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Zhang J, Li F, Shen S, Yang Z, Ji X, Wang X, Liao X, Zhang Y. More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review. Food Chem 2023; 416:135726. [PMID: 36893635 DOI: 10.1016/j.foodchem.2023.135726] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.
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Affiliation(s)
- Jinghao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Fangwei Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Suxia Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Zhaotian Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xingyu Ji
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Yan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China.
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Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis. Int J Mol Sci 2022; 23:ijms232012351. [PMID: 36293229 PMCID: PMC9604016 DOI: 10.3390/ijms232012351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Cystic fibrosis is a genetic disease caused by mutation of the CFTR gene, which encodes a chloride and bicarbonate transporter in epithelial cells. Due to the vast range of geno- and phenotypes, it is difficult to find causative treatments; however, small-molecule therapeutics have been clinically approved in the last decade. Still, the search for novel therapeutics is ongoing, and thousands of compounds are being tested in different assays, often leaving their mechanism of action unknown. Here, we bring together a CFTR-specific compound database (CandActCFTR) and systems biology model (CFTR Lifecycle Map) to identify the targets of the most promising compounds. We use a dual inverse screening approach, where we employ target- and ligand-based methods to suggest targets of 309 active compounds in the database amongst 90 protein targets from the systems biology model. Overall, we identified 1038 potential target–compound pairings and were able to suggest targets for all 309 active compounds in the database.
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Transcriptomics Reveals the Effect of Thymol on the Growth and Toxin Production of Fusarium graminearum. Toxins (Basel) 2022; 14:toxins14020142. [PMID: 35202169 PMCID: PMC8877954 DOI: 10.3390/toxins14020142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/05/2022] [Accepted: 02/11/2022] [Indexed: 12/20/2022] Open
Abstract
Fusarium graminearum is a harmful pathogen causing head blight in cereals such as wheat and barley, and thymol has been proven to inhibit the growth of many pathogens. This study aims to explore the fungistatic effect of thymol on F. graminearum and its mechanism. Different concentrations of thymol were used to treat F. graminearum. The results showed that the EC50 concentration of thymol against F. graminearum was 40 μg/mL. Compared with the control group, 40 μg/mL of thymol reduced the production of Deoxynivalenol (DON) and 3-Ac-DON by 70.1% and 78.2%, respectively. Our results indicate that thymol can effectively inhibit the growth and toxin production of F. graminearum and cause an extensive transcriptome response. Transcriptome identified 16,727 non-redundant unigenes and 1653 unigenes that COG did not annotate. The correlation coefficients between samples were all >0.941. When FC was 2.0 times, a total of 3230 differential unigenes were identified, of which 1223 were up-regulated, and 2007 were down-regulated. Through the transcriptome, we confirmed that the expression of many genes involved in F. graminearum growth and synthesis of DON and other secondary metabolites were also changed. The gluconeogenesis/glycolysis pathway may be a potential and important way for thymol to affect the growth of F. graminearum hyphae and the production of DON simultaneously.
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