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Peng X, Pei C, Qian EW, Du Y, Li JJ. Co-immobilization of a bi-enzymatic cascade into hierarchically porous MIL-53 for efficient 6'-sialyllactose production. NANOSCALE 2024; 16:14932-14939. [PMID: 39046038 DOI: 10.1039/d4nr01775g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
6'-Sialyllactose (6'-SL), the most abundant sialylated human milk oligosaccharide, has attracted attention for its potential application in supplementary infant formulas. Herein, we report a facile strategy to construct a cascade bioreactor for the enzymatic synthesis of 6'-SL by co-immobilizing an enzymatic module consisting of CMP-sialic acid synthase and α-2,6-sialyltransferase into hierarchically porous MIL-53 (HP-MIL-53). The as-prepared HP-MIL-53 showed high enzyme immobilization capacity, reaching 226 mg g-1. Furthermore, the co-immobilized enzymes exhibited higher initial catalytic efficiency, and thermal, pH and storage stability than the free ones. Finally, the 6'-SL yield remained >80% after 13 cycles of use. We expect that HP-MIL-53 would have potential industrial applications in the enzymatic modular synthesis of 6'-SL and other glycans.
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Fan X, Li K, Qin X, Li Z, Du Y. Structural Characterization and Screening for Anti-inflammatory Activity of Polysaccharides with Different Molecular Weights from Astragali Radix. Chem Biodivers 2024; 21:e202400262. [PMID: 38705857 DOI: 10.1002/cbdv.202400262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Astragali Radix polysaccharides (APSs) exhibit a broad spectrum of biological activity, which is mainly related to immune regulation. At present, most available studies focus on total APSs or a certain component of APSs. However, systematic structural study and screening for the anti-inflammatory activity of polysaccharides with different molecular weights (MW) have yet to be conducted. In this study, lipopolysaccharide (LPS)-induced RAW264.7 macrophages were used as a model to investigate the anti-inflammatory activity of APSs and its fractions. The results revealed that fraction APS-I had better anti-inflammatory effects than APS-II. After APS-I was hydrolyzed by trifluoroacetic acid (TFA), the resulting degradation products oligosaccharides were fully methylated. These derivatized oligosaccharides were further analyzed by MALDI-TOF-MS and UPLC-Q-Exactive-MS/MS. The results showed that APS-I was a hetero-polysaccharide with a molecular weight of about 2.0×106 Da, mainly consisting of glucose (46.8 %) and galactose (34.4 %). The degree of polymerization of Astragali Radix oligosaccharides (APOS) was 2-16. APOS were identified as 1,4-glucooligosaccharides and 1,4-galactooligosaccharides. The findings of this study lay the foundation for further elucidation of structure-function relationships of APSs and provide guidance for the development of anti-inflammatory drugs.
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Feng S, Li K, Lv W, Wen Y, Qin X, Li Z, Du Y. Extraction, characterization, antioxidation and anti-inflammatory activity of polysaccharides from Bupleurum chinense based on different molecular weights. Nat Prod Res 2024:1-11. [PMID: 38824676 DOI: 10.1080/14786419.2024.2357667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/14/2024] [Indexed: 06/04/2024]
Abstract
Bupleurum chinense polysaccharide has a wide range of biological activities. In this study, Bupleurum chinense polysaccharides (BPs), BPs-1 (30 kDa) and BPs-2 (2000 kDa) with different molecular weights were isolated and prepared by ultrafiltration interception method. The structures of BPs, BPs-1 and BPs-2 were characterised by monosaccharide composition, GC-MS, Fourier transform infra-red spectroscopy and nuclear magnetic resonance. The results showed that the monosaccharide composition of BPs with different molecular weights was the same, but the proportion was different. BPs, BPs-1 and BPs-2 were mainly connected by Glup-(1→,→2,4)-Araf-(1→,→6)-Glup-(1→). The anti-inflammatory activity screening experiment in vitro showed that BPs-1 had stronger anti-inflammatory effect. Antioxidant experiments showed that BPs-2 had high free radical scavenging activity. This study laid a foundation for elucidating the fine structure and structure-activity relationship of Bupleurum chinense polysaccharides and will promote the product development of Bupleurum chinense polysaccharides.
