Zhiyong Xie’s research while affiliated with Sun Yat-sen University and other places

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Publications (124)


Molecularly imprinted polymer combined with multiple-component covalent organic frameworks for extraction of naringenin enantiomers
  • Article

May 2025

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2 Reads

Food Chemistry

Juanqiong Ma

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Na Yang

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Xingyuan Zhang

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[...]

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Yanlong Chen




Application of Advanced High‐Resolution Mass Spectrometric Techniques for the Analysis of Losartan Potassium Drug Substance Degradation Products: From Nontargeted to Targeted Screening

December 2024

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7 Reads

Journal of Separation Science

Advances in techniques for quality analysis allow for a more detailed examination of drug impurities. High‐resolution mass spectrometry (HRMS) contributes to detecting both known and unknown impurities. In this study, a combination of a nontargeted and targeted screening approach was established and applied to the detailed degradation profile of the losartan potassium (LP) drug substance. Through general unknown comparative screening (GUCS), 35 degradation products (DPs) were detected; of these, 10 DPs were confirmed with reference substances. DP‐1, DP‐2, DP‐3, and DP‐6 were the first characterized, as per previous studies; the other twenty‐four were newly identified. In addition, a liquid chromatography‐tandem mass spectrometry method was developed for the determination of the ten DPs. It was sensitive, with the limit of quantitation of analytes ranging from 0.01 to 0.5 ng mL ⁻¹ . Two newly characterized DPs, DP‐1 and DP‐2, were determined in active pharmaceutical ingredient solutions. This study introduced a new approach using broad screening to analyze degradation impurity profiles in LP drug substance, aiding in the identification of low‐level impurities or those without reference substances. Additionally, the sensitive determination method developed allows for the precise quantification and control of ten DPs at trace levels in LP drug substances or products.



Structure of genetically incorporable unnatural amino acids BCNK, CYPK, and TCOK, which can undergo inverse electron demand Diels‐Alder reaction with tetrazines.
Immunoblotting of cellular PKA−Cα and UBE2L3 abundance after BCN‐mediated bioorthogonal tethering. (a) Structure of tetrazine conjugates 1–4. (b, c) Tetrazine conjugates induced proteasomal degradation of PKA−Cα(135BCNK)‐HA and UBE2L3(90BCNK)‐FLAG in HEK293T cells. HEK293T cells were transiently transfected with plasmids expressing a PylRS(AF)/tRNACUA for BCNK incorporation and a PKA−Cα or UBE2L3 variant. Codon of the amino acid residue designated for BCNK incorporation was changed to TAG to achieve amber suppression. Cells were cultured in the presence or absence of 0.1 mM BCNK for 48 h, followed by treatment with 10 μM of the indicated tetrazine conjugate for 2 h in the absence of BCNK. If required, cells were pretreated with the indicated inhibitor before addition of the tetrazine conjugate. Pretreatment conditions: 10 μM MG‐132 for 2 h; 10 μM bortezomib for 1 h; 10 nM leupeptin for 2 h; 5 μM bafilomycin A1 for 2 h.
Immunoblotting of cellular abundance change of UBE2L6 incorporated with BCNK in different sites in response to tetrazine conjugates 2–4. (a) Structure of UBE2L6 with BCNK incorporation site responsive (in green) and non‐responsive (in red) to degradation induced by tetrazine conjugates (pdb: 1WZV). The enzyme contains a catalytic cysteine residue at position 86. See Figure S3 for the structure in surface and sidechain stick models. (b) Abundance of UBE2L6 variants with BCNK at position 84, 85, 87, 88, 89 or 90 under different conditions. HEK293T cells were transiently transfected with plasmids expressing a PylRS(AF)/tRNACUA for BCNK incorporation and a UBE2L6‐FLAG variant. Codon of the amino acid residue designated for BCNK incorporation was changed to TAG to achieve amber suppression. Cells were cultured in the presence or absence of 0.1 mM BCNK for 48 h, followed by treatment with 10 μM of the indicated tetrazine conjugate for 2 h in the absence of BCNK. For cells cultured in the absence of BCNK, no protein was detected, demonstrating the specificity of BCNK incorporation. Results of variants with BCNK at positions 69, 73, 74, 91, 93, 94, 118, 119 or 122 are shown in Figure S4.
Immunoblotting of cellular abundance change of PKA−Cβ (a) and E2 ubiquitin‐conjugating enzymes (b) bearing BCNK in response to tetrazine conjugates 2–4. HEK293T cells were transiently transfected with plasmids expressing a PylRS(AF)/tRNACUA for BCNK incorporation and a PKA−Cβ or E2 variant. Codon of the amino acid residue designated for BCNK incorporation was changed to TAG to achieve amber suppression. Numbering of PKA−Cβ and E2 enzymes follows the numbering of PKA−Cα and UBE2L3, respectively. Cells were cultured in the presence or absence of 0.1 mM BCNK for 48 h, followed by treatment with 10 μM of the indicated tetrazine conjugate for 2 h in the absence of BCNK.
Effects of unnatural amino acid on protein degradation induced by tetrazine ligation. HEK293T cells were transiently transfected with plasmids expressing a PylRS/tRNACUA for CYPK incorporation or PylRS(AF)/tRNACUA for BCNK or TCOK incorporation, as well as a PKA or E2 variant. Codon of the amino acid residue designated for unnatural amino acid incorporation was changed to TAG to achieve amber suppression. Cells were cultured in the presence or absence of 0.1 mM unnatural amino acid for 48 h, followed by treatment with 10 μM of the indicated tetrazine conjugate for 2 h in the absence of unnatural amino acid.

