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Genome-scale metabolic models applied for human health and biopharmaceutical engineering

Quantitative Biology 2023年第4期11卷 363-375页

作者： Feiran Li Yu Chen Johan Gustafsson Hao Wang YiWang Chong Zhang Xinhui Xing nstitute of biopharmaceutical and health engineering Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina Key Laboratory of Quantitative Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina Department of Biology and Biological engineering Chalmers University of TechnologyGothenburgSweden Key Laboratory for Industrial Biocatalysis Ministry of EducationInstitute of Biochemical EngineeringDepartment of Chemical EngineeringTsinghua University BeijingChina Center for Synthetic and Systems Biology Tsinghua UniversityBejingChina institute of Biomedical health Technology and engineering Shenzhen Bay LaboratoryShenzhenChina

Over the last 15 years,genome-scale metabolic models(GEMs)have been reconstructed for human and model animals,such as mouse and rat,to systematically understand metabolism,simulate multicellular or multi-tissue interplay,understand human diseases,and guide cell factory design for biopharmaceutical protein production.Here,we describe how metabolic networks can be represented using stoichiometric matrices and well-defined constraints for flux simulation.Then,we review the history of GEM development for quantitative understanding of Homo sapiens and other relevant animals,together with their applications.We describe how model develops from H.sapiens to other animals and from generic purpose to precise context-specific simulation.The progress of GEMs for animals greatly expand our systematic understanding of metabolism in human and related animals.We discuss the difficulties and present perspectives on the GEM development and the quest to integrate more biological processes and omics data for future research and translation.We truly hope that this review can inspire new models developed for other mammalian organisms and generate new algorithms for integrating big data to conduct more in-depth analysis to further make progress on human health and biopharmaceutical engineering.

关键词： constraint-based modeling disease genome-scale metabolicmodel metabolism

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Base editor-mediated large-scale screening of functional mutations in bacteria for industrial phenotypes

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Science China(Life Sciences) 2024年第5期67卷 1051-1060页

作者： Yaomeng Yuan Xihao Liao Shuang Li Xin-Hui Xing Chong Zhang MOE Key Laboratory for Industrial Biocatalysis Institute of Biochemical EngineeringDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China institute of Biomedical health Technology and engineering Shenzhen Bay LaboratoryShenzhen 440300China Center for Synthetic and Systems Biology Tsinghua UniversityBeijing 100084China

Base editing,the targeted introduction of point mutations into cellular DNA,holds promise for improving genome-scale functional genome screening to single-nucleotide resolution.Current efforts in prokaryotes,however,remain confined to loss-of-function screens using the premature stop codons-mediated gene inactivation library,which falls far short of fully releasing the potential of base editors.Here,we developed a base editor-mediated functional single nucleotide variant screening pipeline in Escherichia coli.We constructed a library with 31,123 sgRNAs targeting 462 stress response-related genes in E.coli,and screened for adaptive mutations under isobutanol and furfural selective conditions.Guided by the screening results,we successfully identified several known and novel functional mutations.Our pipeline might be expanded to the optimization of other phenotypes or the strain engineering in other microorganisms.

关键词： base editor high-throughput large-scale screening Escherichia coli functional mutation

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Enzyme-metal nanocomposites for antibacterial applications

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Particuology 2022年第5期20卷 134-139页

作者： Jiarong Xiong Xinyi cai Jun Ge Key Lab for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China

Metal nanoparticles have been used as antibacterial agents widely,and the combined use of enzymes and metal nanoparticles promotes antibacterial activity,achieving a synergistic effect.Additionally,enzymes decrease the amounts of metals and increase biocompatibility,thereby reducing toxicity of metals.However,the efficiency of enzymes is hindered when coupled with metals,which causes deactivation in the function of enzymes.How can a balance be struck between metals and enzymes?Although the antibacterial mechanism of metal nanoparticles is relatively clear,how enzyme-metal nanocomposites work against bacteria is not conclusive.Here,we describe several examples on the synthesis of enzyme-metal nanocomposites via co-immobilization or in situ reduction and summarize how enzyme-metal nanocomposites combat microorganisms.

