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Advances in solid-state NMR methods for studying RNA structures and dynamics

Magnetic Resonance Letters 2025年第1期5卷 64-74页

作者： Jinhan He Xiaole Liu Shenlin Wang State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghai200237China

Ribonucleic acid(RNA)structures and dynamics play a crucial role in elucidating RNA functions and facilitating the design of drugs targeting RNA and RNA-protein ***,obtaining RNA structures using conventional biophysical techniques,such as Xray crystallography and solution nuclear magnetic resonance(NMR),presents challenges due to the inherent flexibility and susceptibility to degradation of *** recent years,solid-state NMR(SSNMR)has rapidly emerged as a promising alternative technique for characterizing RNA structure and *** has several distinct advantages,including flexibility in sample states,the ability to capture dynamic features of RNA in solid form,and suitability to character RNAs in various *** decade witnessed the growth of ^(1)H-detected SSNMR methods on RNA,which targeted elucidating RNA topology and base pair dynamics in solid *** have been applied to determine the topology of RNA segment in human immunodeficiency virus(HIV)genome and the base pair dynamics of riboswitch *** advancements have expanded the utility of SSNMR techniques within the RNA research *** review provides a comprehensive discussion of recent progress in ^(1)H-detected SSNMR investigations into RNA structure and *** focus on the established ^(1)H-detected SSNMR methods,sample preparation protocols,and the implementation of rapid data acquisition approaches.

关键词： Solid-state NMR RNA Structure Dynamics Pulse sequences

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Polyvinyl alcohol, N-acetylcysteine, and methyl-β-cyclodextrin exhibit albumin functions in natural killer cell culture

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Journal of Bioscience and Bioengineering 2025年第6期139卷 436-444页

作者： Xu, Ruisheng Zhang, Guofeng Huang, Huimin Zhao, Yuanyuan Tan, Wen-Song Cai, Haibo State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai200237 China

Albumin is a crucial component of serum-free media, playing a significant role in ex vivo cell culture as a lipid carrier and antioxidant. However, purified albumin contains undefined substances, making it challenging to achieve clinical application standards for effector cell culture. This study used natural killer (NK)-92 cells as a model to investigate the effects of the albumin substitute replacing bovine serum albumin (BSA) on cell expansion and metabolism in an in-house-designed, chemically defined, serum-free medium. We selected polyvinyl alcohol (PVA), N-acetylcysteine (NAC), and methyl-β-cyclodextrin (M-β-CD) as an albumin substitute combination and optimized their concentrations by using response surface methodology. The optimized albumin substitute was named PVA-NAC-M-β-CD (PNM). After 8 days of culture, NK-92 cells cultured with the PNM exhibited phenotype and cytotoxic function comparable to cells cultured with different concentrations of BSA. The expansion fold was 89.22 ± 3.55, significantly higher than the 51.23 ± 6.57 observed in the 0.75 g/L BSA group (p © 2025 The Society for Biotechnology, Japan

关键词： Cholesterol

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Sequence-activated chemiluminescence probes:programmable illumination for high-contrast in vivo sensing and imaging

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Science China Chemistry 2025年第1期68卷 26-34页

作者： Yutao Zhang Juan Li Wei-Hong Zhu Zhiqian Guo Shanghai Key Laboratory of Functional Materials Chemistry Joint International Research Laboratory of Precision Chemistry and Molecular EngineeringInstitute of Fine ChemicalsSchool of Chemistry and Molecular EngineeringEast China University of Science and TechnologyShanghai 200237China State Key Laboratory of Bioreactor Engineering Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell MetabolismEast China University of Science&TechnologyShanghai 200237China

Sequence-activated chemiluminescence(CL)technique offers a unique approach to detecting specific biomolecules or cellular events with high sensitivity and spatial *** fundamental principle behind sequence-activated CL probes involves tailoring highly-controllable CL signals in response to specific sequences or events of interest,thus enabling high-contrast signals under complex physiological *** sequential activation could be triggered by enzymes,reactive oxygen species(ROS),biothiols or changes in the *** unique sequence-activated CL probes bestow several advantages,including minimal background,deep-tissue penetration,and the ability of non-invasive or minimally invasive *** sequence-activated CL techniques represent a significant advancement in molecular imaging and *** this mini-review,we focus on the latest developments in sequential CL probes,addressing the technical challenges and discussing the future trajectory by harnessing CL signaling and molecular recognition.

