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Molecular dynamics-driven exploration of peptides targeting SARS-CoV-2,with special attention on ACE2,S protein,M^(pro),and PL^(pro):A review

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BIOCELL 2023年第8期47卷 1727-1742页

作者： MOHAMAD ZULKEFLEE SABRI JOANNA BOJARSKA FAI-CHU WONG tsun-thai chai Green Chemistry and Sustainable Technology Cluster Bioengineering SectionUniversiti Kuala LumpurMalaysian Institute of Chemical and Bioengineering Technology(UniKL MICET)Alor Gajah78000Malaysia Institute of General and Ecological Chemistry Faculty of ChemistryLodz University of TechnologyLodz90-924Poland Department of Chemical Science Faculty of ScienceUniversiti Tunku Abdul RahmanKampar31900Malaysia Center for Agriculture and Food Research Universiti Tunku Abdul RahmanKampar31900Malaysia

Molecular dynamics(MD)simulation is a computational technique that analyzes the movement of a system of particles over a given *** can provide detailed information about the fluctuations and conformational changes of biomolecules at the atomic level over *** recent years,MD has been widely applied to the discovery of peptides and peptide-like molecules that may serve as severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)*** review summarizes recent advances in such explorations,focusing on four protein targets:angiotensin-converting enzyme 2(ACE2),spike protein(S protein),main protease(M^(pro)),and papain-like protease(PL^(pro)).These four proteins are important druggable targets of SARS-CoV-2 because of their roles in viral entry,maturation,and infectivity of the virus.A review of the literature revealed that ACE2,S protein,and M^(pro) have received more attention in MD research than PL^(pro).Inhibitors of the four targets identified by MD simulations included peptides derived from food and other bioresources,peptides designed using the targets as templates,and peptide-like molecules retrieved from *** of the inhibitors have yet to be validated in experimental assays for ***,the role of MD simulation as an efficient tool in the early stages of anti-SARS-CoV-2 drug discovery agents has been demonstrated.

关键词： COVID-19 Anti-SARS-CoV-2 agent Receptor binding domain Computational screening Drug discovery

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Seagrass proteins: Sources of health-promoting agents awaiting exploration?

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Food Innovation and Advances 2023年第1期2卷 18-20页

作者： tsun-thai chai Jillian Lean Sim Ooi Fai-Chu Wong Department of Chemical Science Faculty of ScienceUniversiti Tunku Abdul Rahman31900 KamparMalaysia Center for Agriculture and Food Research Universiti Tunku Abdul Rahman31900 KamparPerakMalaysia Department of Geography Faculty of Arts and Social SciencesUniversiti Malaya50603 Kuala LumpurMalaysia

Seagrasses are marine plants that form economically and ecologically important ecosystems in coastal seas around the *** seaweeds,another group of marine flora,seagrasses are flowering and seed-bearing ***,there are only 72 known species of seagrasses,distributed over six bioregions,spanning from the Temperate North Atlantic to the Temperate Southern Ocean[1].This contrasts with 295,383 species of terrestrial flowering plants[2]and 225,000 species of seaweeds known to science[3].

关键词： ecosystems coastal marine

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Antiviral activity of traditional Chinese medicinal plants Dryopteris crassirhizoma and Morus alba against dengue virus

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Journal of Integrative Agriculture 2020年第4期19卷 1085-1096页

作者： Maqsood MARYAM Kian Keong TE Fai Chu WONG tsun thai chai Gary K K LOW Seng Chiew GAN Hui Yee CHEE Department of Medical Microbiology and Parasitology Faculty of Medicine and Health SciencesUniversiti Putra MalaysiaSerdang 43400Malaysia Faculty of Natural Sciences SBK Women's University QuettaBalochistan 87300Pakistan Department of Chinese Medicine Faculty of Medicine and Health SciencesUniversiti Tunku Abdul RahmanSungai Long CampusKajang 43000Malaysia Department of Chemical Science Faculty of ScienceUniversiti Tunku Abdul Rahman(Kampar Campus)Kampar 31900Malaysia Department of Population Medicine Faculty of Medicine and Health SciencesUniversiti Tunku Abdul Rahman(Sungai Long Campus)Kajang 43000Malaysia Department of Pre-Clinical Sciences Faculty of Medicine and Health SciencesUniversiti Tunku Abdul Rahman(Sungai Long Campus)Kajang 43000Malaysia