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Selective Protein Degradation through Tetrazine Ligation of Genetically Incorporated Unnatural Amino Acids
  • Article
  • Full-text available

October 2024

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29 Reads

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1 Citation

Small molecule‐responsive tags for targeted protein degradation are valuable tools for fundamental research and drug target validation. Here, we show that genetically incorporated unnatural amino acids bearing a strained alkene or alkyne functionality can act as a minimalist tag for targeted protein degradation. Specifically, we observed the degradation of strained alkene‐ or alkyne‐containing kinases and E2 ubiquitin‐conjugating enzymes upon treatment with hydrophobic tetrazine conjugates. The extent of the induced protein degradation depends on the identity of the target protein, unnatural amino acid, and tetrazine conjugate, as well as the site of the unnatural amino acid in the target protein. Mechanistic studies revealed proteins undergo proteasomal degradation after tetrazine tethering, and the identity of tetrazine conjugates influences the dependence of ubiquitination on protein degradation. This work provides an alternative approach for targeted protein degradation and mechanistic insight, facilitating the future development of more effective targeted protein degradation strategies.

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Metabolomic analysis reveals potential role of immunometabolism dysregulation in recurrent pregnancy loss

October 2024

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9 Reads

Background Recurrent pregnancy loss (RPL) affects women's reproductive health seriously, with immune dysfunction playing a key role in its cause, yet the exact mechanisms remain elusive. We aim to investigate potential mechanisms and identify biomarkers linked to RPL. Methods Immune cytokine testing and metabolomic profiling were conducted on the serum of 34 RPL patients and 30 healthy individuals. The metabolic pathways of the differential metabolites were analyzed, and specific metabolites were validated through targeted profiling. Potential biomarkers were identified, and the relationships between immune cytokines and differential metabolites were explored. Results In the RPL group, serum interleukin-6 and interleukin-10 levels were significantly higher, while interleukin-2 and interferon-γ were significantly lower. A total of 296 differential metabolites were detected by untargeted metabolomic profiling between the RPL and control groups, with most linked to amino acid metabolism. Targeted metabolomic profiling of amino acid metabolism revealed upregulation of indole-3-acetic acid, tyrosine, glycine, isoleucine, tryptophan, lysine, aspartic acid, arginine, leucine, threonine, glutamic acid, cystine, and phenylpyruvic acid (PPA) in the RPL group. Moreover, PPA and 5-hydroxy-L-tryptophan showed great potential in predicting RPL in a diagnostic model. Cystine and tyrosine were associated with immune cytokines in correlation analysis. Conclusion The study highlights the role of amino acid metabolism in RPL pathogenesis, suggesting that PPA and 5-HTP may be potential predictive indicators, while cystine and tyrosine may potentially regulate immune responses related to RPL. Further investigation into the molecular mechanisms underlying these findings could potentially result in the creation of novel diagnostic and therapeutic approaches for RPL.



