapten Structure Enhancing Antibody’s Group-specificity: Development of an Immunochromatographic Strip for Tylosin and Tilmicosin in Milk and Water. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.105068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
6
|
Targeted preparation and recognition mechanism of broad-spectrum antibody specific to Aconitum alkaloids based on molecular modeling and its application in immunoassay. Anal Chim Acta 2022; 1222:340011. [DOI: 10.1016/j.aca.2022.340011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/13/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022]
|
7
|
Ren Z, Zhang H, Wang Z, Chen X, Yang L, Jiang H. Progress in Immunoassays of Toxic Alkaloids in Plant-Derived Medicines: A Review. Toxins (Basel) 2022; 14:toxins14030165. [PMID: 35324662 PMCID: PMC8948709 DOI: 10.3390/toxins14030165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Plants are the cradle of the traditional medicine system, assuaging human or animal diseases, and promoting health for thousands of years. However, many plant-derived medicines contain toxic alkaloids of varying degrees of toxicity that pose a direct or indirect threat to human and animal health through accidental ingestion, misuse of plant materials, or through the food chain. Thus, rapid, easy, and sensitive methods are needed to effectively screen these toxic alkaloids to guarantee the safety of plant-derived medicines. Antibodies, due to their inherent specificity and high affinity, have been used as a variety of analytical tools and techniques. This review describes the antigen synthesis and antibody preparation of the common toxic alkaloids in plant-derived medicines and discusses the advances of antibody-based immunoassays in the screening and detection of toxic alkaloids in plants or other related matrices. Finally, the limitations and prospects of immunoassays for toxic alkaloids are discussed.
Collapse
|
8
|
Yang JY, Xie MC, Tan XC, Tian YX, Wang H, Xu ZL, Yuan TT, Xiao YM, Shen YD. Improved molecular softness of tadalafil hapten enhancing antibody performance in immunoassay: Evidence from computational chemistry. J Food Sci 2022; 87:1342-1354. [PMID: 35166370 DOI: 10.1111/1750-3841.16078] [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: 11/19/2021] [Revised: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
The tadalafil-like compounds have appeared recently as adulterants in drinks and healthcare dietary supplements sourced from medicinal and edible food, which may cause illness and even death. In this work, the rationality of haptens was explored by computational chemistry and molecular simulation theories such as frontier molecular orbital (FMO)-based softness (S), three-dimensional (3D) structure, surface electrostatic potential (ESP), and lipophilic potential (LP). An antiserum from hapten H5 with the highest softness and maintaining the appropriate three-dimensional (3D) structure showed the optimal immunoassay performance, indicating an increasing softness was a critical factor for effective hapten. Based on the antibody induced by hapten H5, an indirect competitive enzyme-linked immunosorbent assay (icELISA) method for detecting multiple tadalafil-like adulterants was established. The icELISA showed a limit of detection (LOD), 50% inhibition concentration (IC50 ), and a working range of 0.004-0.396, 0.89-4.27, and 0.094-16.71 ng/ml for tadalafil, amino tadalafil, acetamino tadalafil, nortadalafil, and N-desmethyl ent-tadalafil, respectively. The spiked recoveries of tadalafil-like adulterants in samples ranged from 84.9% to 116.2%. The results of the icELISA and HPLC-MS/MS methods had a good correlation for real samples with the R2 of 0.9955. Specially, this work not only provided a convenient immunoassay method for measuring tadalafil-like adulterants in spirit drinks and dietary supplements in group-screening manner, but also suggested that softness was likely to be a general theory for rational hapten design. PRACTICAL APPLICATION: Rapid monitoring of tadalafil-like adulterants in food samples is very necessary and important for consumers, regulatory agencies, and the food industry.
Collapse
Affiliation(s)
- Jin-Yi Yang
- College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou, China
| | - Mei-Chan Xie
- College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou, China
| | - Xue-Cai Tan
- College of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, China
| | - Yuan-Xin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Hong Wang
- College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou, China
| | - Zhen-Lin Xu
- College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou, China
| | - Ting-Ting Yuan
- Shenzhen Care-green Agriculture Products Testing & Certification Co. Ltd., Shenzhen, China
| | - Yi-Mei Xiao
- Shenzhen Care-green Agriculture Products Testing & Certification Co. Ltd., Shenzhen, China
| | - Yu-Dong Shen
- College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou, China
| |
Collapse
|
9
|
Zhu T, Tao C. Prediction models with multiple machine learning algorithms for POPs: The calculation of PDMS-air partition coefficient from molecular descriptor. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127037. [PMID: 34530267 DOI: 10.1016/j.jhazmat.2021.127037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Polydimethylsiloxane-air partition coefficient (KPDMS-air) is a key parameter for passive sampling to measure POPs concentrations. In this study, 13 QSPR models were developed to predict KPDMS-air, with two descriptor selection methods (MLR and RF) and seven algorithms (MLR, LASSO, ANN, SVM, kNN, RF and GBDT). All models were based on a data set of 244 POPs from 13 different categories. The diverse model evaluation parameters calculated from training and test set were used for internal and external verification. Notably, the Radj2, QBOOT2 and Qext2 are 0.995, 0.980 and 0.951 respectively for GBDT model, showing remarkable superiority in fitting, robustness and predictability compared with other models. The discovery that molecular size, branches and types of the bonds were the main internal factors affecting the partition process was revealed by mechanism explanation. Different from the existing QSPR models based on single category compounds, the models developed herein considered multiple classes compounds, so that its application domain was more comprehensive. Therefore, the obtained models can fill the data gap of missing experimental KPDMS-air values for compounds in the application range, and help researchers better understand the distribution behavior of POPs from the perspective of molecular structure.