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Xu M, Gao Y, Xu Y, Xu T, Ma J, Li J, Yang T, Zhang Y, Du Y, Xu Q. Synthesis of acylated derivatives of alginate oligosaccharides and evaluation of their potential antibacterial activities against Staphylococcus aureus. Int J Biol Macromol 2024; 271:132484. [PMID: 38821795 DOI: 10.1016/j.ijbiomac.2024.132484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/28/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024]
Abstract
Alginate oligosaccharides (AOS) are crucial carbohydrate-based biomaterial used in the synthesis of potential drugs and biological agents, but their antibacterial activities are not significant. In this study, AOS acylated derivatives were synthesized by grafting maleic anhydride (MA) onto AOS at varying ratios. Additionally, their inhibitory effects against Staphylococcus aureus were thoroughly investigated. Characterization of the AOS acylated derivatives (AOS-MA-x, where x = 1, 5, 10, and 20) was conducted using Fourier-transformed infrared spectroscopy, 1H nuclear magnetic resonance spectroscopy, and X-ray diffraction, which confirmed the successful synthesis of these derivatives. The bacteriostatic activity of the AOS-MA derivatives was assessed using growth curves and plate coating method, demonstrating significant antibacterial effects against S. aureus, as compared with AOS. Among these derivatives, AOS-MA-20 exhibited the most potent bacteriostatic activity and was selected for further investigation of its inhibitory mechanism. Scanning electron microscopy analysis revealed that treatment with AOS-MA-20 led to the lysis and rupture of S. aureus cells, expelling their intracellular contents. Moreover, AOS-MA-20 disrupted the integrity of cell wall and cell membrane, impacted ATPase activity, and inhibited the formation of biofilm to some extent, ultimately resulting in bacterial death. These findings lay a foundational framework for the development of environmentally friendly antimicrobial agents.
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Liu Y, Li R, Zhang Y, Jiao S, Xu T, Zhou Y, Wang Y, Wei J, Du W, Fujita M, Du Y, Wang ZA. Unveiling the inverse antimicrobial impact of a hetero-chitooligosaccharide on Candida tropicalis growth and biofilm formation. Carbohydr Polym 2024; 333:121999. [PMID: 38494241 DOI: 10.1016/j.carbpol.2024.121999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
Chitosan and chitooligosaccharide (COS) are renowned for their potent antimicrobial prowess, yet the precise antimicrobial efficacy of COS remains elusive due to scant structural information about the utilized saccharides. This study delves into the antimicrobial potential of COS, spotlighting a distinct hetero-chitooligosaccharide dubbed DACOS. In contrast to other COS, DACOS remarkably fosters the growth of Candida tropicalis planktonic cells and fungal biofilms. Employing gradient alcohol precipitation, DACOS was fractionated, unveiling diverse structural characteristics and differential impacts on C. tropicalis. Notably, in a murine model of systemic candidiasis, DACOS, particularly its 70 % alcohol precipitates, manifests a promotive effect on Candida infection. This research unveils a new pathway for exploring the intricate nexus between the structural attributes of chitosan oligosaccharides and their physiological repercussions, underscoring the imperative of crafting chitosan and COS with meticulously defined structural configurations.
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Pei C, Peng X, Wu Y, Jiao R, Li T, Jiao S, Zhou L, Li J, Du Y, Qian EW. Characterization and application of active human α2,6-sialyltransferases ST6GalNAc V and ST6GalNAc VI recombined in Escherichia coli. Enzyme Microb Technol 2024; 177:110426. [PMID: 38503081 DOI: 10.1016/j.enzmictec.2024.110426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Eukaryotic sialyltransferases play key roles in many physiological and pathological events. The expression of active human recombinant sialyltransferases in bacteria is still challenging. In the current study, the genes encoding human N-acetylgalactosaminide α2,6-sialyltransferase V (hST6GalNAc V) and N-acetylgalactosaminide α2,6-sialyltransferase VI (hST6GalNAc VI) lacking the N-terminal transmembrane domains were cloned into the expression vectors, pET-32a and pET-22b, respectively. Soluble and active forms of recombinant hST6GalNAc V and hST6GalNAc VI when coexpressed with the chaperone plasmid pGro7 were successfully achieved in Escherichia coli. Further, lactose (Lac), Lacto-N-triose II (LNT II), lacto-N-tetraose (LNT), and sialyllacto-N-tetraose a (LSTa) were used as acceptor substrates to investigate their activities and substrate specificities. Unexpectedly, both can transfer sialic acid onto all those substrates. Compared with hST6GalNAc V expressed in the mammalian cells, the recombinant two α2,6-sialyltransferases in bacteria displayed flexible substrate specificities and lower enzymatic efficiency. In addition, an important human milk oligosaccharide disialyllacto-N-tetraose (DSLNT) can be synthesized by both human α2,6-sialyltransferases expressed in E. coli using LSTa as an acceptor substrate. To the best of our knowledge, these two active human α2,6-sialyltransferases enzymes were expressed in bacteria for the first time. They showed a high potential to be applied in biotechnology and investigating the molecular mechanisms of biological and pathological interactions related to sialylated glycoconjugates.