Dengue virus(DENV) has emerged as a major virus that is spread by mosquitoes. Recently, it has spread to more than a hundred nations but continues to lack specific treatable medication. Many traditional Chinese medicinal(TCM) plants are in practice for dengue fever in dengue endemic regions. These traditional medicines persevere with treatments, which modern medicines lack. The study aims to substantiate the anti-dengue potential of some traditional herbs and make them available for further studies to facilitate TCM users. Twelve TCM plants aqueous extracts were evaluated, which are described as cool herbs used for the diseases with high fever. Lead plants were established through detailed in vitro foci forming unit reduction analysis(FFURA) against all four serotypes and validated through quantitative real-time RT-PCR(q RT-PCR). Four plants potentially inhibited the virus in primary phenotypic in vitro evaluation. Two lead plants Dryopteris crassirhizoma(DC) and Morus alba(MA) were identified with half minimal inhibitory concentration(IC50) 130 and 221 μg m L^-1, respectively, while the selectivity indices(SI) were 4.21 and 4.62, respectively. Lead plants equally inhibited all four serotypes of DENV. Time-of-addition analysis suggested that, DC was active at later stages of viral replication, whereas MA was active during the early stages and even showed some prophylactic activity. Liquid chromatography-mass spectrometry(HPLC/MS) analysis revealed presence of flavonoids. DC and MA are identified as potential anti-dengue plants, active against varied stages of dengue virus replication cycle. These results may serve as the base knowledge for further investigation on their combined treatments or integrative treatment with western medicines, which may improve the overall anti-dengue activity in future.

关键词： dengue virus traditional Chinese medicines TCM complementary medicines plant extracts anti-dengue

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Purification and identification of novel cytotoxic oligopeptides from soft coral Sarcophyton glaucum

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2019年第1期20卷 59-70页

作者： Yixian QUAH Nor Ismaliza MOHD ISMAIL Jillian Lean Sim OOI Yang Amri AFFENDI Fazilah ABD MANAN Lai-Kuan TEH Fai-Chu WONG tsun-thai chai Department of Chemical Science Faculty of Science Universiti Tunku Abdul Rahman Department of Biological Science Faculty of Science Universiti Tunku Abdul Rahman Centre for Biodiversity Research Universiti Tunku Abdul Rahman Department of Geography Faculty of Arts and Social Sciences University of Malaya Institute of Biological Sciences Faculty of Science University of Malaya Institute of Ocean and Earth Sciences University of Malaya Department of Biosciences Faculty of Science Universiti Teknologi Malaysia Department of Biomedical Science Faculty of Science Universiti Tunku Abdul Rahman

Globally, peptide-based anticancer therapies have drawn much attention. Marine organisms are a reservoir of anticancer peptides that await discovery. In this study, we aimed to identify cytotoxic oligopeptides from Sarcophyton glaucum. Peptides were purified from among the S. glaucum hydrolysates produced by alcalase, chymotrypsin, papain, and trypsin, guided by a methylthiazolyldiphenyl-tetrazolium bromide(MTT) assay on the human cervical cancer(HeLa) cell line for cytotoxicity evaluation. Purification techniques adopted were membrane ultrafiltration, gel filtration chromatography, solid phase extraction(SPE), and reversed-phase high-performance liquid chromatography(RP-HPLC). Purified peptides were identified by de novo peptide sequencing. From papain hydrolysate, three peptide sequences were identified: AGAPGG, AERQ, and RDTQ(428.45, 502.53, and 518.53 Da, respectively). Peptides synthesized from these sequences exhibited cytotoxicity on HeLa cells with median effect concentration(EC50) values of 8.6, 4.9, and 5.6 mmol/L, respectively, up to 5.8-fold stronger than the anticancer drug 5-fluorouracil. When tested at their respective EC50, AGAPGG, AERQ, and RDTQ showed only 16%, 25%, and 11% cytotoxicity to non-cancerous Hek293 cells, respectively. In conclusion, AERQ, AGAPGG, and RDTQ are promising candidates for future development as peptide-based anticancer drugs.

关键词： Anticancer therapy Bioactive peptide Cytotoxicity HeLa cells Sarcophyton glaucum Soft coral

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Quantum purification for coherent states and its application

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Science China(Physics,Mechanics & Astronomy) 2025年第2期68卷 37-50页

作者： Lei Wang Geng chai Zhengwen Cao Xinlei Chen Kexin Liang Jinye Peng Laboratory of Quantum Information and Technology School of Information Science and TechnologyNorthwest UniversityXi'an 710127China

The inevitable decoherence of quantum states leaks information to the environments and reduces the practical performance of quantum-information *** purification of coherent states provides an easy-to-implement approach to decouple from the environments utilizing the correlation of several ***,repeated transmission of quantum states reduces the randomness of the collectivity and generates security *** this paper,we propose a modified purification scheme and apply it to the continuous-variable quantum secure direct communication(CV-QSDC)protocol based on coherent *** designed purification scheme improves the security capacity of communication systems through the effective suppression of excess noises,accompanied by the maintenance of source-side *** conduct a proof-of-principle experiment of the purification scheme in the CV-QSDC *** appearance of transmitted quantum states in phase space and two-dimensional Gaussian distributions have high goodness of fit at two *** security capability of this system is improved by 43.6%as the excess noise is reduced to 0.58 times the original noise by purification.