Collapse
Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China.
| | - Cuicui Tao
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| |
Collapse
|
10
|
Changing Cross-Reactivity for Different Immunoassays Using the Same Antibodies: Theoretical Description and Experimental Confirmation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many applications of immunoassays involve the possible presence of structurally similar compounds that bind with antibodies, but with different affinities. In this regard, an important characteristic of an immunoassay is its cross-reactivity: the possibility of detecting various compounds in comparison with a certain standard. Based on cross-reactivity, analytical systems are assessed as either high-selective (responding strictly to a specific compound) or low-selective (responding to a number of similar compounds). The present study demonstrates that cross-reactivity is not an intrinsic characteristic of antibodies but can vary for different formats of competitive immunoassays using the same antibodies. Assays with sensitive detection of markers and, accordingly, implementation at low concentrations of antibodies and modified (competing) antigens are characterized by lower cross-reactivities and are, thus, more specific than assays requiring high concentrations of markers and interacting reagents. This effect was confirmed by both mathematical modeling and experimental comparison of an enzyme immunoassay and a fluorescence polarization immunoassay of sulfonamides and fluoroquinolones. Thus, shifting to lower concentrations of reagents decreases cross-reactivities by up to five-fold. Moreover, the cross-reactivities are changed even in the same assay format by varying the ratio of immunoreactants’ concentrations and shifting from the kinetic or equilibrium mode of the antigen-antibody reaction. The described patterns demonstrate the possibility of modulating immunodetection selectivity without searching for new binding reactants.
Collapse
|
11
|
Liu B, Qin Y, Cao M, Shi H, Li S, Sheng W, Wang S. A stable and sensitive enzyme-linked immunosorbent assay (ELISA) for the determination of metsulfuron-methyl residues in foods. J Food Sci 2021; 86:3176-3187. [PMID: 34176121 DOI: 10.1111/1750-3841.15683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/06/2020] [Accepted: 02/14/2021] [Indexed: 11/26/2022]
Abstract
A hapten of metsulfuron-methyl was successfully designed and synthesized from 2-methylester-phenylsulfonamide and succinic anhydride, and the polyclonal antibody against metsulfuron-methyl was prepared by immunization procedure with the hapten-bovine serum albumin conjugate. A stable and sensitive direct competitive enzyme-linked immunosorbent assay (dcELISA) method had been developed under the optimal conditions. The sensitivity (IC50 ) was 37.03 ± 1.87 µg/L, and the detection line (IC15 ) was 1.57 ± 0.11 µg/L. Rice, wheat, oat, flaxseed, milk, and water were chosen to study the recovery test and the recovery rates were 83.11%-117.44% . The matrix effect was eliminated by a simple dilution of the sample extracts. The results from dcELISA were well agreement with the results from HPLC-MS. It was indicated that the developed method had good accuracy and stability. It could be applied for the detection of metsulfuron-methyl residues. It was worth mentioning that the antibody could recognize metsulfuron-methyl and tribenuron-methyl with cross-reactivities of 100% and 49.72%, respectively. In order to understand the cross-reactivity, molecular modeling including molecular alignment and electrostatic potential surfaces were introduced. It was found that the special group of metsulfuron-methyl played an important role, especially on C3 position of the phenyl group. PRACTICAL APPLICATION: A stable, sensitive, and low-cost dc ELISA method had been developed with good accuracy and applied in the determination of metsulfuron-methyl in foods. Molecular simulation was introduced to understand the specificity between the antibody and the analyst. It was a good method to study the cross-reactivity between the antibody and the analyst or analogue.