关键词： Enzyme-metal nanocomposites Applications Preparations Antibacterial mechanisms

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Diffusion process in enzyme-metal hybrid catalysts

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Frontiers of Chemical Science and engineering 2022年第6期16卷 921-929页

作者： Shitong Cui Jun Ge Key Lab for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China

Enzyme-metal hybrid catalysts bridge the gap between enzymatic and heterogeneous catalysis,which is significant for expanding biocatalysis to a broader scope.Previous studies have demonstrated that the enzyme-metal hybrid catalysts exhibited considerably higher catalytic efficiency in cascade reactions,compared with that of the combination of separated enzyme and metal catalysts.However,the precise mechanism of this phenomenon remains unclear.Here,we investigated the diffusion process in enzyme-metal hybrid catalysts using Pd/lipase-Pluronic conjugates and the combination of immobilized lipase(Novozyme 435)and Pd/C as models.With reference to experimental data in previous studies,the Weisz-Prater parameter and efficiency factor of internal diffusion were calculated to evaluate the internal diffusion limitations in these catalysts.Thereafter,a kinetic model was developed and fitted to describe the proximity effect in hybrid catalysts.Results indicated that the enhanced catalytic efficiency of hybrid catalysts may arise from the decreased internal diffusion limitation,size effect of Pd clusters and proximity of the enzyme and metal active sites,which provides a theoretical foundation for the rational design of enzyme-metal hybrid catalysts.

关键词： enzyme-metal hybrid catalyst internal diffusion proximity effect kinetic model

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Targeted therapeutic effects of oral magnetically driven pectin nanoparticles containing chlorogenic acid on colon cancer

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Particuology 2024年第1期84卷 53-59页

作者： Huatai Zhu Limei Zhang Fujia Kou Jingyang Zhao Jiandu Lei Jing He Beijing Key Laboratory of Lignocellulosic Chemistry Beijing Forestry UniversityBeijing100083China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhen518055China

Oral colonic nano-drug delivery system has attracted growing attention in treating colon cancer for their excellent characteristics.However,the unique and complex structure of the gastrointestinal tract is still an obstacle to the safe delivery of drugs targeting sites in colon tumors.Here,we designed magnetically driven dual-targeted oral colonic nanoparticles loaded with chlorogenic acid using pectin and oleic acid-modified iron oxide(Fe3O4@OA).Specific degradation of pectin by pectinase produced by colonic flora and magnetic fields applied to the colon confers specific targeting of nanoparticles to the colon.In order to overcome the challenge of preparing magnetically driven nanoparticles with small and homogeneous particle sizes by a single conventional method,we developed the combined ultrasound-emulsification technique.The average particle size of the prepared nanoparticles was 81.04±1.02 nm,which showed good drug release in the simulated colonic environment.In vitro anticancer studies,the drug-loaded nanoparticles possess an obvious toxicity and apoptosis-inducing ability against cancer cells.Meanwhile,the hemolysis results demonstrated the safety of the nanoplatform(PET/CGA/Fe_(3)O_(4)@OA).This work holds broad prospects as a new treatment modality for colon cancer.

关键词： Pectin Chlorogenic acid Ultrasound-emulsion Magnetically driven Colon cancer Colon targeted

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Graphene-based nanomaterials for cancer therapy and anti-infections

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Bioactive Materials 2022年第8期7卷 335-349页

作者： Yan Wang Juan Li Xiaobin Li Jinping Shi Zhaotan Jiang Can Yang Zhang School of Physics Beijing Institute of TechnologyBeijing100081China Advanced Research institute for Multidisciplinary Science Beijing Institute of TechnologyBeijing100081China Institute of Biopharmaceutical and Health Engineering Shenzhen International Graduate SchoolTsinghua UniversityShenzhen518055China

Graphene-based nanomaterials(GBNMs)has been thoroughly investigated and extensively used in many biomedical fields,especially cancer therapy and bacteria-induced infectious diseases treatment,which have attracted more and more attentions due to the improved therapeutic efficacy and reduced reverse effect.GBNMs,as classic two-dimensional(2D)nanomaterials,have unique structure and excellent physicochemical properties,exhibiting tremendous potential in cancer therapy and bacteria-induced infectious diseases treatment.In this review,we first introduced the recent advances in development of GBNMs and GBNMs-based treatment strategies for cancer,including photothermal therapy(PTT),photodynamic therapy(PDT)and multiple combination therapies.Then,we surveyed the research progress of applications of GBNMs in anti-infection such as antimicrobial resistance,wound healing and removal of biofilm.The mechanism of GBNMs was also expounded.Finally,we concluded and discussed the advantages,challenges/limitations and perspective about the development of GBNMs and GBNMs-based therapies.Collectively,we think that GBNMs could be potential in clinic to promote the improvement of cancer therapy and infections treatment.

