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.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.
3.Facilitators and impediments to home glucose management for patients undergoing bariatric surgery: a qualitative study
Xiaoqian ZHANG ; Lin YAO ; Jinfeng WANG ; Chunxia LIU ; Lihua ZHU ; Xiaoxu DUAN
Chinese Journal of Modern Nursing 2025;31(11):1417-1422
Objective:To explore facilitators and impediments to home glucose management for patients undergoing bariatric surgery based on the consolidated framework for implementation research (CFIR), so as to inform the development of a glucose management pathway after bariatric surgery.Methods:This study was a descriptive phenomenological study. Using purposive sampling method, seven healthcare professionals and 11 patients undergoing bariatric surgery from the General Surgery·Metabolic and Bariatric Center of China-Japan Friendship Hospital were selected from November 2023 to January 2024 for semi-structured interviews. Targeted content analysis was used for the data analysis.Results:A total of six facilitators and six impediments related to the five dimensions of CFIR were distilled. Facilitators included the personalized glucose management program, regular long-term follow-up, multidisciplinary management team, support from family and friends, complication distress, and information technology platform. Impediments involved patterned follow-up, poor accessibility and convenience of resources, role conflict, herd mentality, poor behavioral compliance, and low utilization of digital equipment.Conclusions:Glucose management needs vary in patients after bariatric surgery, with a gradual decline in management compliance. Healthcare professionals should build an "Internet +"home glucose management service model, carry out targeted multidisciplinary team follow-up, and promote the formation of a standardized pathway for patients' home glucose management.
4.Facilitators and impediments to home glucose management for patients undergoing bariatric surgery: a qualitative study
Xiaoqian ZHANG ; Lin YAO ; Jinfeng WANG ; Chunxia LIU ; Lihua ZHU ; Xiaoxu DUAN
Chinese Journal of Modern Nursing 2025;31(11):1417-1422
Objective:To explore facilitators and impediments to home glucose management for patients undergoing bariatric surgery based on the consolidated framework for implementation research (CFIR), so as to inform the development of a glucose management pathway after bariatric surgery.Methods:This study was a descriptive phenomenological study. Using purposive sampling method, seven healthcare professionals and 11 patients undergoing bariatric surgery from the General Surgery·Metabolic and Bariatric Center of China-Japan Friendship Hospital were selected from November 2023 to January 2024 for semi-structured interviews. Targeted content analysis was used for the data analysis.Results:A total of six facilitators and six impediments related to the five dimensions of CFIR were distilled. Facilitators included the personalized glucose management program, regular long-term follow-up, multidisciplinary management team, support from family and friends, complication distress, and information technology platform. Impediments involved patterned follow-up, poor accessibility and convenience of resources, role conflict, herd mentality, poor behavioral compliance, and low utilization of digital equipment.Conclusions:Glucose management needs vary in patients after bariatric surgery, with a gradual decline in management compliance. Healthcare professionals should build an "Internet +"home glucose management service model, carry out targeted multidisciplinary team follow-up, and promote the formation of a standardized pathway for patients' home glucose management.
5.Small tidal volume hyperventilation relieves intraocular and intracranial pressure elevation in prone spinal surgery:a randomized controlled trial
Xuefei DUAN ; Jinfeng WEI ; Anyi LIANG ; Xuexia JI
Journal of Southern Medical University 2024;44(4):660-665
Objective To investigate the effects of different ventilation strategies on intraocular pressure (IOP) and intracranial pressure in patients undergoing spinal surgery in the prone position under general anesthesia. Methods Seventy-two patients undergoing prone spinal surgery under general anesthesia between November, 2022 and June, 2023 were equally randomized into two groups to receive routine ventilation (with Vt of 8mL/kg, Fr of 12-15/min, and etCO2 maintained at 35-40 mmHg) or small tidal volume hyperventilation (Vt of 6 mL/kg, Fr of18-20/min, and etCO2 maintained at 30-35 mmHg) during the surgery. IOP of both eyes (measured with a handheld tonometer), optic nerve sheath diameter (ONSD;measured at 3 mm behind the eyeball with bedside real-time ultrasound), circulatory and respiratory parameters of the patients were recorded before anesthesia (T0), immediately after anesthesia induction (T1), immediately after prone positioning (T2), at 2 h during operation (T3), immediately after supine positioning after surgery (T4) and 30 min after the operation (T5). Results Compared with those at T1, IOP and ONSD in both groups increased significantly at T3 and T4 (P<0.05). IOP was significantly lower in hyperventilation group than in routine ventilation group at T3 and T4 (P<0.05), and ONSD was significantly lower in hyperventilation group at T4 (P<0.05). IOP was positively correlated with the length of operative time (r=0.779, P<0.001) and inversely with intraoperative etCO2 at T3 (r=-0.248, P<0.001) and T4 (r=-0.251, P<0.001). ONSD was correlated only with operation time (r=0.561, P<0.05) and not with IOP (r=0.178, P>0.05 at T3;r=0.165, P>0.05 at T4). Conclusion Small tidal volume hyperventilation can relieve the increase of IOP and ONSD during prone spinal surgery under general anesthesia.