Collapse
Affiliation(s)
- Bing Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
| | - Yue Qin
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Meirong Cao
- Hebei Food Inspection and Research Institute, Hebei Food Safety Key Laboratory, Shijiazhuang, China
| | - Haipeng Shi
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Shijie Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Wei Sheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| |
Collapse
|
12
|
Zhu T, Chen W, Singh RP, Cui Y. Versatile in silico modeling of partition coefficients of organic compounds in polydimethylsiloxane using linear and nonlinear methods. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:123012. [PMID: 32544766 DOI: 10.1016/j.jhazmat.2020.123012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Environmental fate, behavior and effects of hazardous organic compounds have recently received great attention in diverse environmental phases, including water, atmosphere, soil and sediment. Considering polydimethylsiloxane (PDMS) fibers were validated for the wide application in the determination of partition behavior in passive sampling, in this work, several in silico models were established to predict PDMS-water (KPDMS-w), PDMS-air (KPDMS-a) and PDMS-seawater partition coefficients (KPDMS-sw) of diverse chemicals. This is an attempt to combine conventional linear method and popular nonlinear algorithm for the estimation of partition coefficients between PDMS and different environmental media. All of the developed models showed satisfactory goodness-of-fit with high adjusted correlation coefficient (R2adj) and were validated to be robust, stable and predictable by various internal and external validation techniques, deriving a wide series of statistical checks. Moreover, it was found that hydrophobicity, polarizability, charge distribution and molecular size of compounds contributed significantly to the model development by interpreting the selected descriptors. Based on the broad applicability domains (ADs), the current study provides suitable tools to fill the experimental data gap for other compounds and to help researchers better understand the mechanistic basis of adsorption behavior of PDMS.
Collapse
Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China.
| | - Wenxuan Chen
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | | | - Yanran Cui
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99354, United States
| |
Collapse
|
13
|
Zhu T, Yan H, Singh RP, Wang Y, Cheng H. QSPR study on the polyacrylate-water partition coefficients of hydrophobic organic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:17550-17560. [PMID: 31493082 DOI: 10.1007/s11356-019-06389-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
The partition coefficient is essential for the analysis of organic chemicals using solid-phase microextraction (SPME) techniques. In this study, a quantitative structure-property relationship (QSPR) model was developed with chemical descriptors for the prediction of the polyacrylate (PA)-water partition coefficient (KPA-w). The major variables influencing KPA-w in the QSPR model were CrippenlogP (crippen octanal-water partition coefficient), RNCG (relative negative charge-most negative charge/total negative charge), VE2_Dzv (average coefficient sum of the last eigenvector from the Barysz matrix/weighted by van der Waals volume), and ATSC4v (centred Broto-Moreau autocorrelation-lag 4/weighted by van der Waals volume). The relative determination coefficient (R2) and cross-validation coefficient (Q2) were 0.898 and 0.858, respectively, which implied that the model had excellent robustness. Mechanistic interpretation suggested that the factors affecting the partitioning process between PA and water are the hydrophobicity, relative negative charge, and van der Waals volume of a chemical. The results of this study provide a good tool for predicting the log KPA-w values of diverse hydrophobic organic compounds (HOCs) within the applicability domain to reduce experimental costs and the time required for innovation.
Collapse
Affiliation(s)
- Tengyi Zhu
- Jiangsu Provincial Laboratory of Water Environmental Protection Engineering, School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
| | - Heting Yan
- Jiangsu Provincial Laboratory of Water Environmental Protection Engineering, School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | | | - Yajun Wang
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Haomiao Cheng
- Jiangsu Provincial Laboratory of Water Environmental Protection Engineering, School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
| |
Collapse
|
14
|
McGrath G, Rao PSC, Mellander PE, Kennedy I, Rose M, van Zwieten L. Real-time forecasting of pesticide concentrations in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 663:709-717. [PMID: 30731416 DOI: 10.1016/j.scitotenv.2019.01.401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Forecasting pesticide residues in soils in real time is essential for agronomic purposes, to manage phytotoxic effects, and in catchments to manage surface and ground water quality. This has not been possible in the past due to both modelling and measurement constraints. Here, the analytical transient probability distribution (pdf) of pesticide concentrations is derived. The pdf results from the random ways in which rain events occur after pesticide application. First-order degradation kinetics and linear equilibrium sorption are assumed. The analytical pdfs allow understanding of the relative contributions that climate (mean storm depth and mean rainfall event frequency) and chemical (sorption and degradation) properties have on the variability of soil concentrations into the future. We demonstrated the two uncertain reaction parameters can be constrained using Bayesian methods. An approach to a Bayesian informed forecast is then presented. With the use of new rapid tests capable of providing quantitative measurements of soil concentrations in the field, real-time forecasting of future pesticide concentrations now looks possible for the first time. Such an approach offers new means to manage crops, soils and water quality, and may be extended to other classes of pesticides for ecological risk assessment purposes.