关键词： Graphene Phototherapy Cancer therapy Anti-infection 2D materials

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Multi-functional engineered polypeptide-based drug delivery systems for improved cancer therapy

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Green Chemical engineering 2023年第2期4卷 173-188页

作者： Xiaobin Li Junyu Liu Haihong Chen Yaxin Chen Yi Wang Can Yang Zhang Xin-Hui Xing Institute of Biopharmaceutical and Health Engineering Shenzhen International Graduate SchoolTsinghua UniversityShenzhen518055China institute of Biochemical engineering Department of Chemical EngineeringTsinghua UniversityBeijing100084China MOE Key Laboratory for Industrial Biocatalysis Beijing100084China institute of Biomedical health Technology and engineering Shenzhen Bay LaboratoryShenzhen440300China Center for Synthetic and Systems Biology Tsinghua UniversityBeijing100084China

With the rapid development of chemical engineering and biotechnology,polypeptide,as a promising candidate in the biomedical field,has been thoroughly investigated and extensively used as the drug delivery vehicle for diseases treatment,especially cancer,owing to the high biocompatibility,good biodegradability,versatile con-structions,and diverse functions.Engineered polypeptide-based drug delivery system(so-called EPP-DDS)can deliver the cargos to the target site via a specific recognition effect,followed by overcoming the barriers like blood brain barrier(BBB)and releasing them by responding to the microenvironment cues,to improve the therapeutic efficacy and reduce the side-effect.Herein,it's of great importance to conclude and summarize the updates on EPP-DDS developed by chemical engineering methods.In this review,we first summarized the recent updates in the manufacturing of polypeptide and preparation of EPP-DDS based on green biochemical engineering and/or synthetic processes for cancer therapy,including chemotherapy,immunotherapy,photodynamic therapy(PDT),gene therapy,and combination therapy.Then,we surveyed the research progress of inflammation-mediated cancer treatment strategies based on EPP-DDS with high anti-inflammation activity.Finally,we concluded the discovery and green production process of engineered polypeptide,challenges,and perspectives of EPP-DDS.Overall,the EPP-DDS has great potential for cancer therapy in the clinic with improved therapeutic efficacy and reduced adverse effect,which needs the innovation of green biochemical engineering for customized design and production of polypeptides.

关键词： Polypeptide Drug delivery system Cancer therapy Biopharmaceutics Green biochemical engineering

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Andrias davidianus bone peptides alleviates hyperuricemia-induced kidney damage in vitro and in vivo

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Food Science and Human Wellness 2023年

作者： Wei Li Hai-hong Chen Hong-liang Chen Ziyin Li Wei Hu Qin-xuan Zhou Bing Xu Yi Wang Xin-Hui Xing Affiliated Dongguan Hospital Southern Medical University (Dongguan People's Hospital) Center for Synthetic and Systems Biology Tsinghua University Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate School institute of Biomedical health Technology and engineering Shenzhen Bay Laboratory Key Laboratory for Industrial Biocatalysis Ministry of Education institute of Biochemical engineering Department of Chemical engineering

Hyperuricemia (HUA) is a vital risk factor for chronic kidney diseases (CKD) and development of functional foods capable of protecting CKD is of importance. This paper aimed to explore the amelioration effects and mechanism of Andrias davidianus bone peptides (ADBP) on HUA-induced kidney damage. In the present study， we generated the standard ADBP which contained high hydrophobic amino acid and low molecular peptide contents. In vitro results found that ADBP protected uric acid (UA)-induced HK-2 cells from damage by modulating urate transporters and antioxidant defense. In vivo results indicated that ADBP effectively ameliorated renal injury in HUA-induced CKD mice， evidenced by a remarkable decrease in serum UA， creatinine and blood urea nitrogen， improving kidney UA excretion， antioxidant defense and histological kidney deterioration. Metabolomic analysis highlighted fourteen metabolites that could be selected as potential biomarkers and attributed to the amelioration effects of ADBP on CKD mice kidney dysfunction. Intriguingly， ADBP restored the gut microbiome homeostasis in CKD mice， especially with respect to the elevated helpful microbial abundance， and the decreased harmful bacterial abundance. This study demonstrated that ADBP displayed great nephroprotective effects， and has great promise as a food or functional food ingredient for the prevention and treatment of HUA-induced CKD.