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Wu Y, Sun Y, Pei C, Peng X, Liu X, Qian EW, Du Y, Li JJ. Automated chemoenzymatic modular synthesis of human milk oligosaccharides on a digital microfluidic platform. RSC Adv 2024; 14:17397-17405. [PMID: 38813121 PMCID: PMC11134329 DOI: 10.1039/d4ra01395f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
Glycans, along with proteins, nucleic acids, and lipids, constitute the four fundamental classes of biomacromolecules found in living organisms. Generally, glycans are attached to proteins or lipids to form glycoconjugates that perform critical roles in various biological processes. Automatic synthesis of glycans is essential for investigation into structure-function relationships of glycans. In this study, we presented a method that integrated magnetic bead-based manipulation and modular chemoenzymatic synthesis of human milk oligosaccharides (HMOs), on a DMF (Digital Microfluidics) platform. On the DMF platform, enzymatic modular reactions were conducted in solution, and purification of products or intermediates was achieved by using DEAE magnetic beads, circumventing the intricate steps required for traditional solid-phase synthesis. With this approach, we have successfully synthesized eleven HMOs with highest yields of up to >90% on the DMF platform. This study would not only lay the foundation for OPME synthesis of glycans on the DMF platform, but also set the stage for developing automated enzymatic glycan synthesizers based on the DMF platform.
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Li B, Cui J, Xu T, Xu Y, Long M, Li J, Liu M, Yang T, Du Y, Xu Q. Advances in the preparation, characterization, and biological functions of chitosan oligosaccharide derivatives: A review. Carbohydr Polym 2024; 332:121914. [PMID: 38431416 DOI: 10.1016/j.carbpol.2024.121914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Chitosan oligosaccharide (COS), which represent the positively charged basic amino oligosaccharide in nature, is the deacetylated and degraded products of chitin. COS has become the focus of intensive scientific investigation, with a growing body of practical and clinical studies highlighting its remarkable health-enhancing benefits. These effects encompass a wide range of properties, including antibacterial, antioxidant, anti-inflammatory, and anti-tumor activities. With the rapid advancements in chemical modification technology for oligosaccharides, many COS derivatives have been synthesized and investigated. These newly developed derivatives possess more stable chemical structures, improved biological activities, and find applications across a broader spectrum of fields. Given the recent interest in the chemical modification of COS, this comprehensive review seeks to consolidate knowledge regarding the preparation methods for COS derivatives, alongside discussions on their structural characterization. Additionally, various biological activities of COS derivatives have been discussed in detail. Lastly, the potential applications of COS derivatives in biomedicine have been reviewed and presented.
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Huang F, Sun C, Dong J, Wu X, Du Y, Hu Q, Zhou L. Ultra-sensitive fluorescent biosensor for multiple bacteria detection based on CDs/QDs@ZIF-8 and microfluidic fluidized bed. Mikrochim Acta 2024; 191:237. [PMID: 38570419 DOI: 10.1007/s00604-024-06303-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
An ultra-sensitive fluorescent biosensor based on CDs/QDs@ZIF-8 and microfluidic fluidized bed was developed for rapid and ultra-sensitive detection of multiple target bacteria. The zeolitic imidazolate frameworks (ZIF-8) act as the carrier to encapsulate three kinds of fluorescence signal molecules from the CDs/QDs@ZIF-8 signal amplification system. Besides, three kinds of target pathogenic bacteria were automatically, continuously, and circularly captured by the magnetic nanoparticles (MNPs) in the microfluidic fluidized bed. The neutral Na2EDTA solution was the first time reported to not only dissolve the ZIF-8 frameworks from the MNPs-bacteria-CDs/QDs@ZIF-8 sandwich complexes, but also release the CDs/QDs from sandwich complexes with no loss of fluorescence signal. Due to the advantages of signal amplification and automated sample pretreatment, the proposed fluorescent biosensor can simultaneously detect Escherichia coli O157:H7, Salmonella paratyphi A, and Salmonella paratyphi B as low as 101 CFU/mL within 1.5 h, respectively. The mean recovery in spiked milk samples can reach 99.18%, verifying the applicability of this biosensor in detecting multiple bacteria in real samples.
