1.EvoNB: A protein language model-based workflow for nanobody mutation prediction and optimization.
Danyang XIONG ; Yongfan MING ; Yuting LI ; Shuhan LI ; Kexin CHEN ; Jinfeng LIU ; Lili DUAN ; Honglin LI ; Min LI ; Xiao HE
Journal of Pharmaceutical Analysis 2025;15(6):101260-101260
The identification and optimization of mutations in nanobodies are crucial for enhancing their therapeutic potential in disease prevention and control. However, this process is often complex and time-consuming, which limit its widespread application in practice. In this study, we developed a workflow, named Evolutionary-Nanobody (EvoNB), to predict key mutation sites of nanobodies by combining protein language models (PLMs) and molecular dynamic (MD) simulations. By fine-tuning the ESM2 model on a large-scale nanobody dataset, the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced. The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies. Additionally, we selected four widely representative nanobody-antigen complexes to verify the predicted effects of mutations. MD simulations analyzed the energy changes caused by these mutations to predict their impact on binding affinity to the targets. The results showed that multiple mutations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target, further validating the potential of this workflow for designing and optimizing nanobody mutations. Additionally, sequence-based predictions are generally less dependent on structural absence, allowing them to be more easily integrated with tools for structural predictions, such as AlphaFold 3. Through mutation prediction and systematic analysis of key sites, we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes. The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.
2.Disorder of phospholipid metabolism in the renal cortex and medulla contributes to acute tubular necrosis in mice after cantharidin exposure using integrative lipidomics and spatial metabolomics.
Tianmu HE ; Kexin LIN ; Lijuan XIONG ; Wen ZHANG ; Huan ZHANG ; Cancan DUAN ; Xiaofei LI ; Jianyong ZHANG
Journal of Pharmaceutical Analysis 2025;15(7):101210-101210
Cantharidin (CTD), a natural compound used to treat multiple tumors in the clinic setting, has been limited due to acute kidney injury (AKI). However, the major cause of AKI and its underlying mechanism remain to be elucidated. Serum creatinine (SCr) and blood urea nitrogen (BUN) were detected through pathological evaluation after CTD (1.5 mg/kg) oral gavage in mice in 3 days. Kidney lipidomics based on ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to investigate lipids disorder after CTD exposure in mice. Then, spatial metabolomics based on matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) was used to detect the kidney spatial distribution of lipids. Integrative analysis was performed to reveal the spatial lipid disorder mechanism and verify key lipids in vitro. The results showed that the levels of SCr and BUN were increased, and tubular necrosis was observed in mouse kidneys, resulting in acute tubular necrosis (ATN) in CTD-induced AKI. Then, lipidomics results revealed that after CTD exposure, 232 differential lipid metabolites and 11 pathways including glycerophospholipid (GP) and sphingolipid (SL) metabolism were disrupted. Spatial metabolomics revealed that 55 spatial differential lipid metabolites and nine metabolic pathways were disturbed. Subsequently, integrative analysis found that GP metabolism was stimulated in the renal cortex and medulla, whereas SL metabolism was inhibited in the renal cortex. Up-regulated lysophosphatidylcholine (LysoPC) (18:2(9Z,12Z)), LysoPC (16:0/0:0), glycerophosphocholine, and down-regulated sphingomyelin (SM) (d18:0/16:0), SM (d18:1/24:0), and SM (d42:1) were key differential lipids. Among them, LysoPC (16:0/0:0) was increased in the CTD group at 1.1196 μg/mL, which aggravated CTD-induced ATN in human kidney-2 (HK-2) cells. LysoPC acyltransferase was inhibited and choline phosphotransferase 1 (CEPT1) was activated after CTD intervention in mice and in HK-2 cells. CTD induces ATN, resulting in AKI, by activating GP metabolism and inhibiting SL metabolism in the renal cortex and medulla, LysoPC (16:0/0:0), LysoPC acyltransferase, and CEPT1 may be the therapeutic targets.