Collapse
Affiliation(s)
- Gavan McGrath
- Ishka Solutions, Nedlands 6009, Australia; Teagasc, Environment, Soils and Water Department, Johnstown Castle, Wexford, Ireland; School of Agriculture and Environment, University of Western Australia, 6009 Perth, Australia.
| | - P Suresh C Rao
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN 47907, USA; Agronomy Department, Purdue University, West Lafayette, IN 47907, USA
| | - Per-Erik Mellander
- Teagasc, Environment, Soils and Water Department, Johnstown Castle, Wexford, Ireland
| | - Ivan Kennedy
- Sydney Institute of Agriculture, University of Sydney, Sydney 2006, Australia
| | - Michael Rose
- Wollongbar Primary Industries Institute, NSW Department of Primary Industries, Wollongbar, 2477, Australia
| | - Lukas van Zwieten
- Wollongbar Primary Industries Institute, NSW Department of Primary Industries, Wollongbar, 2477, Australia
| |
Collapse
|
15
|
Buglak AA, Zherdev AV, Lei HT, Dzantiev BB. QSAR analysis of immune recognition for triazine herbicides based on immunoassay data for polyclonal and monoclonal antibodies. PLoS One 2019; 14:e0214879. [PMID: 30943259 PMCID: PMC6447172 DOI: 10.1371/journal.pone.0214879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/21/2019] [Indexed: 12/03/2022] Open
Abstract
A common task in the immunodetection of structurally close compounds is to analyze the selectivity of immune recognition; it is required to understand the regularities of immune recognition and to elucidate the basic structural elements which provide it. Triazines are compounds of particular interest for such research due to their high variability and the necessity of their monitoring to provide safety for agricultural products and foodstuffs. We evaluated the binding of 20 triazines with polyclonal (pAb) and monoclonal (mAb) antibodies obtained using atrazine as the immunogenic hapten. A total of over 3000 descriptors were used in the quantitative structure-activity relationship (QSAR) analysis of binding activities (pIC50). A comparison of the two enzyme immunoassay systems showed that the system with pAb is much easier to describe using 2D QSAR methodology, while the system with mAb can be described using the 3D QSAR CoMFA. Thus, for the 3D QSAR model of the polyclonal antibodies, the main statistical parameter q2 (‘leave-many-out’) is equal to 0.498, and for monoclonal antibodies, q2 is equal to 0.566. Obviously, in the case of pAb, we deal with several targets, while in the case of mAb the target is one, and therefore it is easier to describe it using specific fields of molecular interactions distributed in space.
Collapse
Affiliation(s)
- Andrey A. Buglak
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- St. Petersburg State University, St. Petersburg, Russia
- * E-mail:
| | - Anatoly V. Zherdev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Hong-Tao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou, China
| | - Boris B. Dzantiev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
16
|
Zhang X, He K, Zhang D, Huang Z. Production and characterization of a monoclonal antibody for Pefloxacin and mechanism study of antibody recognition. Biosci Biotechnol Biochem 2019; 83:633-640. [DOI: 10.1080/09168451.2018.1562876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
ABSTRACT
In this report, an artificial antigen (PFLX–BSA: Pefloxacin connected bovine serum albumin) was successfully prepared. The monoclonal antibody against pefloxacin was produced and characterized using a direct competitive ELISA. The linear range of detection was 0.115–6.564 µg/L. The limit of detection defined as IC15 was 0.170 ± 0.05 µg/L and the IC50 was 0.902 ± 0.03 µg/L. The antibody variable region genes were amplified, assembled, and sequenced. A three–dimensional structural model of the variable region was constructed to study the mechanism of antibody recognition using molecular docking analysis. Three predicted essential amino acids, Thr53, Arg97 of heavy chain and Thr52 of light chain, were mutated to verify the theoretical model. Three mutants lost binding activity significantly against pefloxacin as predicted. These may provide useful insights for studying antigen–antibody interaction mechanisms to improve antibody affinity maturation in vitro.
Collapse
Affiliation(s)
- Xiuyuan Zhang
- Food Safety Centre of Hebei North University, Hebei North University, Zhangjiakou, China
- College of Food Engineering, Henan University of Animal Husbandry & Economy, Zhenzhou, China
| | - Kuo He
- Food Safety Centre of Hebei North University, Hebei North University, Zhangjiakou, China
| | - Donghao Zhang
- Food Safety Centre of Hebei North University, Hebei North University, Zhangjiakou, China
| | - Zhihong Huang
- Food Safety Centre of Hebei North University, Hebei North University, Zhangjiakou, China
| |
Collapse
|
17
|
Wang J, Peng T, Zhang X, Xie S, Zheng P, Yao K, Ke Y, Wang Z, Jiang H. Application of quantitative structure-activity relationship analysis on an antibody and alternariol-like compounds interaction study. J Mol Recognit 2019; 32:e2776. [PMID: 30663161 DOI: 10.1002/jmr.2776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/23/2018] [Accepted: 12/24/2018] [Indexed: 11/06/2022]
Abstract
The antigen-antibody interaction determines the sensitivity and specificity of competitive immunoassay for hapten detection. In this paper, the specificity of a monoclonal antibody against alternariol-like compounds was evaluated through indirect competitive ELISA. The results showed that the antibody had cross-reactivity with 33 compounds with the binding affinity (expressed by IC50 ) ranging from 9.4 ng/mL to 12.0 μg/mL. All the 33 compounds contained a common moiety and similar substituents. To understand how this common moiety and substituents affected the recognition ability of the antibody, a three-dimensional quantitative structure-activity relationship (3D-QSAR) between the antibody and the 33 alternariol-like compounds was constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The q2 values of the CoMFA and CoMSIA models were 0.785 and 0.782, respectively, and the r2 values were 0.911 and 0.988, respectively, indicating that the models had good predictive ability. The results of 3D-QSAR showed that the most important factor affecting antibody recognition was the hydrogen bond mainly formed by the hydroxyl group of alternariol, followed by the hydrophobic force mainly formed by the methyl group. This study provides a reference for the design of new hapten and the mechanisms for antibody recognition.