关键词： chemiluminescnece sequence-activation in-vivo bioimaging cyclic peroxide

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Photocalibrated NO release from the zinc ion fiuorescent probe based on naphthalimide and its application in living cells

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Chinese Chemical Letters 2025年第4期36卷 323-326页

作者： Zhixiao Xiong Shanni Qiu Yuyu Wang Houna Duan Yi Xiao Yufang Xu Weiping Zhu Xuhong Qian State Key Laboratory of Bioreactor Engineering Shanghai Key Laboratory of Chemical BiologySchool of PharmacyEast China University of Science and TechnologyShanghai 200237China Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism School of PharmacyEast China University of Science and TechnologyShanghai 200237China State Key Laboratory of Fine Chemicals Dalian University of TechnologyDalian 116024China

A highly sensitive zinc ion fiuorescent probe NOD-NY with controlled release of nitric oxide was designed,synthesized and used for tracking intracellular zinc ions in living A549 ***-NY was prepared from naphthalimide as the fiuorophore and N,N-bis(2-pyridylmethyl)amine as the zinc ion recognition receptor,the amide N atom of the naphthalimide was connected to *** the irradiation of ultraviolet light,NOD-NY can quantitatively release nitric oxide and generate a highly sensitive zinc ion probe Zn-HN,accompanied by a red-shift process of maximum ultraviolet absorption from 350 nm to 450 *** addition of Zn^(2+)to the solutions of Zn-HN,a remarkable fiuorescence enhancement was observed,which could be attributed to the photo-induced electron transfer(PET)*** replaced the nbutylamine on NOD-NY with diethylene glycolamine or triphenylphosphine structures,NOD-AY with good biocompatibility and NOD-BY that can target mitochondria were obtained *** addition,the nitric oxide released by NOD-NY enriched in lysosome can diffuse into *** released nitric oxide can stimulate metallothionein to release zinc ions,and the light-induced in situ generated zinc ion probe Zn-HN can have a highly sensitive fiuorescence response to free zinc ions in living A549 cells.

关键词： Naphthalimide Fluorescent probe Nitric oxide donor Zinc ion Photocalibration

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Two-Step Synthesis of a Dolutegravir Intermediate DTG-6 in a Microfluidized Bed Cascade System: Route Design and Kinetic Study

Chem and Bio Engineering

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Chem and Bio engineering 2025年第3期2卷 182-191页

作者： Xue, Xiao Xie, Chengmin Qian, Guozhi Shang, Minjing Qiu, Min Jiang, Rongkun Pasha, Mohsin Zhong, Zihao Wang, Zhijun Liu, Shu Zhang, Hua Su, Yuanhai School of Chemistry and Chemical Engineering Key Laboratory of Thin Film and Microfabrication Ministry of Education Shanghai Jiao Tong University Shanghai200240 China State Key Laboratory of Bioreactor Engineering Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology Shanghai200237 China Shanghai Desano Pharmaceuticals Co. Ltd. Shanghai201203 China

In the existing two-step method for the preparation of DTG-6 (i.e., an important intermediate of the anti-HIV drug Dolutegravir (DTG)), a strong base is required to neutralize the homogeneous strong acid catalyst of the first step to make the reaction solution weakly acidic for the DTG-5 cyclization in the second step. The DTG-6 yield in the two-step synthesis is affected by the reaction of the strong base with the carboxyl group on the generated intermediate DTG-5. In this article, a solid acid catalyst, titanium cation-exchanged montmorillonite (Ti4+-mont), was used in the microfluidized bed to catalyze the conversion of DTG-4 to DTG-5. DTG-5 can be directly cyclized with (R)-3-aminobutanol (RABO) to form DTG-6 without the introduction of a strong base into the reaction solution. After the parametric screening on the flow rate, solid acid type, temperature, residence time, and solvent type, the DTG-6 yield increased from 90% (in our previous work) to 95% in the microfluidized bed cascade system. Due to the easy separation of heterogeneous catalyst, the utilization of a microfluidized bed not only simplified operations, but also improved synthetic efficiency. Moreover, the kinetics of the cyclization of unstable intermediate DTG-5 with RABO was investigated and verified by means of experimental data. © 2024 The Authors. Co-published by Zhejiang University and American Chemical Society.