6.Relationship between plasma mtDNA,tissue MIP1α,MCP-1 and recovery of hip function in patients with hip fractures
Zhonglei SU ; Yuntao GUO ; Jinfeng LIU ; Wenjuan WANG ; Yuantao DUAN ; Xin'an GUO
Journal of Clinical Surgery 2024;32(11):1200-1204
Objective To analyze the relationship between plasma mitochondrial DNA(mtDNA),macrophage inflammatory protein-1α(MIP1α)and monocyte chemotactic protein 1(MCP-1)in vastus lateralis tissues and postoperative muscle atrophy,recovery of hip function in patients with hip fractures.Methods A total of 86 patients with hip fractures and 43 patients with coxitis in Jinan Eighth People's Hospital were enrolled as hip fracture group and coxitis group between October 2020 and October 2022,respectively.The lateral muscle tissues were collected as samples during surgery.The level of plasma mtDNA was detected by real-time fluorescence quantitative polymerase chain reaction.Before surgery,levels of serum interleukin-6(IL-6)and tumor necrosis factor α(TNF-α)were detected by enzyme-linked immunosorbent assay.Before surgery,cross-sectional areas of types Ⅰ and Ⅱ vastus lateralis fibers were detected by immunofluorescence method.Before surgery,expression levels of MIP1α and MCP-1 proteins in lateral muscle tissues were detected by Western blot.All patients with hip fracture were effectively followed up for 6 months after surgery.At 3 and 6 months after surgery,total lean mass(TLM)and unaffected limb lean mass(ULLM)were detected by DXA.Results The level of plasma mtDNA in hip fracture group was higher than that in coxitis group before surgery[(4.12±0.53)vs(2.37±0.36),P<0.05],levels of serum IL-6 and TNF-α were higher than those in coxitis group[(34.68±6.14)pg/ml,(21.54±4.12)pg/ml vs(12.74±3.06)pg/ml,(10.81±2.71)pg/ml,P<0.05],cross-sectional areas of types Ⅰ and Ⅱ vastus lateralis fibers were smaller than those in coxitis group[(4321.45±441.36)μm2,(2384.38±247.11)μm2 vs(5417.63±553.27)μm2,(3569.24±368.22)μm2,P<0.05],and expression levels of MIP1α and MCP-1 proteins were higher than those in coxitis group[(2.34±0.25),(2.47±0.28)vs(1.18±0.15),(1.95±0.23),P<0.05].In patients with hip fracture after 6 months of follow-up,there were 53 cases with good prognosis and 33 cases with poor prognosis.The level of plasma mtDNA in poor prognosis group was higher than that in good prognosis group before surgery[(4.53±0.52)vs(3.87±0.44),P<0.05],levels of serum IL-6 and TNF-α were higher than those in good prognosis group[(35.97±5.32)pg/ml,(20.74±4.27)pg/ml vs(33.51±5.16)pg/ml,(22.83±4.33)pg/ml,P<0.05],cross-sectional areas of types Ⅰ and Ⅱ vastus lateralis fibers were smaller than those in good prognosis group[(4174.26±434.60)μm2,(2309.56±246.18)μm2 vs(4394.42±450.12)μm2,(2430.97±250.72)μm2,P<0.05],and expression levels of MIP1α and MCP-1 proteins were higher than those in good prognosis group[(2.47±0.28),(1.95±0.23)vs(2.26±0.24),(1.82±0.21),P<0.05].TLM and ULLM at 6 months after surgery were lower than those at 3 months after surgery in good prognosis group and poor prognosis group(P<0.05).At 3 and 6 months after surgery,there was no significant different in TLM or ULLM between good prognosis group and poor prognosis group(P>0.05).Conclusion Traumatic stress injury will increase level of plasma mtDNA in patients with hip fracture,which will induce the increase of systemic inflammatory indexes(serum IL-6,TNF-α)and inflammatory factors(MCP-1,MIP1α)levels,aggravate muscle atrophy and cause postoperative decline of hip function.