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Li J, Xu T, Zheng Y, Liu D, Zhang C, Li J, Wang ZA, Du Y. In Silico Study on a Binding Mechanism of ssDNA Aptamers Targeting Glycosidic Bond-Containing Small Molecules. Anal Chem 2024; 96:5056-5064. [PMID: 38497564 DOI: 10.1021/acs.analchem.4c00927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aptamer-based detection targeting glycoconjugates has attracted significant attention for its remarkable potential in identifying structural changes in saccharides in different stages of various diseases. However, the challenges in screening aptamers for small carbohydrates or glycoconjugates, which contain highly flexible and diverse glycosidic bonds, have hindered their application and commercialization. In this study, we investigated the binding conformations between three glycosidic bond-containing small molecules (GlySMs; glucose, N-acetylneuraminic acid, and neomycin) and their corresponding aptamers in silico, and analyzed factors contributing to their binding affinities. Based on the findings, a novel binding mechanism was proposed, highlighting the central role of the stem structure of the aptamer in binding and recognizing GlySMs and the auxiliary role of the mismatched bases in the adjacent loop. Guided by this binding mechanism, an aptamer with a higher 6'-sialyllactose binding affinity was designed, achieving a KD value of 4.54 ± 0.64 μM in vitro through a single shear and one mutation. The binding mechanism offers crucial guidance for designing high-affinity aptamers, enhancing the virtual screening efficiency for GlySMs. This streamlined workflow filters out ineffective binding sites, accelerating aptamer development and providing novel insights into glycan-nucleic acid interactions.
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Wei J, Liu D, Xu T, Zhu L, Jiao S, Yuan X, Wang ZA, Li J, Du Y. Variations in metabolic enzymes cause differential changes of heparan sulfate and hyaluronan in high glucose treated cells on chip. Int J Biol Macromol 2023; 253:126627. [PMID: 37660864 DOI: 10.1016/j.ijbiomac.2023.126627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/17/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Glycocalyx dysfunction is believed as the first step in diabetic vascular disease. However, few studies have systematically investigated the influence of HG on the glycocalyx as a whole and its major constituent glycans towards one type of cell. Furthermore, most studies utilized traditional two-dimensional (2D) cultures in vitro, which can't provide the necessary fluid environment for glycocalyx. Here, we utilized vascular glycocalyx on chips to evaluate the changes of glycocalyx and its constituent glycans in HG induced HUVECs. Fluorescence microscopy showed up-regulation of hyaluronan (HA) but down-regulation of heparan sulfate (HS). By analyzing the metabolic enzymes of both glycans, a decrease in the ratio of synthetic/degradative enzymes for HA and an increase in that for HS were demonstrated. Two substrates (UDP-GlcNAc, UDP-GlcA) for the synthesis of both glycans were increased according to omics analysis. Since they were firstly pumped into Golgi apparatus to synthesize HS, less substrates may be left for HA synthesis. Furthermore, the differential changes of HA and HS were confirmed in vessel slides from db/db mice. This study would deepen our understanding of impact of HG on glycocalyx formation and diabetic vascular disease.
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Yu W, Li Y, Liu D, Wang Y, Li J, Du Y, Gao GF, Li Z, Xu Y, Wei J. Evaluation and Mechanistic Investigation of Human Milk Oligosaccharide against SARS-CoV-2. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16102-16113. [PMID: 37856320 DOI: 10.1021/acs.jafc.3c04275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Four human milk oligosaccharides (HMOs), 3'-sialyllactose (3'-SL), 6'-sialyllactose (6'-SL), 2'-fucosyllactose (2'-FL), and 3-fucosyllactose (3-FL), were assessed for their possible antiviral activity against the SARS-CoV-2 spike receptor binding domain (RBD) in vitro. Among them, only 2'-FL/3-FL exhibited obvious antibinding activity against direct binding and trans-binding in competitive immunocytochemistry and enzyme-linked immunosorbent assays. The antiviral effects of 2'-FL/3-FL were further confirmed by pseudoviral assays with three SARS-Cov-2 mutants, with a stronger inhibition effect of 2'-FL than 3-FL. Then, 2'-FL/3-FL were studied with molecular docking and microscale thermophoresis analysis, showing that the binding sites of 2'-FL on RBD were involved in receptor binding, in addition to a tighter bond between them, thus enabling 2'-FL to be more effective than 3-FL. Moreover, the immunomodulation effect of 2'-FL was preliminary evaluated and confirmed in a human alveolus chip. These results would open up possible applications of 2'-FL for the prevention of SARS-CoV-2 infections by competitive binding inhibition.
