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Chen Q, Ge Y, He X, Li S, Fang Z, Li C, Chen H. Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning. Food Chem 2024; 460:140741. [PMID: 39128372 DOI: 10.1016/j.foodchem.2024.140741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins through virtual-screening. A prediction model was established by machine-learning. Virtual-screening retained four lengths of peptides, including 3-6. Molecular-docking recognized their binding sites with XO and showed residues W, F, and G were the key amino acids. Datasets of XO inhibitory peptides therewith were established. The optimal model was used to generalize the peptides reported. Results showed that the R2 of the tripeptide, tetrapeptide, pentapeptide and hexapeptide in the generalisation test were R2 = 0.81, R2 = 0.82, R2 = 0.83 and R2 = 0.83, respectively. Overall, this work can serve as a reference for explaining the activity mechanism of XO inhibitory peptides and predicting the activity of XO inhibitory peptides.
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Affiliation(s)
- Qian Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Yuxi Ge
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Xiaoyu He
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Shanshan Li
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Zhengfeng Fang
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Cheng Li
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China.
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Abstract
Antibodies and T cell receptors (TCRs) are the fundamental building blocks of adaptive immunity. Repertoire-scale functionality derives from their epitope-binding properties, just as macroscopic properties like temperature derive from microscopic molecular properties. However, most approaches to repertoire-scale measurement, including sequence diversity and entropy, are not based on antibody or TCR function in this way. Thus, they potentially overlook key features of immunological function. Here we present a framework that describes repertoires in terms of the epitope-binding properties of their constituent antibodies and TCRs, based on analysis of thousands of antibody-antigen and TCR-peptide-major-histocompatibility-complex binding interactions and over 400 high-throughput repertoires. We show that repertoires consist of loose overlapping classes of antibodies and TCRs with similar binding properties. We demonstrate the potential of this framework to distinguish specific responses vs. bystander activation in influenza vaccinees, stratify cytomegalovirus (CMV)-infected cohorts, and identify potential immunological "super-agers." Classes add a valuable dimension to the assessment of immune function.
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Zhu Z, Chen Y, Jia N, Zhang W, Hou H, Xue C, Wang Y. Identification of three novel antioxidative peptides from Auxenochlorella pyrenoidosa protein hydrolysates based on a peptidomics strategy. Food Chem 2021; 375:131849. [PMID: 34942500 DOI: 10.1016/j.foodchem.2021.131849] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022]
Abstract
Auxenochlorella pyrenoidosa is recognized as a potential sustainable protein material in food industry, however, its application remains still very limited. Herein, this study aimed to investigate the antioxidative properties of Auxenochlorella pyrenoidosa protein hydrolysates and identify novel antioxidative peptides from protein hydrolysates through a workflow mainly including enzymatic hydrolysis, peptidome quantification, quantitative structure-activity relationship (QSAR) modeling, in silico screening, and validation. Three novel antioxidative peptides including AGWACLVG, IDLAY and YPLDL were identified from protein hydrolysates by papain with the hydrolysis time of 4 h, in which, AGWACLVG showed strong 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity with the IC50 value of 68.88 µM and Trolox equivalent antioxidative capacity of 6.20 ± 0.23 mmol TE/g. This study suggested that Auxenochlorella pyrenoidosa protein hydrolysates could be used as potential antioxidative ingredients in food industry, and the identification of novel antioxidative peptides would contribute to the construction of more robust QSAR models in the future.
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Affiliation(s)
- Zihao Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; College of Food Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yuyang Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Nan Jia
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Wenhan Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hu Hou
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yanchao Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
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Tong JB, Bai M, Zhao X. QSAR study by the RASMS method of DABO derivatives as HIV-1 reverse transcriptase non-nucleoside inhibitors. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617070204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Comprehensive comparison of twenty structural characterization scales applied as QSAM of antimicrobial dodecapeptides derived from Bac2A against P. aeruginosa. J Mol Graph Model 2017; 71:88-95. [DOI: 10.1016/j.jmgm.2016.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 11/02/2016] [Accepted: 11/06/2016] [Indexed: 02/04/2023]
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Tong J, Li L, Bai M, Li K. A New Descriptor of Amino Acids-SVGER and its Applications in Peptide QSAR. Mol Inform 2016; 36. [PMID: 27739658 DOI: 10.1002/minf.201501023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 09/27/2016] [Indexed: 11/10/2022]
Abstract
In the study of peptide quantitative structure activity relationship (QSAR), a new descriptor of amino acids (SVGER) was calculated. It was applied in two peptides which are angiotensin converting enzyme inhibitors and bitter tasting threshold of di-peptide. QSAR models were built by stepwise multiple regression-multiple linear regression (SMR-MLR) and stepwise multiple regression-partial least square regression (SMR-PLS). In the SMR-MLR models for angiotensin converting enzyme inhibitors, the squared cross-validation correlation coefficient (QLOO2 ) was 0.907, squared correlation coefficient between predicted and observed activities (Rcum2 ) was 0.977 and external multiple correlation coefficient (Qext2 ) was 0.867. The corresponding data for the bitter tasting threshold of di-peptide were 0.802, 0.966, 0.719. While in the SMR-PLS model, QLOO2 , Rcum2 and Qext2 were 0.804, 0.915, 0.858 for angiotensin converting enzyme inhibitors and 0.782, 0.881, 0.747 for bitter tasting threshold of di-peptide. Our results showed that descriptor SVGER can afford good account of relationships between activity and structure of peptide drugs.
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Affiliation(s)
- Jianbo Tong
- Shaanxi University of Science & Technology, Xi'an, PR China
| | - Lingxiao Li
- Shaanxi University of Science & Technology, Xi'an, PR China
| | - Min Bai
- Shaanxi University of Science & Technology, Xi'an, PR China
| | - Kangnan Li
- Shaanxi University of Science & Technology, Xi'an, PR China
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To Determine Biologically Important Mutations in Oxytocin. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Quantitative structure–activity relationship studies of diarylpyrimidine derivatives as anti-HIV drugs using new three-dimensional structure descriptors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0770-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Doucet JP, Doucet-Panaye A, Devillers J. Structure-activity relationship study of trifluoromethylketones: inhibitors of insect juvenile hormone esterase. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:481-499. [PMID: 23721304 DOI: 10.1080/1062936x.2013.792499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The juvenile hormone esterase (JHE) regulates juvenile hormone titre in insect hemolymph during its larval development. It has been suggested that JHE could be targeted for use in insect control. This enzyme can also be considered as involved in the phenomenon of endocrine disruption by xenobiotics in beneficial insects. Consequently, there is a need to know the characteristics of the molecules able to act on the JHE. Trifluoromethylketones (TFKs) are the most potent JHE inhibitors found to date and different quantitative structure-activity relationships (QSARs) have been derived for this group of chemicals. In this context, a set of 181 TFKs (118 active and 63 inactive compounds), tested on Trichoplusia ni for their JHE inhibition activity and described by physico-chemical descriptors, was split into different training and test sets to derive structure-activity relationship (SAR) models from support vector classification (SVC). A SVC model including 88 descriptors and derived from a Gaussian kernel was selected for its predictive performances. Another model computed only with 13 descriptors was also selected due to its mechanistic interpretability. This study clearly illustrates the difficulty in capturing the essential structural characteristics of the TFKs explaining their JHE inhibitory activity.
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Affiliation(s)
- J P Doucet
- ITODYS, UMR 7086, Université Paris 7, Paris, France.
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Tong J, Chen Y, Liu S, Xu X. QSAR studies of antituberculosis drug using three-dimensional structure descriptors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0502-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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