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Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 Mpro inhibitors

Acta Pharmaceutica Sinica B 2024年第1期14卷 87-109页

作者： Letian Song Shenghua Gao Bing Ye Mianling Yang Yusen Cheng Dongwei Kang Fan Yi Jin-Peng Sun Luis Menéndez-Arias Johan Neyts Xinyong Liu Peng Zhan Department of Medicinal Chemistry Key Laboratory of Chemical Biology(Ministry of Education)School of Pharmaceutical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China Shenzhen Research Institute of Shandong University Shenzhen 518057China The key laboratory of Infection and Immunity of Shandong Province Department of PharmacologySchool of Basic Medical SciencesShandong UniversityJinan 250012China key laboratory Experimental Teratology of the Ministry of Education Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China Centro de Biologı´a Molecular“Severo Ochoa”(Consejo Superior de Investigaciones Cientı´ficas&Autonomous University of Madrid) Madrid 28049Spain KU Leuven Department of Microbiology and ImmunologyRega Institute for Medical ResearchLaboratory of Virology and ChemotherapyLeuven 3000Belgium

The main protease(M^(pro))of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life *** covalent M^(pro)inhibitor nirmatrelvir(in combination with ritonavir,a pharmacokinetic enhancer)and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic *** antiviral drugs are needed to fight the pandemic,while non-covalent M^(pro)inhibitors could be promising alternatives due to their high selectivity and favorable *** non-covalent M^(pro)inhibitors with desirable properties have been developed based on available crystal structures of M^(pro).In this article,we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent M^(pro)inhibitors,followed by a general overview and critical analysis of the available *** viewpoints and insights into current strategies for the development of non-covalent M^(pro)inhibitors are also discussed.

关键词： COVID-19 SARS-CoV-2 Main protease Non-covalent inhibitors Medicinal chemistry strategies

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Spatiotemporal evolution and assembly processes of ammonia-oxidizing prokaryotic communities in 1 000-year-old coastal reclaimed soils

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Pedosphere 2024年第4期34卷 709-725页

作者： Sarfraz HUSSAIN Yifan YIN Senlin LIU Shanshan YAN Dongjie CHEN Hui CAO Feng WANG key laboratory of Agricultural Environmental microbiology Ministry of Agriculture and Rural AffairsCollege of Life SciencesNanjing Agricultural UniversityNanjing 210095China Institute of Eco-Environmental Sciences Ningbo Academy of Agricultural SciencesNingbo 315040China

Coastal marshes are transitional areas between terrestrial and aquatic *** are sensitive to climate change and anthropogenic *** recent decades,the reclamation of coastal marshes has greatly increased,and its effects on microbial communities in coastal marshes have been studied with great *** of these studies have explained the short-term spatiotemporal variation in soil microbial community ***,the impact of reclamation on the community composition and assembly processes of functional microbes(e.g.,ammonia-oxidizing prokaryotes)is often *** this study,using quantitative polymerase chain reaction and the Ion S5™XL sequencing platform,we investigated the spatiotemporal dynamics,assembly processes,and diversity patterns of ammonia-oxidizing prokaryotes in 1000-year-old reclaimed coastal salt *** taxonomic and phylogenetic diversity and composition of ammonia oxidizers showed apparent spatiotemporal variations with soil *** null modelling-based analysis showed that across all sites,the archaeal ammonia-oxidizing community was assembled by a deterministic process(84.71%),and deterministic processes were also dominant(55.2%)for ammonia-oxidizing bacterial communities except for communities at 60 years of *** assembly process and nitrification activity in reclaimed soils were positively *** abundance of the amoA gene and changes in ammonia-oxidizing archaeal and bacterial diversities significantly affected the nitrification activity in reclaimed *** findings suggest that long-term coastal salt marsh reclamation affects nitrification by modulating the activities of ammonia-oxidizing microorganisms and regulating their community structures and assembly *** results provide a better understanding of the effects of long-term land reclamation on soil nitrogen-cycling microbial communities.