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Li C, Tang T, Du Y, Jiang L, Yao Z, Ning L, Zhu B. Ulvan and Ulva oligosaccharides: a systematic review of structure, preparation, biological activities and applications. BIORESOUR BIOPROCESS 2023; 10:66. [PMID: 38647949 PMCID: PMC10991135 DOI: 10.1186/s40643-023-00690-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 04/25/2024] Open
Abstract
Ulva is one of the main green algae causing green tide disasters. Ulvan is the primarily component polysaccharide of the cell wall of Ulva and its complex structure and monosaccharide composition resulted in various biological activities. However, the high-value and effective utilization of extracted ulvan have been obstructed by limitations ranging from large molecular weight and low solubility to poor bioavailability. Ulva oligosaccharide obtained by degrading ulvan can not only ideally retain the various biological activities of ulvan very well but also effectively solve the problems of low solubility and poor bioavailability. The preparation and biological activity studies of ulvan and Ulva oligosaccharides have become a hot spot in the field of marine biological resources development research. At present, the comprehensive reviews of ulvan and Ulva oligosaccharides are still scarce. What are overviewed in this paper are the chemical composition, structure, extraction, and purification of ulvan and Ulva oligosaccharides, where research progress on the biological activities of ulvan and Ulva oligosaccharides is summarized and prospected. A theoretical and practical basis has been provided for further research on ulvan and Ulva oligosaccharides, as well as the high-value development and effective utilization of marine algae resources.
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Li B, Han L, Ma J, Zhao M, Yang B, Xu M, Gao Y, Xu Q, Du Y. Synthesis of acylated derivatives of chitosan oligosaccharide and evaluation of their potential antifungal agents on Fusarium oxysporum. Carbohydr Polym 2023; 314:120955. [PMID: 37173050 DOI: 10.1016/j.carbpol.2023.120955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/16/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Chitosan oligosaccharide (COS) is an important carbohydrate-based biomaterial for synthesizing candidate drugs and biological agents. This study synthesized COS derivatives by grafting acyl chlorides of different alkyl chain lengths (C8, C10, and C12) onto COS molecules and further investigated their physicochemical properties and antimicrobial activity. The COS acylated derivatives were characterized using Fourier transform infrared spectroscopy, 1H nuclear magnetic resonance spectroscopy, X-ray diffraction, and thermogravimetric analysis. COS acylated derivatives were successfully synthesized and possessed high solubility and thermal stability. As for the evaluation of antibacterial activity, COS acylated derivatives did not significantly inhibit Escherichia coli and Staphylococcus aureus, but they significantly inhibited Fusarium oxysporum, which was superior to that of COS. Transcriptomic analysis revealed that COS acylated derivatives exerted antifungal activity mainly by downregulating the expression of efflux pumps, disrupting cell wall integrity, and impeding normal cell metabolism. Our findings provided a fundamental theory for the development of environmentally friendly antifungal agents.
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Li J, Liu Y, Liu D, Xu T, Zhang C, Li J, Wang ZA, Du Y. In Silico Selection and Validation of High-Affinity ssDNA Aptamers Targeting Paromomycin. Anal Chem 2023. [PMID: 37384819 DOI: 10.1021/acs.analchem.3c01575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Glycans are promising for disease diagnosis since glycan biosynthesis is significantly affected by disease states, and glycosylation changes are probably more pronounced than protein expression during the transformation to the diseased condition. Glycan-specific aptamers can be developed for challenging applications such as cancer targeting; however, the high flexibility of glycosidic bonds and scarcity of studies on glycan-aptamer binding mechanisms increased the difficulty of screening. In this work, the model of interactions between glycans and ssDNA aptamers synthesized based on the sequence of rRNA genes was developed. Our simulation-based approach revealed that paromomycin as a representative example of glycans is preferred to bind base-restricted stem structures of aptamers because they are more critical in stabilizing the flexible structures of glycans. Combined experiments and simulations have identified two optimal mutant aptamers. Our work would provide a potential strategy that the glycan-binding rRNA genes could act as the initial aptamer pools to accelerate aptamer screening. In addition, this in silico workflow would be potentially applied in the more extensive in vitro development and application of RNA-templated ssDNA aptamers targeting glycans.
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Sun Y, Wu Y, Ma D, Li JJ, Liu X, You Y, Lu J, Liu Z, Cheng X, Du Y. Digital microfluidics-engaged automated enzymatic degradation and synthesis of oligosaccharides. Front Bioeng Biotechnol 2023; 11:1201300. [PMID: 37415787 PMCID: PMC10320006 DOI: 10.3389/fbioe.2023.1201300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023] Open
Abstract
Glycans are an important group of natural biopolymers, which not only play the role of a major biological energy resource but also as signaling molecules. As a result, structural characterization or sequencing of glycans, as well as targeted synthesis of glycans, is of great interest for understanding their structure-function relationship. However, this generally involves tedious manual operations and high reagent consumptions, which are the main technical bottlenecks retarding the advances of both automatic glycan sequencing and synthesis. Until now, automated enzymatic glycan sequencers or synthesizers are still not available on the market. In this study, to promote the development of automation in glycan sequencing or synthesis, first, programmed degradation and synthesis of glycans catalyzed by enzymes were successfully conducted on a digital microfluidic (DMF) device by using microdroplets as microreactors. In order to develop automatic glycan synthesizers and sequencers, a strategy integrating enzymatic oligosaccharide degradation or synthesis and magnetic manipulation to realize the separation and purification process after enzymatic reactions was designed and performed on DMF. An automatic process for enzymatic degradation of tetra-N-acetyl chitotetraose was achieved. Furthermore, the two-step enzymatic synthesis of lacto-N-tetraose was successfully and efficiently completed on the DMF platform. This work demonstrated here would open the door to further develop automatic enzymatic glycan synthesizers or sequencers based on DMF.