3.Analysis of Animal Model of Chronic Heart Failure Based on Combination of Diseases and Syndromes of Traditional Chinese Medicine and Western Medicine
Xueyan ZHANG ; Kexin ZHANG ; You YU ; Huan ZHANG ; Yingzhu DUAN ; Rui YU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(12):239-247
Chronic heart failure (CHF) represents the terminal stage of cardiovascular diseases, and its prevalence remains high in China. In this study, existing animal models of CHF were retrieved and categorized. In combination with the characteristics of CHF from traditional Chinese medicine (TCM) and Western medicine perspectives, the models were weighted, and their clinical consistency was evaluated. The advantages and disadvantages of the models were assessed. Among them, models with higher TCM clinical consistency included the doxorubicin-induced model, the isoproterenol-induced model, and the left anterior descending coronary artery ligation model, each with a TCM consistency rate of 90%. The animal model established by the left anterior descending coronary artery ligation showed a high degree of clinical consistency with Western medicine, with a consistency rate of 82%. Each model exhibited its own advantages and disadvantages, with a general lack of modeling methods combining diseases and syndromes of TCM and Western medicine. At present, the inducement factors used for animal models are relatively singular, mainly reflecting the etiology and pathogenesis of Western medicine, with insufficient correlation to the pathogenesis of TCM. The characteristics of TCM syndromes are not fully represented, and the consistency between TCM and Western medicine is generally not high. TCM has the advantage of a multi-dimensional syndrome differentiation and treatment approach. It is necessary to integrate the characteristics of diseases and syndromes of TCM and Western medicine, adopt multi-factor modeling methods to reflect the pathological process of CHF, improve existing models, and establish animal models of CHF that better align with the characteristics of clinical diseases and syndromes of TCM and Western medicine, so as to provide a reliable reference for clinical prevention and treatment.
4.Analysis of Animal Model of Chronic Heart Failure Based on Combination of Diseases and Syndromes of Traditional Chinese Medicine and Western Medicine
Xueyan ZHANG ; Kexin ZHANG ; You YU ; Huan ZHANG ; Yingzhu DUAN ; Rui YU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(12):239-247
Chronic heart failure (CHF) represents the terminal stage of cardiovascular diseases, and its prevalence remains high in China. In this study, existing animal models of CHF were retrieved and categorized. In combination with the characteristics of CHF from traditional Chinese medicine (TCM) and Western medicine perspectives, the models were weighted, and their clinical consistency was evaluated. The advantages and disadvantages of the models were assessed. Among them, models with higher TCM clinical consistency included the doxorubicin-induced model, the isoproterenol-induced model, and the left anterior descending coronary artery ligation model, each with a TCM consistency rate of 90%. The animal model established by the left anterior descending coronary artery ligation showed a high degree of clinical consistency with Western medicine, with a consistency rate of 82%. Each model exhibited its own advantages and disadvantages, with a general lack of modeling methods combining diseases and syndromes of TCM and Western medicine. At present, the inducement factors used for animal models are relatively singular, mainly reflecting the etiology and pathogenesis of Western medicine, with insufficient correlation to the pathogenesis of TCM. The characteristics of TCM syndromes are not fully represented, and the consistency between TCM and Western medicine is generally not high. TCM has the advantage of a multi-dimensional syndrome differentiation and treatment approach. It is necessary to integrate the characteristics of diseases and syndromes of TCM and Western medicine, adopt multi-factor modeling methods to reflect the pathological process of CHF, improve existing models, and establish animal models of CHF that better align with the characteristics of clinical diseases and syndromes of TCM and Western medicine, so as to provide a reliable reference for clinical prevention and treatment.
5.Cancer Incidence in Five Continents and China:Review and Prospect
Siwei ZHANG ; Rongshou ZHENG ; Kexin SUN ; Lingbin DU ; Qingsheng WANG ; Xibin SUN ; Jijun DUAN ; Wenqiang WEI
China Cancer 2025;34(6):417-429
The Cancer Incidence in Five Continents(CI5)database are jointly maintained by the International Agency for Research on Cancer(IARC)and the International Association of Cancer Registries(IACR),both affiliated to the World Health Organization.This paper provides a histori-cal overview of cancer registration efforts in China,systematically summarizes the journey and en-deavors of Chinese cancer registries as they were incorporated into IARC and CI5.Furthermore,it offers a perspective on the strategies for advancing the high-quality development of cancer registra-tion activities within the nation.