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Enzymes immobilized in wood-derived cellulose scaffold for constructing a novel modular bioreactor

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Green Chemical engineering 2023年第1期4卷 39-48页

作者： Zhihong Zhang Mengchen Jin Guiru Chen Jiandu Lei Luying Wang Jun Ge Beijing Key Laboratory of Lignocellulosic Chemistry Beijing Forestry UniversityBeijing100083China Key Lab for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China MOE engineering Research Center of Forestry Biomass Materials and Bioenergy Beijing Forestry UniversityBeijing100083China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen518055China institute of Biomedical health Technology and engineering Shenzhen Bay LaboratoryShenzhen518107China

Modular bioreactors can provide a flexible platform for constructing complex multi-step pathways,which may be a solution for maximizing reactions and overcoming the complexity of multi-enzyme systems.Here,we selected wood-derived cellulose scaffold as a support for enzyme immobilization and constructed the modular bioreactor.Cellulose scaffold was prepared after removing lignin from wood,followed by citric acid functionalization and the addition of glutaraldehyde finally allowed the cross-linking of enzymes.Three enzymes,horseradish peroxidase(HRP),glucose oxidase(GOD),and catalase(CAT),were separately immobilized,resulting in the immobilized enzyme amount to over 40 mg/g.The introduction of carboxyl groups from citric acid facilitated the rapid enzyme adsorption on the support surface and immobilized enzymes possess~65%expressed activity.Modular bioreactors were constructed by using the immobilized enzymes.With the immobilized HRP module,reactor showed desired catalytic performance with the phenol degradation rate of>90%.Also,a pH regulation can occur in the bioreactors for preserving enzyme activities and neutralizing acid products.In the GOD/CAT modular bioreactor,the cascade reaction with adjusting pH values can achieve a 95%yield of sodium gluconate and exhibit a favorable reusability of 5 operation cycles.

关键词： Wood Immobilized enzyme Citric acid Modular bioreactor Cascade reaction

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Isolation and characterization of novel peptides from fermented products of Lactobacillus for ulcerative colitis prevention and treatment

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Food Science and Human Wellness 2022年第6期11卷 1464-1474页

作者： Dong He Wen Zeng Yi Wang Yifan Xing Kang Xiong Nan Su Chong Zhang Yuan Lu Xinhui Xing School of Chemical engineering and Light Industry Guangdong University of TechnologyGuangzhou 510006China Key Laboratory for Industrial Biocatalysis Ministry of EducationInstitute of Biochemical EngineeringDepartment of Chemical EngineeringChina Center for Synthetic and Systems BiologyTsinghua UniversityBeijing 100084China Center for Synthetic and Systems Biology Tsinghua UniversityBeijing 100084China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China institute of Biomedical health Technology and engineering Shenzhen Bay LaboratoryShenzhen 440300China

Ulcerative colitis(UC)is an incurable and highly complex digestive disease affecting millions of people worldwide.Compared to the current therapeutic drugs,bioactive peptides are more promising and safe substances as functional foods or drugs for the prevention and treatment of UC.The alcohol-soluble components from fermentation broth by fresh wheat germ and apple(AC-WGAF)were found to be effective in UC prevention in dextran sulfate sodium-induced mice in vivo.Herein,4 novel peptides are identifi ed from AC-WGAF by membrane ultrafi ltration,recycling preparative high-performance liquid chromatography,and matrix-assisted laser desorption–ionization time-of-fl ight/time-of-fl ight mass spectrometry,possessing anticolitis activity via using an in vitro model.One of those peptides named T24(PVLGPVRGPFPLL)exhibited the most remarkable anti-colitis activity by preventing tight junction protein loss,maintaining epithelial barrier integrity,and promoting cell proliferation during in vitro and in vivo studies by regulating mitogen-activated protein kinase signaling pathways.Thus,T24 is a promising peptide as a functional food or novel drug for UC prevention and treatment.

关键词： Ulcerative colitis Peptide Fermentation product Intestinal epithelial barrier Cell proliferation Mitogen-activated protein kinase signaling pathways

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