关键词： Reaction intermediates

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Artificial signal transduction triggered by molecular photoisomerization in lipid membranes

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Chinese Chemical Letters 2025年第4期36卷 264-267页

作者： Kai Ye Zhicheng Ye Chuantao Wang Zhilai Luo Cheng Lian Chunyan Bao Shanghai Key Laboratory of Functional Materials Chemistry School of Chemistry&Molecular EngineeringEast China University of Science&TechnologyShanghai 200237China State Key Laboratory of Bioreactor Engineering Shanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismSchool of pharmacyEast China University of Science and TechnologyShanghai 200237China

Inspired by the light-dependent signal transduction in nature, we herein report a fully synthetic receptor AZO with the capacity of transmembrane signaling, working by photo-induced change of molecular conformation. Our receptor has an anchoring group, a rigid and photoresponsive transmembrane unit and a precatalyst tailgroup. After doping in lipid membranes, AZO is membrane anchored and the extended trans-isomer enables the tailgroup to bind with intravesicular Zn^(2+), thereby achieving enzyme activation and triggering downstream events(ester hydrolysis). However, the shortened cis-isomer pulls the tailgroup into lipids, thereby preventing the complexation and all transduction processes. Upon alternative irradiation of ultraviolet(UV) and visible light, the transduction process can be reversible switch between“ON” and “OFF”, achieving light signal transduction. This study provides a new strategy for future design of artificial signal transduction receptors.

关键词： Artificial signal transduction Photoisomerization Azobenzene ON/OFF switch Lipid membranes

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Sequence and taxonomic feature evaluation facilitated the discovery of alcohol oxidases

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Synthetic and Systems Biotechnology 2025年第3期10卷 907-915页

作者： Han, Yilei Ding, Xuwei Tan, Junjian Sun, Yajuan Duan, Yunjiang Liu, Zheng Zheng, Gaowei Lu, Diannan Department of Chemical Engineering Tsinghua University Beijing 100084 China State Key Laboratory of Bioreactor Engineering Shanghai Collaborative Innovation Center for Biomanufacturing East China University of Science and Technology Shanghai 200237 China

Recent advancements in data technology offer immense opportunities for the discovery and development of new enzymes for the green synthesis of chemicals. Current protein databases predominantly prioritize overall sequence matches. The multi-scale features underpinning catalytic mechanisms and processes, which are scattered across various data sources, have not been sufficiently integrated to be effectively utilized in enzyme mining. In this study, we developed a sequence- and taxonomic-feature evaluation driven workflow to discover enzymes that can be expressed in E. coli and catalyze chemical reactions in vitro, using alcohol oxidase (AOX) for demonstration, which catalyzes the conversion of methanol to formaldehyde. A dataset of 21 reported AOXs was used to construct sequence scoring rules based on features, including sequence length, structural motifs, catalytic-related residues, binding residues, and overall structure. These scoring rules were applied to filter the results from HMM-based searches, yielding 357 candidate sequences of eukaryotic origin, which were categorized into six classes at 85 % sequence similarity. Experimental validation was conducted in two rounds on 31 selected sequences representing all classes. Among these selected sequences, 19 were expressed as soluble proteins in E. coli, and 18 of these soluble proteins exhibited AOX activity, as predicted. Notably, the most active recombinant AOX exhibited an activity of 8.65 ± 0.29 U/mg, approaching the highest activity of native eukaryotic enzymes. Compared to the established UniProt-annotation-based workflow, this feature-evaluation-based approach yielded a higher probability of highly active recombinant AOX (from 8.3 % to 19.4 %), demonstrating the efficiency and potential of this multi-dimensional feature evaluation method in accelerating the discovery of active enzymes. © 2025 The Authors

关键词： alcohol oxidase Enzyme discovery Machine learning sequence similiarty network

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Artificial cascade biocatalysis for the synthesis of 2-aminocyclohexanols with contiguous stereocenters

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Chinese Journal of Catalysis 2025年第1期68卷 345-355页

作者： Fei-Xiang Dong Tian Jin Xiaojuan Yu Hong-Yue Wang Qi Chen Jian-He Xu Gao-Wei Zheng State Key Laboratory of Bioreactor Engineering Shanghai Collaborative Innovation Center for BiomanufacturingEast China University of Science and TechnologyShanghai 200237China State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan 430062HubeiChina

Chiral cyclic amino alcohols with contiguous stereocenters are key building blocks in the synthesis of bioactive molecules and *** cascade biocatalysis represents an attractive method for the synthesis of chiral molecules bearing multiple stereocenters from readily available *** we reported an artificial cascade biocatalysis comprising an epoxide hydrolase,an alcohol dehydrogenase,and a reductive aminase or an amine *** can be utilized to access all four stereoisomers of 2-aminocyclohexanol with two contiguous stereocenters in high yields(up to 95%)and excellent stereoselectivity(up to 98%de)starting from readily available cyclohexene oxide without isolation of the ***,the biocatalytic cascade has been successfully extended to the production of structurally diverse 2-(alkylamino)cyclohexanols by replacing ammonia with different organic amines.