关键词： quantum purification coherent state quantum secure direct communication

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Resilient Nonlinear MPC With a Dynamic Event-Triggered Strategy Under DoS Attacks

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IEEE/CAA Journal of Automatica Sinica 2025年第3期12卷 642-644页

作者： Shuang Shen Runqi chai Yuanqing Xia Senchun chai the School of Automation Beijing Institute of Technology

Dear Editor,This letter deals with the stabilization of a resilient model predictive control (MPC) algorithm with a dynamic event-triggered mechanism subject to Denial-of-Service (Do S) attacks. Different from previous works, this letter is based on the designed threshold function to dynamically trigger and gives the upper bound conditions for intersampling intervals with attack and attack-free scenarios to converge.

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Decentralized Federated Learning Algorithm Under Adversary Eavesdropping

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IEEE/CAA Journal of Automatica Sinica 2025年第2期12卷 448-456页

作者： Lei Xu Danya Xu Xinlei Yi Chao Deng Tianyou chai Tao Yang the State Key Laboratory of Synthetical Automation for Process Industries Northeastern University the Department of Mechanical Engineering University of Victoria Shanghai Institute of Intelligent Science and Technology Tongji University IEEE the Institute of Advanced Technology Nanjing University of Posts and Telecommunications

In this paper, we study the decentralized federated learning problem, which involves the collaborative training of a global model among multiple devices while ensuring data *** classical federated learning, the communication channel between the devices poses a potential risk of compromising private information. To reduce the risk of adversary eavesdropping in the communication channel, we propose TRADE(transmit difference weight) concept. This concept replaces the decentralized federated learning algorithm's transmitted weight parameters with differential weight parameters, enhancing the privacy data against eavesdropping. Subsequently, by integrating the TRADE concept with the primal-dual stochastic gradient descent(SGD)algorithm, we propose a decentralized TRADE primal-dual SGD algorithm. We demonstrate that our proposed algorithm's convergence properties are the same as those of the primal-dual SGD algorithm while providing enhanced privacy protection. We validate the algorithm's performance on fault diagnosis task using the Case Western Reserve University dataset, and image classification tasks using the CIFAR-10 and CIFAR-100 datasets,revealing model accuracy comparable to centralized federated learning. Additionally, the experiments confirm the algorithm's privacy protection capability.

关键词： Adversary eavesdropping decentralized federated learning privacy protection stochastic gradient descent

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Insight into the sorption and desorption pattern of pyrrolizidine alkaloids and their N-oxides in acidic tea(Camellia sinensis)plantation soils

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Journal of Environmental Sciences 2025年第2期148卷 350-363页

作者： Yuting Lu Haolei Han Yuexing Yi Yunfeng chai ChenWang Xiangchun Zhang Xiangde Yang Hongping Chen Tea Research Institute Chinese Academy of Agricultural SciencesHangzhou 310008China Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China School of Chemical Engineering and Materials Zhejiang University of TechnologyHangzhou 310008China Key Laboratory of Tea Quality and Safety&Risk Assessment Ministry of AgricultureHangzhou 310008China Key Laboratory of Tea Quality and Safety Control Ministry of Agriculture and Rural AffairsHangzhou 310000China

Pyrrolizidine alkaloids(PAs)and their N-oxides(PANOs)are phytotoxins produced by various plant species and have been emerged as environmental *** sorption/desorption behaviors of PAs/PANOs in soil are crucial due to the horizontal transfer of these natural products from PA-producing plants to soil and subsequently absorbed by plant *** study firstly investigated the sorption/desorption behaviors of PAs/PANOs in tea plantation soils with distinct *** amounts for seneciphylline(Sp)and seneciphylline-N-oxide(SpNO)in three acidic soils ranged from 2.9 to 5.9μg/g and 1.7 to 2.8μg/g,*** percentages for Sp and SpNO were from 22.2%to 30.5%and 36.1%to 43.9%.In the mixed PAs/PANOs systems,stronger sorption of PAs over PANOs was occurred in tested ***,the Freundlich models more precisely described the sorption/desorption *** exchange capacity,sand content and total nitrogen were identified as major influencing factors by linear regression ***,the soils exhibiting higher sorption capacities for compounds with greater *** were more likely to migrate within soils and be absorbed by tea *** contributes to the understanding of environmental fate of PAs/PANOs in tea plantations and provides basic data and clues for the development of PAs/PANOs reduction technology.

