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Kodchakorn K, Kongtawelert P. Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity. PLoS One 2022; 17:e0277745. [PMID: 36395151 PMCID: PMC9671323 DOI: 10.1371/journal.pone.0277745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic caused by a virus that can be transmitted from human to human via air droplets has changed the quality of life and economic systems all over the world. The viral DNA has mutated naturally over time leading to the diversity of coronavirus victims which has posed a serious threat to human security on a massive scale. The current variants have developed in a dominant way and are considered "Variants of Concern" by the World Health Organization (WHO). In this work, Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants were obtained to evaluate whether naturally occurring mutations have strengthened viral infectivity. We apply reliable in silico structural dynamics and energetic frameworks of the mutated S-RBD protein for ACE2-binding to analyze and compare the structural information related to the wild-type. In particular, the hotspot residues at Q493, Q498, and N501 on the S-RBD protein were determined as contributing factors to the employment stability of the relevant binding interface. The L452R mutation induces an increment of the hydrogen bonds formed by changing the Q493 environment for ACE2 binding. Moreover, the Q493K exchange in Omicron enables the formation of two additional salt bridges, leading to a strong binding affinity by increased electrostatic interaction energy. These results could be used in proposing concrete informative data for a structure-based design engaged in finding better therapeutics against novel variants.
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Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
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Shi W, Huo X, Ding X, Zhu P, Wan Y, Lu X, Feng R, Yu Q, Wang X. Rapid screening of illegally added drugs in functional food using a miniature ion trap mass spectrometer. Food Chem 2022; 386:132808. [PMID: 35364493 DOI: 10.1016/j.foodchem.2022.132808] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/04/2022]
Abstract
With the expansion of the functional food market, the qualification assessment of these products has become a major challenge, and efficient analytical tools are urgently needed. Here, a miniature mass spectrometer (MS) with self-aspiration capillary electrospray ionization (SACESI) source and ion trap analyzer was developed for rapid screening of various illegally added drugs in functional foods. No chromatographic separation was required, but a simplified two-step pretreatment method was developed to reduce the operational procedures and time consumption of the entire analysis. SACESI source uses capillary action to drive solution injection, which utilizes a simple structure and convenient operation to constitute a kind of disposable MS detection solution. To achieve accurate and automatic identification, an intelligent recognition algorithm with steps of spectrum preprocessing, characteristic peak matching, and support vector machine learning was constructed. The relative accuracy of rapid screening of 31 suspicious drugs in various samples is up to 99.78%. It achieves 100% correct identification for the 55 batches of actual samples captured by on-site inspection, which demonstrates the feasibility of the proposed analytical system and strategy in food safety applications.
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Affiliation(s)
- Wenyan Shi
- Division of Advanced Manufacturing, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xinming Huo
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Xinyue Ding
- Division of Advanced Manufacturing, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Peiyuan Zhu
- Shenzhen Han Industrial Technologies Co.Ltd., Shenzhen 518055, China
| | - Yutong Wan
- Shenzhen Chin Instrument Co., Ltd., Shenzhen 518055, China
| | - Xinqiong Lu
- Shenzhen Chin Instrument Co., Ltd., Shenzhen 518055, China
| | - Rui Feng
- Research Institute for Frontier Science, Beihang University, Beijing 100191, China
| | - Quan Yu
- Division of Advanced Manufacturing, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Xiaohao Wang
- Division of Advanced Manufacturing, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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