关键词： Biocatalysis Enzyme cascade Aminoalcohol Reductive aminase Amine dehydrogenase

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Photoswitchable molecular assembly for controlled chloride transport across the lipid membranes

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Science China Chemistry 2025年

作者： Chuantao Wang Kai Ye Zexin Yan Shinan Ma Juejiao Fan Chunyan Bao Shanghai Key Laboratory of Functional Materials Chemistry School of Chemistry & Molecular Engineering East China University of Science and Technology State Key Laboratory of Bioreactor Engineering Shanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismSchool of Pharmacy East China University of Science and Technology

Inspired by nature, biomimetic photoregulated ion transporters have attracted great interest because of the spatial and temporal control over ion transport, in which photocontrollable anion transport remains a very challenging task. Herein, we demonstrate an anionophore AZC for photoregulating anion transport with a high selectivity for chloride over hydroxide across the lipid membranes. Our strategy is based on a well-designed bidentate iodo-triazole anion receptor equipped with an azobenzene moiety, which recognizes Cl-by C–I halogen bonding and C–H hydrogen bonding and switches its states in the lipid membranes from inactive aggregates to active single molecules through azobenzene photoisomerization, thereby achieving controllable Cl-transport. Compared with trans-AZC, cis-AZC exhibits much higher ion transport activity with an EC50（the effective concentration required for 50% activity） value at 28 nM, which is one of the highest reported activities to date for halogen bonding anionophores. Finally, it allows the modulation of Cl-transport upon reversible photoisomerization of AZC using alternative ultraviolet and visible light irradiation. This work provides a new strategy for designing stimuli-responsive anion transporters and paves the way for potential applications in remotely controlled membrane transport and treatment of related diseases.

关键词：

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Glibenclamide targets MDH2 to relieve aging phenotypes through metabolism-regulated epigenetic modification

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Signal Transduction and Targeted Therapy 2025年第3期10卷 1652-1666页

作者： Zhifan Mao Wenwen Liu Rong Zou Ling Sun Shuman Huang Lingyu Wu Liru Chen Jiale Wu Shijie Lu Zhouzhi Song Xie Li Yunyuan Huang Yong Rao Yi-You Huang Baoli Li Zelan Hu Jian Li State Key Laboratory of Bioreactor Engineering Shanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismFrontiers Science Center for Materialbiology and Dynamic ChemistryShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghai 200237China Key Laboratory of Tropical Biological Resources of Ministry of Education and Hainan Engineering Research Center for Drug Screening and EvaluationSchool of Pharmaceutical SciencesHainan UniversityHaikou 570228China Hubei Key Laboratory of Genetic Regulation and Integrative Biology School of Life SciencesCentral China Normal UniversityWuhanChina Key Laboratory of Xinjiang Phytomedicine Resource and Utilization Ministry of EducationSchool of PharmacyShihezi UniversityShihezi 832003China

Mitochondrial metabolism-regulated epigenetic modification is a driving force of aging and a promising target for therapeutic *** malate dehydrogenase(MDH2),an enzyme in the TCA cycle,was identified as an anti-aging target through activity-based protein profiling in present *** expression level of MDH2 was positively correlated with the cellular senescence in Mdh2 knockdown or overexpression ***(Gli),a classic anti-glycemic drug,was found to inhibit the activity of MDH2 and relieve fibroblast senescence in an MDH2-dependent *** anti-aging effects of Gli were also further validated in vivo,as it extended the lifespan and reduced the frailty index of naturally aged *** specific Mdh2 knockdown eliminated Gli’s beneficial effects in naturally aged mice,reducing p^(16INK4a) expression and hepatic ***,MDH2 inhibition or knockdown disrupted central carbon metabolism,then enhanced the methionine cycle flux,and subsequently promoted histone ***,the tri-methylation of H3K27,identified as a crucial methylation site in reversing cellular senescence,was significantly elevated in hepatic tissues of naturally aged mice with Mdh2 *** together,these findings reveal that MDH2 inhibition or knockdown delays the aging process through metabolic-epigenetic *** research not only identified MDH2 as a potential therapeutic target and Gli as a lead compound for anti-aging drug development,but also shed light on the intricate interplay of metabolism and epigenetic modifications in aging.

关键词： metabolism glibenclamide cellular senescence MDH therapeutic interventionmitochondrial malate dehydrogenase mdh epigenetic modification aging inhibit activ

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