Collapse
Affiliation(s)
- Jianyi Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| | - Tao Peng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| | - Xiya Zhang
- College of Food Science and Technology, Henan Agricultural University, Henan, People's Republic of China
| | - Sanlei Xie
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| | - Pimiao Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| | - Kai Yao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| | - Yuebin Ke
- Key Laboratory of Molecular Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Zhanhui Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| | - Haiyang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing, People's Republic of China
| |
Collapse
|
18
|
Liu C, Dou X, Zhang L, Kong W, Wu L, Duan Y, Yang M. Development of a broad-specificity antibody-based immunoassay for triazines in ginger and the quantitative structure-activity relationship study of cross-reactive molecules by molecular modeling. Anal Chim Acta 2018; 1012:90-99. [PMID: 29475478 DOI: 10.1016/j.aca.2018.01.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 11/29/2022]
Abstract
In the present study, molecular modeling and principle component analysis (PCA) were used to select appropriate haptens for group detection of triazine herbicides. Four new structures together with three reported triazine derivatives were chosen for the screening of immunizing and coating haptens. A total of 31 triazines coupled with a 3D-QSAR methodology were employed to investigate the relationship between antigen-antibody recognition and molecular structures, the results of which revealed that the antibodies may recognize triazines from the side of molecules with the distinguishing atom and a steric volume matching with the spatial structure of antibodies. Finally, a broad-specificity heterologous immunoassay was developed for determining 10 triazine herbicides in ginger, where the detection limits were 2.5-15.1 μg kg-1 and recoveries were 67.9-102.6%. This study may broaden insight into triazine-antibody interactions and benefit designing novel performance-enhanced antibodies. The developed immunoassay can be further used for triazine detection in other complicated matrices.
Collapse
Affiliation(s)
- Congmin Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Xiaowen Dou
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Lei Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Weijun Kong
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Liu Wu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China; College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, 130118, China
| | - Yaping Duan
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China; College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, 130118, China
| | - Meihua Yang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|
19
|
Substructure-activity relationship studies on antibody recognition for phenylurea compounds using competitive immunoassay and computational chemistry. Sci Rep 2018; 8:3131. [PMID: 29449597 PMCID: PMC5814414 DOI: 10.1038/s41598-018-21394-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Based on the structural features of fluometuron, an immunizing hapten was synthesized and conjugated to bovine serum albumin as an immunogen to prepare a polyclonal antibody. However, the resultant antibody indicated cross-reactivity with 6 structurally similar phenylurea herbicides, with binding activities (expressed by IC50 values) ranging from 1.67 µg/L to 42.71 µg/L. All 6 phenylurea herbicides contain a common moiety and three different substitutes. To understand how these three different chemical groups affect the antibody-phenylurea recognition activity, quantum chemistry, using density function theory (DFT) at the B3LYP/6-311++ G(d,p) level of theory, was employed to optimize all phenylurea structures, followed by determination of the 3D conformations of these molecules, pharmacophore analysis, and molecular electrostatic potential (ESP) analysis. The molecular modeling results confirmed that the geometry configuration, pharmacophore features and electron distribution in the substituents were related to the antibody binding activity. Spearman correlation analysis further elucidated that the geometrical and electrostatic properties on the van der Waals (vdW) surface of the substituents played a critical role in the antibody-phenylurea recognition process.
Collapse
|
20
|
Doses of Immunogen Contribute to Specificity Spectrums of Antibodies against Aflatoxin. Toxins (Basel) 2017; 9:toxins9050172. [PMID: 28534846 PMCID: PMC5450720 DOI: 10.3390/toxins9050172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/03/2017] [Accepted: 05/17/2017] [Indexed: 11/17/2022] Open
Abstract
Research about antibody specificity spectra was conducted to develop single-specific antibodies or broad-specific antibodies. Aflatoxins, as one class of high-toxicity mycotoxins, were selected as the research targets to investigate the effect of the immunogen dose on antibody specificity spectra. For this aim, 16 monoclonal antibodies were induced by low or high doses of aflatoxin B1-BSA, and 34 monoclonal antibodies were induced by low or high doses of aflatoxin M1-BSA. The specificities of the antibodies induced, whether by aflatoxin B1 conjugate or aflatoxin M1 conjugate, indicated that the low dose of the immunogen induced a narrow spectrum of antibody specificity, while the high dose of the immunogen showed an advantage to form a broad spectrum of antibody specificity. Therefore, this report provides important information for the development of new antibodies against small molecules like aflatoxins.