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Wang J, Liu Z, Pan X, Wang N, Li L, Du Y, Li J, Li M. Structural and Biochemical Analysis Reveals Catalytic Mechanism of Fucoidan Lyase from Flavobacterium sp. SA-0082. Mar Drugs 2022; 20:md20080533. [PMID: 36005536 PMCID: PMC9410043 DOI: 10.3390/md20080533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Fucoidans represent a type of polyanionic fucose-containing sulfated polysaccharides (FCSPs) that are cleaved by fucoidan-degrading enzymes, producing low-molecular-weight fucoidans with multiple biological activities suitable for pharmacological use. Most of the reported fucoidan-degrading enzymes are glycoside hydrolases, which have been well studied for their structures and catalytic mechanisms. Little is known, however, about the rarer fucoidan lyases, primarily due to the lack of structural information. FdlA from Flavobacterium sp. SA-0082 is an endo-type fucoidan-degrading enzyme that cleaves the sulfated fuco-glucuronomannan (SFGM) through a lytic mechanism. Here, we report nine crystal structures of the catalytic N-terminal domain of FdlA (FdlA-NTD), in both its wild type (WT) and mutant forms, at resolutions ranging from 1.30 to 2.25 Å. We show that the FdlA-NTD adopts a right-handed parallel β-helix fold, and possesses a substrate binding site composed of a long groove and a unique alkaline pocket. Our structural, biochemical, and enzymological analyses strongly suggest that FdlA-NTD utilizes catalytic residues different from other β-helix polysaccharide lyases, potentially representing a novel polysaccharide lyase family.
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Wen F, Zhang X, Guo J, Liang Z, Cheng Q, Wang C, Yu H, Du Y, Huang S, Li J, Li Y. Emergence of H3N8 avian influenza viruses possessing tri-basic hemagglutinin cleavage sites in China. J Infect 2022; 85:e112-e114. [PMID: 35788010 DOI: 10.1016/j.jinf.2022.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
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Jing B, Xia K, Zhang C, Jiao S, Zhu L, Wei J, Wang ZA, Chen N, Tu P, Li J, Du Y. Chitosan Oligosaccharides Regulate the Occurrence and Development of Enteritis in a Human Gut-On-a-Chip. Front Cell Dev Biol 2022; 10:877892. [PMID: 35557948 PMCID: PMC9086312 DOI: 10.3389/fcell.2022.877892] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/30/2022] [Indexed: 12/22/2022] Open
Abstract
Past studies on the protective effects of chitosan oligosaccharides (COS) on inflammatory bowel disease (IBD) commonly rely on animal models, because traditional cell culture systems couldn't faithfully mimic human intestinal physiology. Here a novel human gut-on-a-chip microsystem was established to further explore the regulatory effects of COS on the occurrence and development of human enteritis. By constructing an intestinal injury model caused by dextran sodium sulfate (DSS) on the chip, this study proved that COS can reduce intestinal epithelial injury by promoting the expression of the mucous layer for the first time. By establishing an inflammatory bowel disease model on the chip caused by E. coli 11775, this study demonstrated that COS can protect the intestinal epithelial barrier and vascular endothelial barrier by inhibiting the adhesion and invasion of E. coli 11775 for the first time. In addition, similar to the results in vivo, COS can decrease the inflammatory response by reducing the expression of toll-like receptor 4 protein and reducing the nuclear DNA binding rate of nuclear factor kappa-B protein on this chip. In summary, COS can be used as a potential drug to treat human IBD and the human gut-on-a-chip would be used as a platform for quick screening drugs to treat human IBD in future.