6.Disorder of phospholipid metabolism in the renal cortex and medulla contributes to acute tubular necrosis in mice after cantharidin exposure using integrative lipidomics and spatial metabolomics
Tianmu HE ; Kexin LIN ; Lijuan XIONG ; Wen ZHANG ; Huan ZHANG ; Cancan DUAN ; Xiaofei LI ; Jianyong ZHANG
Journal of Pharmaceutical Analysis 2025;15(7):1526-1541
Cantharidin(CTD),a natural compound used to treat multiple tumors in the clinic setting,has been limited due to acute kidney injury(AKI).However,the major cause of AKI and its underlying mechanism remain to be elucidated.Serum creatinine(SCr)and blood urea nitrogen(BUN)were detected through pathological evaluation after CTD(1.5 mg/kg)oral gavage in mice in 3 days.Kidney lipidomics based on ultra-high performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS)was used to investigate lipids disorder after CTD exposure in mice.Then,spatial metabolomics based on matrix-assisted laser desorption/ionization-mass spectrometry imaging(MALDI-MSI)was used to detect the kidney spatial distribution of lipids.Integrative analysis was performed to reveal the spatial lipid disorder mechanism and verify key lipids in vitro.The results showed that the levels of SCr and BUN were increased,and tubular necrosis was observed in mouse kidneys,resulting in acute tubular necrosis(ATN)in CTD-induced AKI.Then,lipidomics results revealed that after CTD exposure,232 differential lipid metabolites and 11 pathways including glycerophospholipid(GP)and sphingolipid(SL)metabolism were disrupted.Spatial metabolomics revealed that 55 spatial differential lipid metabolites and nine metabolic pathways were disturbed.Subsequently,integrative analysis found that GP metabolism was stimulated in the renal cortex and medulla,whereas SL metabolism was inhibited in the renal cortex.Up-regulated lysophosphatidylcholine(LysoPC)(18∶2(9Z,12Z)),LysoPC(16∶0/0∶0),glycerophosphocholine,and down-regulated sphingomyelin(SM)(d18∶0/16:0),SM(d 18∶1/24:0),and SM(d42∶1)were key differential lipids.Among them,LysoPC(16∶0/0∶0)was increased in the CTD group at 1.1196 μg/mL,which aggravated CTD-induced ATN in human kidney-2(HK-2)cells.LysoPC acyltransferase was inhibited and choline phos-photransferase 1(CEPT1)was activated after CTD intervention in mice and in HK-2 cells.CTD induces ATN,resulting in AKI,by activating GP metabolism and inhibiting SL metabolism in the renal cortex and medulla,LysoPC(16:0/0:0),LysoPC acyltransferase,and CEPT1 may be the therapeutic targets.
7.EvoNB:A protein language model-based workflow for nanobody mutation prediction and optimization
Danyang XIONG ; Yongfan MING ; Yuting LI ; Shuhan LI ; Kexin CHEN ; Jinfeng LIU ; Lili DUAN ; Honglin LI ; Min LI ; Xiao HE
Journal of Pharmaceutical Analysis 2025;15(6):1334-1343
The identification and optimization of mutations in nanobodies are crucial for enhancing their thera-peutic potential in disease prevention and control.However,this process is often complex and time-consuming,which limit its widespread application in practice.In this study,we developed a work-flow,named Evolutionary-Nanobody(EvoNB),to predict key mutation sites of nanobodies by combining protein language models(PLMs)and molecular dynamic(MD)simulations.By fine-tuning the ESM2 model on a large-scale nanobody dataset,the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced.The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies.Additionally,we selected four widely representative nanobody-antigen complexes to verify the predicted effects of mutations.MD simulations analyzed the energy changes caused by these mu-tations to predict their impact on binding affinity to the targets.The results showed that multiple mu-tations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target,further validating the potential of this workflow for designing and optimizing nanobody mutations.Additionally,sequence-based predictions are generally less dependent on structural absence,allowing them to be more easily integrated with tools for structural predictions,such as AlphaFold 3.Through mutation prediction and systematic analysis of key sites,we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes.The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.