Collapse
|
21
|
Li YF, Sun YM, Beier RC, Lei HT, Gee S, Hammock BD, Wang H, Wang Z, Sun X, Shen YD, Yang JY, Xu ZL. Immunochemical techniques for multianalyte analysis of chemical residues in food and the environment: A review. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2016.12.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
22
|
Kar S, Roy K, Leszczynski J. On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
23
|
Nanomaterials-Based Platforms for Environmental Monitoring. PAST, PRESENT AND FUTURE CHALLENGES OF BIOSENSORS AND BIOANALYTICAL TOOLS IN ANALYTICAL CHEMISTRY: A TRIBUTE TO PROFESSOR MARCO MASCINI 2017. [DOI: 10.1016/bs.coac.2017.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
|
24
|
He K, Du X, Sheng W, Zhou X, Wang J, Wang S. Crystal Structure of the Fab Fragment of an Anti-ofloxacin Antibody and Exploration of Its Specific Binding. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2627-2634. [PMID: 26963935 DOI: 10.1021/acs.jafc.5b05882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The limited knowledge on the mechanism of interactions between small contaminants and the corresponding antibodies greatly inhibits the development of enzyme-linked immunosorbent assay methods. In this study, the crystal structure of a Fab fragment specific for ofloxacin was obtained. On the basis of the crystal characteristics, the modeling of the interactions between ofloxacin and the Fab revealed that TYR31 and HIS99 of the heavy chain and MET20 and GLN79 of the light chain formed a hydrophobic region and that SER52 and ALA97 of the heavy chain and TYR35 of the light chain formed a salt bridge and two hydrogen bonds for specific binding. The key roles of SER52 and ALA97 were further confirmed by site-directed mutation. A specificity analysis using 14 ofloxacin analogues indicates that the length of the bond formed between the piperazine ring and the antibody plays key roles in specific recognition. This work helps to clarify the mechanisms through which antibodies recognize small molecules and improve immune detection methods.
Collapse
Affiliation(s)
- Kuo He
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology , Tianjin 300457, People's Republic of China
- Hebei North University , Zhangjiakou, Hebei 075000, People's Republic of China
| | - Xinjun Du
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology , Tianjin 300457, People's Republic of China
| | - Wei Sheng
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology , Tianjin 300457, People's Republic of China
| | - Xiaonan Zhou
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology , Tianjin 300457, People's Republic of China
| | - Junping Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology , Tianjin 300457, People's Republic of China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology , Tianjin 300457, People's Republic of China
| |
Collapse
|
25
|
Jammer S, Rizkov D, Gelman F, Lev O. Quantitative structure-activity relationship correlation between molecular structure and the Rayleigh enantiomeric enrichment factor. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2015; 17:1370-1376. [PMID: 26153539 DOI: 10.1039/c5em00084j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It was recently demonstrated that under environmentally relevant conditions the Rayleigh equation is valid to describe the enantiomeric enrichment - conversion relationship, yielding a proportional constant called the enantiomeric enrichment factor, εER. In the present study we demonstrate a quantitative structure-activity relationship model (QSAR) that describes well the dependence of εER on molecular structure. The enantiomeric enrichment factor can be predicted by the linear Hansch model, which correlates biological activity with physicochemical properties. Enantioselective hydrolysis of sixteen derivatives of 2-(phenoxy)propionate (PPMs) have been analyzed during enzymatic degradation by lipases from Pseudomonas fluorescens (PFL), Pseudomonas cepacia (PCL), and Candida rugosa (CRL). In all cases the QSAR relationships were significant with R(2) values of 0.90-0.93, and showed high predictive abilities with internal and external validations providing QLOO(2) values of 0.85-0.87 and QExt(2) values of 0.8-0.91. Moreover, it is demonstrated that this model enables differentiation between enzymes with different binding site shapes. The enantioselectivity of PFL and PCL was dictated by electronic properties, whereas the enantioselectivity of CRL was determined by lipophilicity and steric factors. The predictive ability of the QSAR model demonstrated in the present study may serve as a helpful tool in environmental studies, assisting in source tracking of unstudied chiral compounds belonging to a well-studied homologous series.
Collapse
Affiliation(s)
- S Jammer
- The Casali Center of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | | | | | | |
Collapse
|
26
|
Mu H, Wang B, Xu Z, Sun Y, Huang X, Shen Y, Eremin SA, Zherdev AV, Dzantiev BB, Lei H. Stereospecific recognition and quantitative structure–activity relationship between antibodies and enantiomers: ofloxacin as a model hapten. Analyst 2015; 140:1037-45. [DOI: 10.1039/c4an02155j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, ofloxacin stereoisomers were chosen as a simple model to investigate the stereospecific recognition of chiral haptens and antibodies.