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Xu Y, Li Y, You X, Pei C, Wang Z, Jiao S, Zhao X, Lin X, Lü Y, Jin C, Gao GF, Li J, Wang Q, Du Y. Novel Insights Into the Sulfated Glucuronic Acid-Based Anti-SARS-CoV-2 Mechanism of Exopolysaccharides From Halophilic Archaeon Haloarcula hispanica. Front Chem 2022; 10:871509. [PMID: 35572116 PMCID: PMC9091367 DOI: 10.3389/fchem.2022.871509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/25/2022] [Indexed: 11/15/2022] Open
Abstract
The pandemic caused by SARS-CoV-2 is the most widely spread disease in the 21st century. Due to the continuous emergence of variants across the world, it is necessary to expand our understanding of host-virus interactions and explore new agents against SARS-CoV-2. In this study, it was found exopolysaccharides (EPSs) from halophilic archaeon Haloarcula hispanica ATCC33960 can bind to the spike protein of SARS-CoV-2 with the binding constant KD of 2.23 nM, block the binding of spike protein to Vero E6 and bronchial epithelial BEAS-2B cells, and inhibit pseudovirus infection. However, EPSs from the gene deletion mutant △HAH_1206 almost completely lost the antiviral activity against SARS-CoV-2. A significant reduction of glucuronic acid (GlcA) and the sulfation level in EPSs of △HAH_1206 was clearly observed. Our results indicated that sulfated GlcA in EPSs is possible for a main structural unit in their inhibition of binding of SARS-CoV-2 to host cells, which would provide a novel antiviral mechanism and a guide for designing new agents against SARS-CoV-2.
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Zhang J, Zhang M, Lin R, Du Y, Wang L, Yao Q, Zannettino A, Zhang H. Chondrogenic preconditioning of mesenchymal stem/stromal cells within a magnetic scaffold for osteochondral repair. Biofabrication 2022; 14. [PMID: 35226893 DOI: 10.1088/1758-5090/ac5935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/28/2022] [Indexed: 12/11/2022]
Abstract
Stem cell therapy using mesenchymal stromal/stem cells (MSCs) represents a novel approach to treating severe diseases, including osteoarthritis (OA). However, the therapeutic benefit of MSCs is highly dependent on their differentiation state, which can be regulated by many factors. Herein, three-dimensional (3D) magnetic scaffolds were successfully fabricated by incorporating magnetic nanoparticles (MNPs) into electrospun gelatin nanofibers. When positioned near a rotating magnet (f= 0.5 Hz), the magnetic scaffolds with the embedded MSCs were driven upward/downward in the culture container to induce mechanical stimulation to MSCs due to spatial confinement and fluid flow. The extracellular matrix-mimicking scaffold and the alternating magnetic field significantly enhanced chondrogenesis instead of osteogenesis. Furthermore, the fibre topography could be tuned with different compositions of the coating layer on MNPs, and the topography had a significant impact on MSC differentiation. Selective up-regulation of chondrogenesis-related genes (COL2A1andACAN) was found for the magnetic scaffolds with citric acid-coated MNPs (CAG). In contrast, osteogenesis-related genes (RUNX2andSPARC) were selectively and significantly up-regulated for the magnetic scaffolds with polyvinylpyrrolidone-coated MNPs (PVPG). Prior to implantation in vivo, chondrogenic preconditioning of MSCs within the CAG scaffolds under a dynamic magnetic field resulted in superior osteochondral repair. Hence, the magnetic scaffolds together with an in-house rotating magnet device could be a novel platform to initiate multiple stimuli on stem cell differentiation for effective repair of osteochondral defects.
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Li K, Li XQ, Li GX, Cui LJ, Qin XM, Li ZY, Du YG, Liu YT, Li AP, Zhao XY, Fan XH. Relationship Between the Structure and Immune Activity of Components From the Active Polysaccharides APS-II of Astragali Radix by Enzymolysis of Endo α-1,4-Glucanase. Front Pharmacol 2022; 13:839635. [PMID: 35281923 PMCID: PMC8913491 DOI: 10.3389/fphar.2022.839635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Astragali Radix polysaccharides (APSs) have a wide range of biological activities. Our preliminary experiment showed that APS-Ⅱ (10 kDa) was the main immunologically active component of APSs. However, the characteristic structure related to activity of APS-Ⅱ needs further verification and clarification. In this study, APS-II was degraded by endo α-1,4-glucosidase. The degraded products with different degrees of polymerization [1–3 (P1), 3–6 (P2), 7–14 (P3), and 10–18 (P4)] were obtained using a polyacrylamide gel chromatography column. The structural features of the different products were characterized by HPGPC, monosaccharide composition, Fourier transform infrared spectrum, GC–MS, nuclear magnetic resonance, and UPLC-ESI-QTOF-MS analysis. Specific immune and non-specific immune cell tests were used to identify the most immunogenic fractions of the products. The backbone of P4 was speculated to be α-D-1,4-linked glucans and rich in C2 (25.34%) and C6 (34.54%) branches. Immune screening experiments indicated that the activity of P4 was better than that of APS-II and the other three components. In this research, the relationship between the structure of APS-Ⅱ and the immune activity from the degradation level of polysaccharides was studied, laying a foundation for the quality control and product development of APSs.