8.The comparison of ferroptosis characteristics and motor deficits in Parkinson's disease mouse models
Haiyan LI ; Mengzhu LI ; Mengxuan CHEN ; Da GAO ; Kexin DUAN ; Lijun ZHAO ; Meiling ZHU
The Journal of Practical Medicine 2025;41(22):3501-3509
Objective To compare ferroptosis characteristics and motor dysfunction across different mouse models of Parkinson's disease(PD).Methods Animal models of PD were divided into five groups:the control group,sham-operated group,6-hydroxydopamine(6-OHDA)group,1-methyl-4-phenyl-1,2,3,6-tetrahydropyri-dine(MPTP)group,and lipopolysaccharide(LPS)group.Differences in ferroptosis-related features and motor dysfunction across these groups were evaluated through behavioral observation,histopathological examination,protein analysis,and assessment of lipid peroxidation and oxidative stress levels.Results In all three model groups,the number of TH-positive neurons in the substantia nigra on the lesioned side was significantly reduced,accompanied by evident neuronal degeneration and a marked decrease in Nissl bodies.Behavioral assessments revealed that the 6-OHDA group displayed the most severe motor deficits.In the substantia nigra,FTH1 protein expression was significantly downregulated in the 6-OHDA,LPS,and MPTP groups(P<0.01,P<0.05,P<0.01),respectively,while GPX4 expression was also reduced(P<0.001,P<0.001,P<0.01).Malondialdehyde(MDA)levels were significantly elevated in both the 6-OHDA and MPTP groups(P<0.05,P<0.05).Glutathione(GSH)assays demonstrated markedly reduced levels in the 6-OHDA,MPTP,and LPS groups(P<0.01,P<0.001,P<0.001).Reactive oxygen species(ROS)detection revealed a significant increase in the MPTP and LPS groups(P<0.05,P<0.05).Conclusion The 6-OHDA model is well suited for studying PD-related behaviors and the underlying mechanisms of motor symptoms,the MPTP model is particularly effective for investigating the ferroptosis pathway,and the LPS model serves as a valuable complement for research on neuroinflammation mechanisms.
9.Effect of Baofei Yiqi pill on improving immune function of patients with lung cancer
Qingfei WANG ; Kexin CHENG ; Xiaoying ZOU ; Yumeng ZHU ; Linjian DUAN
China Modern Doctor 2025;63(4):57-60
Objective To explore the effect of Baofei Yiqi pill on immune function of patients with lung cancer.Methods A total of 100 patients with lung cancer diagnosed and treated in Leping Hospital of Traditional Chinese Medicine from September 2020 to September 2023 were selected and divided into experimental group and control group according to random number table method,with 50 cases in each group.The control group was treated with docetaxel combined with cisplatin,and the experimental group was treated with Baofei Yiqi pill on the basis of control group.Both groups were treated with 3 cycles of chemotherapy.The clinical efficacy,quality of life,changes in weight,immune function and adverse reactions were compared between two groups.Results The total response rate of experimental group was significantly higher than that of control group(x2=14.620,P<0.001).After treatment,the Karnofsky performance status score and weight of experimental group were significantly higher than those of control group(P<0.05),and the levels of CD3+,CD4+and CD4+/CD8+in experimental group were significantly higher than those in control group,and the levels of CD8+was significantly lower than than in control group(P<0.05).The incidence of gastrointestinal reactions in experimental group was significantly lower than that in control group(P<0.05).There was no significant difference in the incidence of abnormal renal function and liver function between two groups(P>0.05).Conclusion Baofei Yiqi pill can effectively improve the immune function of patients with lung cancer,improve the quality of life of patients,reduce the adverse reactions of chemotherapy,and alleviate the disease of patients to a certain extent,which is worthy of promotion and application.
10.Effect of Baofei Yiqi pill on improving immune function of patients with lung cancer
Qingfei WANG ; Kexin CHENG ; Xiaoying ZOU ; Yumeng ZHU ; Linjian DUAN
China Modern Doctor 2025;63(4):57-60
Objective To explore the effect of Baofei Yiqi pill on immune function of patients with lung cancer.Methods A total of 100 patients with lung cancer diagnosed and treated in Leping Hospital of Traditional Chinese Medicine from September 2020 to September 2023 were selected and divided into experimental group and control group according to random number table method,with 50 cases in each group.The control group was treated with docetaxel combined with cisplatin,and the experimental group was treated with Baofei Yiqi pill on the basis of control group.Both groups were treated with 3 cycles of chemotherapy.The clinical efficacy,quality of life,changes in weight,immune function and adverse reactions were compared between two groups.Results The total response rate of experimental group was significantly higher than that of control group(x2=14.620,P<0.001).After treatment,the Karnofsky performance status score and weight of experimental group were significantly higher than those of control group(P<0.05),and the levels of CD3+,CD4+and CD4+/CD8+in experimental group were significantly higher than those in control group,and the levels of CD8+was significantly lower than than in control group(P<0.05).The incidence of gastrointestinal reactions in experimental group was significantly lower than that in control group(P<0.05).There was no significant difference in the incidence of abnormal renal function and liver function between two groups(P>0.05).Conclusion Baofei Yiqi pill can effectively improve the immune function of patients with lung cancer,improve the quality of life of patients,reduce the adverse reactions of chemotherapy,and alleviate the disease of patients to a certain extent,which is worthy of promotion and application.

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