Collapse
Affiliation(s)
- Hongtao Mu
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University/Guangdong Provincial Engineering & Technique Research Centre of Food Safety Detection and Risk Assessment
- Guangzhou 510642
- China
| | - Baoling Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University/Guangdong Provincial Engineering & Technique Research Centre of Food Safety Detection and Risk Assessment
- Guangzhou 510642
- China
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University/Guangdong Provincial Engineering & Technique Research Centre of Food Safety Detection and Risk Assessment
- Guangzhou 510642
- China
| | - Yuanming Sun
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University/Guangdong Provincial Engineering & Technique Research Centre of Food Safety Detection and Risk Assessment
- Guangzhou 510642
- China
| | - Xinan Huang
- Tropical Medicine Institute
- Guangzhou University of Chinese Medicine
- Guangzhou 510405
- China
| | - Yudong Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University/Guangdong Provincial Engineering & Technique Research Centre of Food Safety Detection and Risk Assessment
- Guangzhou 510642
- China
| | - Sergei A. Eremin
- A.N. Bach Institute of Biochemistry
- Russian Academy of Sciences
- Moscow 119071
- Russia
- Faculty of Chemistry
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry
- Russian Academy of Sciences
- Moscow 119071
- Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry
- Russian Academy of Sciences
- Moscow 119071
- Russia
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University/Guangdong Provincial Engineering & Technique Research Centre of Food Safety Detection and Risk Assessment
- Guangzhou 510642
- China
| |
Collapse
|
27
|
Li Y, Zhao F, Zhao L, Yang Z. Development of a Broad-Specificity Immunoassay for Determination of Organophosphorus Pesticides Using Dual-Generic Hapten Antigens. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9906-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
Sharma P, Kukkar M, Ganguli AK, Bhasin A, Suri CR. Plasmon enhanced fluoro-immunoassay using egg yolk antibodies for ultra-sensitive detection of herbicide diuron. Analyst 2013; 138:4312-20. [DOI: 10.1039/c3an00505d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
29
|
Yuan M, Na Y, Li L, Liu B, Sheng W, Lu X, Kennedy I, Crossan A, Wang S. Computer-aided molecular modeling study on antibody recognition of small molecules: an immunoassay for triazine herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:10486-93. [PMID: 23043348 DOI: 10.1021/jf303256r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Most immunoassays for determination of small molecules are still designed on the basis of the "trial and error" method, due to the lack of understanding of antibody recognition. In the present study, we developed a heterologous indirect competitive enzyme-linked immunosorbent assay for determination of triazine herbicides, with limits of detection for 11 triazines ranging from 0.05 to 29.4 μg/L. Mechanisms of the antigen-antibody interaction were studied by computer-aided molecular modeling (CAMM)-based quantitative structure-activity relationship analyses. Co-effects of the analytes' substructural hydrophobic, electrostatic, and steric fields on antibody recognition were further revealed. Hydrophobicity of the antigens was demonstrated to have the most important impact. Even less exposed substituents provided hydrophobic force to the antigen-antibody interaction. Dislocated orientation of analyte functional groups could lead to steric hindrance and hydrophobic misleading of antibody recognition. This may happen even when the antigens contained the same substituent as the hapten. Frontier orbital energies also affect the reaction significantly. This study highlights of the power of CAMM-based analyses, providing insights into antibody recognition of small molecules.
Collapse
Affiliation(s)
- Meng Yuan
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Gertzen CGW, Gohlke H. From Hansch-Fujita Analysis to AFMoC: A Road to Structure-Based QSAR. Mol Inform 2012; 31:698-704. [PMID: 27476451 DOI: 10.1002/minf.201200015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 07/10/2012] [Indexed: 11/05/2022]
Abstract
Since the pioneering effort of Hansch and Fujita, quantitative structure-activity relationships (QSAR) have proved valuable in optimizing lead structures. Enriching classical 3D-QSAR analysis, which exploits the three-dimensional structure of ligands, with structural information of the target has helped to improve the interpretability of the derived models and to increase their predictive power. One such method is the Adaption of Fields for Molecular Comparison (AFMoC) approach where protein-specifically adapted knowledge-based pair-potentials are tailored to one particular protein by considering additional structural and energetic information about ligands. Here, we summarize applications of AFMoC, describe recent developments, and provide an outlook on how to improve the method.
Collapse
Affiliation(s)
- Christoph G W Gertzen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf fax: +49-211-8113847
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf fax: +49-211-8113847.