关键词： ammonia oxidizer beta nearest taxon index coastal salt marshes community assembly deterministic process nitrification rate stochastic process

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Transforming growth factor-beta 1 enhances discharge activity of cortical neurons

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Neural Regeneration Research 2025年第2期20卷 548-556页

作者： Zhihui Ren Tian Li Xueer Liu Zelin Zhang Xiaoxuan Chen Weiqiang Chen Kangsheng Li Jiangtao Sheng Department of microbiology and immunology Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular ImmunopathologyShantou University Medical CollegeShantouGuangdong ProvinceChina Department of Neurosurgery First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdong ProvinceChina

Transforming growth factor-beta 1(TGF-β1)has been extensively studied for its pleiotropic effects on central nervous system *** neuroprotective or neurotoxic effects of TGF-β1 in specific brain areas may depend on the pathological process and cell types ***-gated sodium channels(VGSCs)are essential ion channels for the generation of action potentials in neurons,and are involved in various neuroexcitation-related ***,the effects of TGF-β1 on the functional properties of VGSCs and firing properties in cortical neurons remain *** this study,we investigated the effects of TGF-β1 on VGSC function and firing properties in primary cortical neurons from *** found that TGF-β1 increased VGSC current density in a dose-and time-dependent manner,which was attributable to the upregulation of Nav1.3 *** VGSC current density and Nav1.3 expression were significantly abolished by preincubation with inhibitors of mitogen-activated protein kinase kinase(PD98059),p38 mitogen-activated protein kinase(SB203580),and Jun NH2-terminal kinase 1/2 inhibitor(SP600125).Interestingly,TGF-β1 significantly increased the firing threshold of action potentials but did not change their firing rate in cortical *** findings suggest that TGF-β1 can increase Nav1.3 expression through activation of the ERK1/2-JNK-MAPK pathway,which leads to a decrease in the firing threshold of action potentials in cortical neurons under pathological ***,this contributes to the occurrence and progression of neuroexcitatory-related diseases of the central nervous system.

关键词： central nervous system cortical neurons ERK firing properties JNK Nav1.3 p38 transforming growth factor-beta 1 traumatic brain injury voltage-gated sodium currents

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Elucidating microbial iron corrosion mechanisms with a hydrogenase-deficient strain of Desulfovibrio vulgaris

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mLife 2024年第2期3卷 269-276页

作者： Di Wang Toshiyuki Ueki Peiyu Ma Dake Xu Derek R.Lovley Electrobiomaterials Institute Key Laboratory for Anisotropy and Texture of Materials(Ministry of Education)Northeastern UniversityShenyangChina Shenyang National laboratory for Materials Science Northeastern UniversityShenyangChina Department of microbiology University of MassachusettsAmherstMAUSA

Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal *** is substantial debate over their corrosion *** investigated Fe^(0) corrosion with Desulfovibrio vulgaris,the sulfate reducer most often employed in corrosion *** were grown with both lactate and Fe^(0) as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive ***^(0) was corroded in cultures of a *** hydrogenase-deficient mutant with the 1:1 correspondence between Fe^(0) loss and H_(2) accumulation expected for Fe^(0) oxidation coupled to H+reduction to H_(2).This result and the extent of sulfate reduction indicated that *** was not capable of direct Fe^(0)-to-microbe electron transfer even though it was provided with a supplementary energy source in the presence of abundant ferrous *** in the hydrogenase-deficient mutant cultures was greater than in sterile controls,demonstrating that H_(2) removal was not necessary for the enhanced corrosion observed in the presence of *** parental H_(2)-consuming strain corroded more Fe^(0) than the mutant strain,which could be attributed to H_(2) oxidation coupled to sulfate reduction,producing sulfide that further stimulated Fe^(0) *** results suggest that H_(2) consumption is not necessary for microbially enhanced corrosion,but H_(2) oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate *** finding that *** was incapable of direct electron uptake from Fe^(0) reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes.

关键词： electrobiocorrosion electron transfer hydrogen transfer microbial corrosion sulfate-reducing microbes

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Glutamate oxidase-integrated biomimetic Fe_(3)O_(4) hybrids as cascade nanozymes for glutamate detection

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Particuology 2024年第5期88卷 192-200页

作者： Peikun Li Yanchao Wang Xiuyan Luo Zixin Geng Jiahui Jia Ruirui Wang Jiandong Cui Hongjie Bian Shiru Jia State key laboratory of Food Nutrition and Safety Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin300457China Sports Department Hebei University of Science and TechnologyShijiazhang050000China Research Center for Fermentation Engineering of Hebei College of Bioscience and BioengineeringHebei University of Science and TechnologyShijiazhang050000China

Herein,a new nanozyme/natural enzyme hybrid biosensor was established for ultrasensitive l-glutamic acid(L-Glu)*** Fe_(3)O_(4) nanoparticles with peroxidase-like activity and stability was used as a nanozyme and carrier for immobilizing l-Glutamate oxidase(GLOD)through Schiffff base reaction to construct a chem-enzyme cascade *** resultant Fe_(3)O_(4)-GOLD exhibited a wide linear range(10−500μM)and a low detection limit of 6.03μM for L-Glu ***,the Fe_(3)O_(4)-GOLD exhibited excellent pH stability,thermal stability,reusability and storage *** repeated nine cycles,Fe_(3)O_(4)-GOLD still retained 70%of its initial ***,Fe_(3)O_(4)-GOLD maintained 50%of its initial activity after storage for 20 days,while free GLOD only retained 20%of its initial *** strategy of integrating biomimetic Fe 3 O4 and natural enzymes for cascade catalysis makes it possible to design an efficient and stable chemo-enzyme composite catalysts,which are promising for applications in biosensing and biomimetic catalysis.