Identification and Function Analysis of Novel Hypoglycemic and Antioxidant Peptides from Chickpea

August 2024

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21 Reads

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3 Citations

Plant Foods for Human Nutrition

Chickpea is rich in protein and has been demonstrated to possess hypoglycaemic effects. However, the specific bioactive ingredients and mechanisms underlying their hypoglycaemic effects remain unclear. In this study, enzymatic hydrolysis and gel permeation chromatography were used to extract chickpea bioactive peptide (CBP) from chickpea protein. One of the products, CBP-75-3, was found to inhibit α-glucosidase (GAA) activity and significantly increase the viability of insulin resistant (IR) cells. Moreover, CBP-75-3 significantly increased the rate of glucose consumption and glycogen synthesis in IR-HepG2 cells. Moreover, CBP-75-3 decreased the levels of malondialdehyde and increased the levels of superoxide dismutase, glutathione, and glutathione peroxidase. Subsequently, 29 novel bioactive peptides in CBP-75-3 were identified by LC‒MS/MS, and the potential hypoglycaemic targets of these novel bioactive peptides were investigated using molecular docking. Based on the results, the residues of the novel bioactive peptides interact with GAA through hydrogen bonding (especially LLR, FH, RQLPR, KGF and NFQ by binding to the substrate binding pocket or the active centre of GAA), thereby inhibiting GAA activity and laying a foundation for its hypoglycaemic activity. In short, the novel bioactive peptides isolated and identified from chickpea can effectively exert hypoglycaemic effects and increase the antioxidant capacity of IR-HepG2 cells. This study reveals that CBP-75-3, a natural hypoglycaemic ingredient, has potential for applications in functional foods and provides a theoretical basis for the development and application of CBP in the future.


Citations (71)


... It leverages databases to identify potential drug targets and pathways in the context of various diseases (Kibble et al. 2015). By employing methods like molecular docking and experimental validation, network pharmacology enhances the understanding of the multifaceted interactions of herbal medicines and their active targets (Yao et al. 2024;Wu et al. 2024;Deng et al. 2024). ...

Reference:

Decoding the anti-hypertensive mechanism of α-mangostin based on network pharmacology, molecular docking and experimental validation
Identification and screening of potential anti-pneumonia active ingredients and targets of Qing-Kai-Ling Oral Liquid via UHPLC-Q-Exactive Orbitrap Mass Spectrometry based on data post-processing
  • Citing Article
  • September 2024

Journal of Chromatography A

... Plant-derived peptides have demonstrated significant effectiveness in alleviating T2DM, making them promising candidates for the development of anti-diabetic drugs [10,29,30]. Almond is a widely-consumed nut and long-term intake was beneficial to alleviating insulin resistance in patients with T2DM [14][15][16]. ...

Identification and Function Analysis of Novel Hypoglycemic and Antioxidant Peptides from Chickpea

Plant Foods for Human Nutrition

... The primary BA CA was increased by an inulin fiber diet, leading to IL-33 upregulation and worsen-ing DSS-induced murine colitis and human IBD, which are likely mediated by group 2 innate lymphoid cells (ILC2s) and eosinophils [80]. In DSS-induced colitis, CA, CDCA, and LCA regulated RORγt + T reg levels via VDR [81], and UDCA, isoalloLCA, and 3-oxoLCA increased the proportion of ILC3s in the intestine [82], thereby improving epithelial barrier integrity and alleviating colitis. Other metabolites, including short-chain fatty acids, also work with the immune system to regulate BAs; for example, tumor necrosis factor (TNF-α), interferon-γ (IFN-γ), and butyrate-inhibited TCA uptake by Caco-2 cells, possibly through the PI3K and JAK/STAT1 pathways [83]. ...

Gallic acid attenuates murine ulcerative colitis by promoting group 3 innate lymphocytes, affecting gut microbiota, and bile acid metabolism
  • Citing Article
  • June 2024

The Journal of Nutritional Biochemistry

... In previous work, bivalent aptamers are usually used to deliver siRNA for targeted therapy, but it may need complicated design due to integration of siRNA sequences [40][41][42]. Circular bivalent aptamers have also been reported to deliver therapeutics with enhanced stability, while enzyme-catalyzed ligation make the synthesis of circular bivalent aptamers not easy [43][44][45]. Compared to the reported bivalent aptamer complex, the developed BADD can be fast constructed through simple DNA self-assembly and noncovalent intercalation of Dox without difficult sequence design. ...