| |
Collapse
|
31
|
Yuan L, Wei W, Liu S. Label-free electrochemical immunosensors based on surface-initiated atom radical polymerization. Biosens Bioelectron 2012; 38:79-85. [DOI: 10.1016/j.bios.2012.05.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 05/05/2012] [Accepted: 05/07/2012] [Indexed: 11/30/2022]
|
32
|
Investigating the quantitative structure-activity relationships for antibody recognition of two immunoassays for polycyclic aromatic hydrocarbons by multiple regression methods. SENSORS 2012; 12:9363-74. [PMID: 23012547 PMCID: PMC3444105 DOI: 10.3390/s120709363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/12/2012] [Accepted: 06/25/2012] [Indexed: 01/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous contaminants found in the environment. Immunoassays represent useful analytical methods to complement traditional analytical procedures for PAHs. Cross-reactivity (CR) is a very useful character to evaluate the extent of cross-reaction of a cross-reactant in immunoreactions and immunoassays. The quantitative relationships between the molecular properties and the CR of PAHs were established by stepwise multiple linear regression, principal component regression and partial least square regression, using the data of two commercial enzyme-linked immunosorbent assay (ELISA) kits. The objective is to find the most important molecular properties that affect the CR, and predict the CR by multiple regression methods. The results show that the physicochemical, electronic and topological properties of the PAH molecules have an integrated effect on the CR properties for the two ELISAs, among which molar solubility (Sm) and valence molecular connectivity index (3χv) are the most important factors. The obtained regression equations for RisC kit are all statistically significant (p < 0.005) and show satisfactory ability for predicting CR values, while equations for RaPID kit are all not significant (p > 0.05) and not suitable for predicting. It is probably because that the RisC immunoassay employs a monoclonal antibody, while the RaPID kit is based on polyclonal antibody. Considering the important effect of solubility on the CR values, cross-reaction potential (CRP) is calculated and used as a complement of CR for evaluation of cross-reactions in immunoassays. Only the compounds with both high CR and high CRP can cause intense cross-reactions in immunoassays.
Collapse
|
33
|
Aragay G, Pino F, Merkoçi A. Nanomaterials for Sensing and Destroying Pesticides. Chem Rev 2012; 112:5317-38. [DOI: 10.1021/cr300020c] [Citation(s) in RCA: 394] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Gemma Aragay
- Nanobioelectronics
and Biosensors
Group, Catalan Institute of Nanotechnology, UAB Campus, 08193 Bellaterra,
Barcelona, Spain
| | - Flavio Pino
- Nanobioelectronics
and Biosensors
Group, Catalan Institute of Nanotechnology, UAB Campus, 08193 Bellaterra,
Barcelona, Spain
| | - Arben Merkoçi
- Nanobioelectronics
and Biosensors
Group, Catalan Institute of Nanotechnology, UAB Campus, 08193 Bellaterra,
Barcelona, Spain
- ICREA,
Barcelona, Spain
| |
Collapse
|
34
|
Peng J, Feng LN, Zhang K, Li XH, Jiang LP, Zhu JJ. Calcium Carbonate-Gold Nanocluster Hybrid Spheres: Synthesis and Versatile Application in Immunoassays. Chemistry 2012; 18:5261-8. [DOI: 10.1002/chem.201102876] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 12/31/2011] [Indexed: 01/01/2023]
|
35
|
Na Y, Sheng W, Yuan M, Li L, Liu B, Zhang Y, Wang S. Enzyme-linked immunosorbent assay and immunochromatographic strip for rapid detection of atrazine in water samples. Mikrochim Acta 2012. [DOI: 10.1007/s00604-012-0772-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
36
|
Cui Y, Tang D, Liu B, Chen H, Zhang B, Chen G. Biofunctionalized dendritic polyaniline nanofibers for sensitive electrochemical immunoassay of biomarkers. Analyst 2012; 137:1656-62. [DOI: 10.1039/c2an15848e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
37
|
Lei H, Liu J, Song L, Shen Y, Haughey SA, Guo H, Yang J, Xu Z, Jiang Y, Sun Y. Development of a highly sensitive and specific immunoassay for determining chrysoidine, a banned dye, in soybean milk film. Molecules 2011; 16:7043-57. [PMID: 21849932 PMCID: PMC6264186 DOI: 10.3390/molecules16087043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/07/2011] [Accepted: 08/11/2011] [Indexed: 11/30/2022] Open
Abstract
A highly specific and sensitive indirect competitive enzyme-linked immunosorbent assay (icELISA)was developed for the first time for the detection of chrysoidine, a dye banned in soybean milk film. Two haptens with different spacer arms were synthesized to produce antibodies. Both homologous and heterologous immunoassay formats were compared to enhance the icELISA sensitivity. The heterologous icELISA exhibited better performance, with an IC(50) (50% inhibitory concentration) of 0.33 ng/mL, a limit of detection (LOD, 10% inhibitory concentration) of 0.04 ng/mL, and a limit of quantitation (LOQ, 20%-80% inhibitory concentration) from 0.09 to 4.9 ng/mL. The developed icELISA was high sensitive and specific, and was applied to determine chrysoidine in fortified soybean milk film samples. The results were in good agreement with that obtained by high-performance liquid chromatography (HPLC) analyses.
Collapse
Affiliation(s)
- Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Jin Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Lijun Song
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Yudong Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Simon A. Haughey
- Institute of Agri-Food and Land Use, Queen’s University Belfast, Belfast BT9 5AG, Northern Ireland, UK; (S.A.H.)
| | - Haoxian Guo
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Jinyi Yang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| | - Yueming Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Yuanming Sun
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong, China; (H.L.); (J.L.); (L.S.); (Y.S.); (H.G.); (J.Y.); (Z.X.)
| |
Collapse
|