关键词： Fe_(3)O_(4) nanozyme GLOD Chemo-enzymes Glutamate detection

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Soil microbial ecology through the lens of metatranscriptomics

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Soil Ecology Letters 2024年第3期6卷 1-15页

作者： Jingjing Peng Xi Zhou Christopher Rensing Werner Liesack Yong-Guan Zhu State key laboratory of Nutrient Use and Management College of Resources and Environmental SciencesNational Academy of Agriculture Green DevelopmentKey Laboratory of Plant-Soil InteractionsMinistry of EducationChina Agricultural UniversityBeijing 100193China Institute of Environmental microbiology College of Resource and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China Max Planck Institute for Terrestrial microbiology Marburg 35043Germany State key laboratory of Urban and Regional Ecology Research Centre for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China key laboratory of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental *** double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional *** contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA *** this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional *** particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and *** review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

关键词： metatranscriptomics mRNA MAGs rhizobiont resistome virome

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The infection kinetics and transmission potential of two Guaico Culex viruses in Culex quinquefasciatus mosquitoes

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Virologica Sinica 2024年第2期39卷 228-234页

作者： Ru-Yi Chen Teng Zhao Jing-Jing Guo Feng Zhu Na-Na Zhang Xiao-Feng Li Hai-Tao Liu Fei Wang Yong-Qiang Deng Cheng-Feng Qin College of Bioscience and Bioengineering Jiangxi Agricultural UniversityNanchang330045China State key laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China School of Life Sciences Southwest Forestry UniversityKunming650224China

Guaico Culex virus(GCXV)is a newly identified segmented Jingmenvirus from Culex *** in Central and South *** genome of GCXV is composed of four or five single-stranded positive RNA ***,the infection kinetics and transmission capability of GCXV in mosquitoes remain *** this study,we used reverse genetics to rescue two GCXVs(4S and 5S)that contained four and five RNA segments,respectively,in C6/36 *** in vitro characterization revealed that the two GCXVs exhibited comparable replication kinetics,protein expression and viral ***,GCXV RNAs were detected in the bodies,salivary glands,midguts and ovaries of Culex quinquefasciatus at 4–10 days after oral *** addition,two GCXVs can colonize *** eggs,resulting in positive rates of 15%–35%for the second gonotrophic *** conclusion,our results demonstrated that GCXVs with four or five RNA segments can be detected in *** eggs during the first and second gonotrophic cycles after oral infection.

关键词： Guaico Culex virus(GCXV) Jingmenvirus Culex quinquefasciatus Vertical transmission

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Chronic social defeat stress‑induced depression reduces BCG efficacy by promoting regulatory T‑cell levels in mice

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Animal Diseases 2024年第2期4卷 115-126页

作者： Rohit Tyagi Xi Chen Atika Dhar Bing Yang Wei Zhou Aikebaier Reheman Yingying Lei Gang Cao National key laboratory of Agricultural microbiology College of Veterinary MedicineHuazhong Agricultural UniversityWuhan 430070China National Institute of immunology New Delhi 110067India College of Animal Science and Technology Tarim UniversityAlar 843300China Bio‑Medical Center Huazhong Agricultural UniversityWuhan 430070China

Despite the initial successes of the Bacillus Calmette-Guerin(BCG)vaccine in children,its efficacy against tuberculosis is highly *** is a lack of understanding about how mental conditions influence BCG ***,we used the chronic social defeat stress(CSDS)model to explore the effects of depression on BCG vaccination *** observed higher lung and spleen bacterial loads and a lower organ index in depressed compared to BCG ***,a relatively lower T cell protective efficacy was observed in both compared to control and BCG mice via a mycobacterium growth inhibition assay(MGIA).Cytokine expression of IL-12p40,IL-1β,IL-17,TNF-αand IFN-γwas reduced,whereas the expression of IL-10 and IL-5 was increased in the spleen of both compared to BCG ***,the proportions of CD4^(+)IFN-γ^(+),CD8^(+)IFN-γ^(+)T lymphocytes and CD4^(+)effector/central memory T cells were reduced in the splenocytes of the depressed BCG *** promotes CD4^(+)regulatory T cells(Treg)and myeloid-derived suppressor cell(MDSC)generation in depressed mice,contributing to the reduced pro-inflammatory immune response upon BCG *** study provides insight into the decreased protective immunity by BCG vaccination attributable to depression in mice.