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Li R, Zhu L, Liu D, Wang W, Zhang C, Jiao S, Wei J, Ren L, Zhang Y, Gou X, Yuan X, Du Y, Wang ZA. High molecular weight chitosan oligosaccharide exhibited antifungal activity by misleading cell wall organization via targeting PHR transglucosidases. Carbohydr Polym 2022; 285:119253. [DOI: 10.1016/j.carbpol.2022.119253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/12/2022] [Accepted: 02/11/2022] [Indexed: 11/02/2022]
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Cao R, Yu H, Long H, Zhang H, Hao C, Shi L, Du Y, Jiao S, Guo A, Ma L, Wang Z. Low Deacetylation Degree Chitosan Oligosaccharide Protects against IL-1β Induced Inflammation and Enhances Autophagy Activity in Human Chondrocytes. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2021; 33:517-531. [PMID: 34704529 DOI: 10.1080/09205063.2021.1996962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Osteoarthritis (OA) is a degenerative joint disease, which can lead to joint pain, stiffness, deformity and dysfunction, that seriously affects the quality of life in patients. At present, the treatments of OA mainly include early pharmacological treatment and late joint replacement. However, current pharmacological treatment has limited efficacy and undesired side effects.Chitosan oligosaccharide (COS) is a kind of nontoxic and biodegradable oligo-saccharide, which is composed of 2-20 glucosamine or N-acetylglucosamine linked by β-1,4 glycosidic bond. Studies have shown that COS has significant biological properties like antimicrobial, anti-inflammatory, antioxidant, and anti-tumor, as well as immunoregulation ability. However, the effects of COS on OA have not been clarified. In this study, we explored the protective effects of COS with different degrees of deacetylation on chondrocytes stimulated by interleukin 1β (IL-1β) in vitro.The results showed that IL-1β inhibited cell proliferation and promoted cell apoptosis. Besides that, IL-1β increased the expression of the major chondro-degrading genes MMP13 and ADAMTS-5, while decreased the expression of COL2A and ACAN. COS with different degrees of deacetylation (HDACOS, MDACOS, LDACOS) had different effects on IL-1β induced inflammation. LDACOS had the most obvious anti-inflammatory effects to inhibit the expression of MMP13 and ADAMTS-5 while promoted the expression of COL2A and ACAN. In addition, we found that the expression of autophagy-related gene Beclin-1 was up-regulated, and the ratio of LC3-II/LC3-I was increased in the LDACOS group. Furthermore, transmission electron microscopy (TEM) analysis showed that the number of intracellular autophagosomes increased significantly with the treatment of LDACOS. Based on our research, we suggested that LDACOS could inhibit chondrocytes inflammation and promote cell autophagy, and might be a protective drug for the treatment of OA.
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Zhu C, Liu Z, Ren L, Jiao S, Zhang X, Wang Q, Li Z, Du Y, Li JJ. Overexpression and biochemical characterization of a truncated endo-α (1 → 3)-fucoidanase from alteromonas sp. SN-1009. Food Chem 2021; 353:129460. [PMID: 33725543 DOI: 10.1016/j.foodchem.2021.129460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/23/2022]
Abstract
Endo-fucoidanases are important in structural analysis of fucoidans and preparation of fuco-oligosaccharides. However their enzymological properties and analysis of degradation products are scarcely investigated. Truncated endo-α (1 → 3)-fucoidanase Fda1 (tFda1B from Alteromonas sp. was overexpressed and characterized, showing highest activity at pH 7.0, 35 °C, and 1.0 M NaCl. Its Km and kcat were 3.88 ± 0.81 mg/mL and 0.82 ± 0.17 min-1. Fe3+ and Mn2+ enhanced activity by 100% and 19.5% respectively. Co2+ and Cu2+ completely inactivated tFda1B, whereas Ni2+, Mg2+, Zn2+, Pb2+, Ca2+, Ba2+ and Li+ decreased activity by 58.8%, 56.0%, 50.6%, 47.7%, 28.9%, 15.6% and 37.5%, respectively. Catalytic residues were identified through structure and sequence alignment, and confirmed by mutagenesis. Degradation products of Kjellmaniella crassifolia fucoidan by tFda1B were characterized by LC-ESI-MS/MS, confirming tFda1B belongs to endo-(1 → 3)-fucoidanases, and backbone of K. crassifolia fucoidan is 1 → 3 fucoside linkage. This endo-α (1 → 3)-fucoidanase would be useful for elucidating fucoidan structures, and be used as a food enzyme.
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