关键词： Pyrrolizidine alkaloids Sorption-desorption behavior Tea plantation system Acidic soil Linear regression model

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Dissolved carbon in biochar:Exploring its chemistry,iron complexing capability,toxicity in natural redox environment

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Journal of Environmental Sciences 2025年第1期147卷 217-229页

作者： Chaochao Lai Juhong Zhan Qiuyun chai Changlu Wang Xiaoxia Yang Huan He Bin Huang Xuejun Pan Faculty of Environmental Science and Engineering Kunming University of Science and TechnologyKunming 650500China Research Institute for Environmental Innovation(Suzhou)Tsinghua Suzhou 215163China

Dissolved black carbon(DBC)plays a crucial role in the migration and bioavailability of iron in ***,the properties of DBC releasing under diverse pyrolysis conditions and dissolving processes have not been systematically ***,the compositions of DBC released from biochar through redox processes dominated by bacteria and light were thoroughly *** was found that the DBC released from straw biochar possess more oxygen-containing functional groups and aromatic *** content of phenolic and carboxylic groups in DBC was increased under influence of microorganisms and light,*** concentration of phenolic hydroxyl groups increased from 10.0~57.5 mmol/gC to 6.6~65.2 mmol/gC,and the concentration of carboxyl groups increased from49.7~97.5 mmol/gC to 62.1~113.3 mmol/*** the impacts of DBC on pyrite dissolution andmicroalgae growth were also *** complexing Fe^(3+)was proved to play a predominant role in the dissolution of ferrous mineral in DBC *** to complexing between iron ion and DBC,the amount of dissolved Fe in aquatic water may rise as a result of elevated number of aromatic components with oxygen containing groups and low molecular weight generated under light ***-DBC complexations in solution significantly promoted microalga growth,which might be attributed to the stimulating effect of dissolved Fe on the chlorophyll *** results of study will deepen our understanding of the behavior and ultimate destiny of DBC released into an iron-rich environment under redox conditions.

关键词： Dissolved black carbon Bacteria Light Iron complexes Toxicity

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Synthesis ofδ-MnO_(2)via ozonation routine for low temperature formaldehyde removal

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Journal of Environmental Sciences 2025年第1期147卷 642-651页

作者： Guijun Fan Yacong Guo Shaohua chai Le Zhang Jian Guan Guojun Ma Ning Han Yunfa Chen State Key Laboratory of Multiphase Complex Systems Institute of Process EngineeringChinese Academy of SciencesBeijing 100190China College of Chemical Engineering University of Chinese Academy of SciencesBeijing 100049China Key Laboratory of Science and Technology on Particle Materials Institute of Process EngineeringChinese Academy of SciencesBeijing 361021China Key Laboratory for Mechanics in Fluid Solid Coupling Systems Institute of MechanicsChinese Academy of SciencesBeijing 100190China School of Petrochemical Engineering&Environment Zhejiang Ocean UniversityZhoushan 316022China

Nowadays,it is still a challenge to prepared high efficiency and low cost formaldehyde(HCHO)removal catalysts in order to tackle the long-living indoor air ***,δ-MnO_(2)is successfully synthesized by a facile ozonation strategy,where Mn^(2+)is oxidized by ozone(O_(3))bubble in an alkaline *** presents one of the best catalytic properties with a low 100%conversion temperature of 85℃for 50 ppm of HCHO under a GHSV of 48,000 mL/(g·hr).As a comparison,more than 6 times far longer oxidation time is needed if O3 is replaced by O_(2).Characterizations show that ozonation process generates a different intermediate of tetragonalβ-HMnO_(2),which would favor the quick transformation into the final productδ-MnO_(2),as compared with the relatively more thermodynamically stable monoclinicγ-HMnO_(2)in the O_(2)***,HCHO is found to be decomposed into CO_(2)via formate,dioxymethylene and carbonate species as identified by room temperature insitu diffuse reflectance infrared fourier transform *** these results show great potency of this facile ozonation routine for the highly activeδ-MnO_(2)synthesis in order to remove the HCHO contamination.

关键词： δ-MnO_(2) Ozone oxidation HCHO oxidation In-situ DRIFTS

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