关键词： BCG Vaccine efficacy Treg Immune suppression Depression

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Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

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mLife 2024年第2期3卷 277-290页

作者： Pan Zhang Biliang Zhang Yuan-Yuan Ji Jian Jiao Ziding Zhang Chang-Fu Tian State key laboratory of Plant Environmental Resilience and College of Biological SciencesChina Agricultural UniversityBeijingChina MOA key laboratory of Soil microbiology and Rhizobium Research CenterChina Agricultural UniversityBeijingChina Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina State key laboratory of Livestock and Poultry Biotechnology Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function,while accessory genes are dispensable,particularly in nutrient-rich ***,this assumption is seldom tested genetically within the pangenome *** this study,we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open *** evaluate the robustness of fitness category assignment,Tn-seq data for three independent mutant libraries per strain were analyzed by three methods,which indicates that the Hidden Markov Model(HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size,outperforming the Bayesian and Monte Carlo simulation-based ***,the HMM method was used to classify the fitness *** genes,categorized as essential(ES),advantage(GA),and disadvantage(GD)genes for growth,are enriched in core genes,while nonessential genes(NE)are over-represented in accessory *** ES/GA genes showed a lower fitness effect than core ES/GA *** degrees in the cofitness network decrease in the order of ES,GD,and GA/*** addition to accessory genes,1599 out of 3284 core genes display differential essentiality across test *** the pangenome core,both shared quasi-essential(ES and GA)and strain-dependent fitness genes are enriched in similar functional *** analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.

关键词： cofitnessnetwork pangenome Tn-seq

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The protective effects of fermented vinegar on acute alcohol-induced hepatic and neuro-toxicity by regulating ethanol metabolism and gut microbiota

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Food Science and Human Wellness 2024年

作者： Yuan Meng Yunfan Liu Ting Xia Beibei Geng Yinglei Tian Hailong Cao Jin Yan Xiaoqi Pang Kai Liang Yufeng Yan Min Wang State key laboratory of Food Nutrition and Safety， key laboratory of Industrial Fermentation microbiology， College of Biotechnology， Tianjin University of Science and Technology Department of Gastroenterology and Hepatology， General Hospital， Tianjin Medical University， National key Clinical Specialty， Tianjin Institute of Digestive Diseases， Tianjin key laboratory of Digestive Diseases Shanxi Provincial key laboratory for Vinegar Fermentation Science and Engineering， Shanxi Zilin Vinegar Industry Co.， Ltd.

Alcohol abuse constitutes a significant health hazard， leading to various organ damage， notably the liver and brain. Shanxi aged vinegar (SAV) is one of the famous fermented and functional foods containing a variety of bioactive ingredients with beneficial effects on the human body. This study aimed to explore the potential protective effect of SAV in alleviating acute alcohol intoxication (AAI) in mice. It was found that SAV at 2.5 mg/kg BW effectively ameliorated the decline in behavioral abilities following alcohol consumption， characterized by a shortened sobering period. SAV reduces alcohol-induced liver damage by inhibiting hepatic function enzymes and oxidative stress levels. Additionally， SAV mitigated the overactivation of microglia and the downregulation of neurotransmitter levels (AchE， 5-HT， and DA)， thereby reducing ethanol-induced brain damage. Meanwhile， SAV significantly decreased concentrations of alcohol and acetaldehyde in the blood and increased ADH and ALDH activities in the liver， indicating enhancement of ethanol metabolism. Moreover， we found that some gut microbiota including Verrucomicrobiota， Akkermansia， and Enterococcus were downregulated after SAV treatment in mice with AAI. These bacteria showed a negative correlation with anti-oxidative markers (GSH and CAT) and enzymes related to ethanol metabolism pathways (ADH and ALDH)， and a positive correlation with hepatic function markers (ALT， AST， and MDA)， alcohol metabolites (alcohol and acetaldehyde) and neurotransmitters (AchE， 5-HT， and DA). However， Bacteroidota， norank＿f＿Muribaculaceae， and Alistipes exhibited the opposite direction. These findings suggest that SAV possesses protective effects against hepatic and neuro-toxicity， and could be a potential functional food for AAI prevention.

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