A Bivalent Aptamer-Based DNA Agonist for EGFR Signaling Effectively Alleviates Ulcerative Colitis In Vivo
  • Citing Article
  • June 2024

ACS Chemical Biology

... 129 In addition to directly supplementing live P. distasonis, its outer membrane vesicles inhibited the proliferation of CT26 colon cancer cells in vitro and suppressed tumor growth in CT26 tumor-bearing mice. 130 Nevertheless, one study reported that an increased abundance of P. distasonis was negatively associated with Kupffer cells and positively associated with liver metastasis of CRC after vancomycin supplementation. Here is a lack of direct evidence that P. distasonis is the trigger for liver metastasis in CRC. ...

Parabacteroides distasonis-Derived Outer Membrane Vesicles Enhance Antitumor Immunity Against Colon Tumors by Modulating CXCL10 and CD8 T Cells

... In recent years, the application of functional materials in chiral separation and detection technologies has been widely studied, including covalent organic framework (COFs) [8,9], metal-organic framework (MOFs) [10], porous organic cage (POCs) [11], and some other porous organic materials [12]. Li et al. [13] summarized the development of porous organic materials as chiral separation media for the selective separation of enantiomers. ...

Construction of dual-chiral covalent organic frameworks for enantioselective separation
  • Citing Article
  • May 2024

Journal of Chromatography A

... To control the interactions of different membrane proteins, Liu et al. developed a bivalent linker composed of two different aptamers, which modulated the heterodimerization of receptor tyrosine kinases from different families, thus enabling the stimulation of EGFR1 and c-Met signal transduction pathways. 129 Yang et al. constructed a nongenetically engineered artificial DNA mechanoreceptor, which could sense the exerted tensile forces through an allosteric DNA switch. This design implemented a force-triggered dynamic DNA assembly that promoted receptor dimerization and enhanced downstream signaling in the force-receiving cells. ...

Utilizing bivalent aptamers as first DNA agonist to activate RTKs heterodimer of different families
  • Citing Article
  • March 2024

Chinese Chemical Letters

... Furthermore, compared to shorter-chain PFAS, which depends on electrostatic interactions, long-chain PFAS is more easily absorbed (Zahmatkesh et al. 2024;Thompson et al. 2024). Gong et al. (Gong et al. 2024) created a cationic-fluorinated (CF)-COF by post-modification, which they then utilised as a magnetic solid-phase extraction adsorbent for the adsorption of PFASs. Eight long-chain PFASs in food were identified using a unique approach that combined CF-COF-based magnetic solid-phase extraction with LC-MS/MS. ...

Rapidly enrichment and detection of per-and polyfluoroalkyl substances in foods using a novel bifunctional covalent organic framework
  • Citing Article
  • March 2024

Food Chemistry

... In terms of immune modulation, probiotics maintain immune homeostasis and prevent excessive immune responses that can damage intestinal tissues. For instance, Lactobacillus acidophilus and its metabolite ursodeoxycholic acid (UDCA) alleviate UC symptoms by activating the RapGap/PI3K-AKT/NF-κB signaling pathway, regulating Treg cells and M1 macrophages [52]. Similarly, Lactobacillus johnsonii alleviates colonic inflammation by producing indole-3-lactic acid (ILA), which activates the aryl hydrocarbon receptor (AhR) [53]. ...

Lactobacillus acidophilus and its metabolite ursodeoxycholic acid ameliorate ulcerative colitis by promoting Treg differentiation and inhibiting M1 macrophage polarization

... Inflammatory bowel disease (IBD) is a chronic intermittent disease primarily affecting the rectal and colon mucosa (15,16). It is characterized by intestinal inflammation and damage to the epithelial barrier (17). IBD has gained significant attention in recent years due to its detrimental impact on host health. ...

Berberine alleviates inflammation and suppresses PLA2-COX-2-PGE2-EP2 pathway through targeting gut microbiota in DSS-induced ulcerative colitis
  • Citing Article
  • December 2023

Biochemical and Biophysical Research Communications