7.Small tidal volume hyperventilation relieves intraocular and intracranial pressure elevation in prone spinal surgery:a randomized controlled trial
Xuefei DUAN ; Jinfeng WEI ; Anyi LIANG ; Xuexia JI
Journal of Southern Medical University 2024;44(4):660-665
Objective To investigate the effects of different ventilation strategies on intraocular pressure (IOP) and intracranial pressure in patients undergoing spinal surgery in the prone position under general anesthesia. Methods Seventy-two patients undergoing prone spinal surgery under general anesthesia between November, 2022 and June, 2023 were equally randomized into two groups to receive routine ventilation (with Vt of 8mL/kg, Fr of 12-15/min, and etCO2 maintained at 35-40 mmHg) or small tidal volume hyperventilation (Vt of 6 mL/kg, Fr of18-20/min, and etCO2 maintained at 30-35 mmHg) during the surgery. IOP of both eyes (measured with a handheld tonometer), optic nerve sheath diameter (ONSD;measured at 3 mm behind the eyeball with bedside real-time ultrasound), circulatory and respiratory parameters of the patients were recorded before anesthesia (T0), immediately after anesthesia induction (T1), immediately after prone positioning (T2), at 2 h during operation (T3), immediately after supine positioning after surgery (T4) and 30 min after the operation (T5). Results Compared with those at T1, IOP and ONSD in both groups increased significantly at T3 and T4 (P<0.05). IOP was significantly lower in hyperventilation group than in routine ventilation group at T3 and T4 (P<0.05), and ONSD was significantly lower in hyperventilation group at T4 (P<0.05). IOP was positively correlated with the length of operative time (r=0.779, P<0.001) and inversely with intraoperative etCO2 at T3 (r=-0.248, P<0.001) and T4 (r=-0.251, P<0.001). ONSD was correlated only with operation time (r=0.561, P<0.05) and not with IOP (r=0.178, P>0.05 at T3;r=0.165, P>0.05 at T4). Conclusion Small tidal volume hyperventilation can relieve the increase of IOP and ONSD during prone spinal surgery under general anesthesia.
8.Comparison of QT interval prolongation incidence in cardiology intensive care unit patients treated with moxifloxacin versus levofloxacin and analysis of related risk factors
Chao WEN ; Xiaoxia TANG ; Jinfeng ZHANG ; Man DUAN ; Gang CHEN ; Wenwen ZHU ; Ya WANG
Adverse Drug Reactions Journal 2024;26(7):412-416
Objective:To investigate the differences in the incidence of QT interval prolongation between moxifloxacin and levofloxacin in anti-infective therapy among cardiology intensive care unit (CCU) patients, and to analyze the risk factors for QT interval prolongation.Methods:The data of patients who received anti-infective treatments with moxifloxacin and levofloxacin in CCU of Xiaogan Central Hospital from January 2020 to December 2022 were collected and analyzed retrospectively. The clinical characteristics in the 2 groups were compared. Potential influencing factors of QT interval prolongation were analyzed using univariate regression analysis. Variables with P<0.2 were included in a logistic regression model for multivariate analysis. The effect values were expressed as odds ratio ( OR) and its 95% confidence interval ( CI). Results:A total of 146 patients were included in the study, with 76 patients in the moxifloxacin group and 70 patients in the levofloxacin group. In the moxifloxacin group, 18 out of 76 patients (23.68%) experienced QT interval prolongation, while in the levofloxacin group, 6 out of 70 patients (8.57%) experienced QT interval prolongation; the difference between the 2 groups was statistically significant ( P=0.025). There were no statistically significant differences in other factors between the 2 groups. Univariate regression analysis showed that female ( OR=2.958, 95% CI: 1.144-7.647, P=0.025), myocardial infarction ( OR=2.958, 95% CI: 1.144-7.647, P=0.025), concomitant use of amiodarone ( OR=2.569, 95% CI: 1.042-6.337, P=0.040) and escitalopram were influencing factors of QT interval prolongation. Factors with P<0.2 were entered in the multivariate logistic regression analysis, and the results showed that female ( OR=3.616, 95% CI: 1.240-10.538, P=0.019), hypokalemia ( OR=2.953, 95% CI: 1.263-6.905, P=0.012), and myocardial infarction ( OR=3.026, 95% CI: 1.057-8.666, P=0.039) were independent risk factors for QT interval prolongation. Conclusions:Moxifloxacin is associated with a higher incidence of QT interval prolongation compared to levofloxacin. Female and patients with hypokalemia and myocardial infarction have high risks for QT interval prolongation.
9.Comparison of QT interval prolongation incidence in cardiology intensive care unit patients treated with moxifloxacin versus levofloxacin and analysis of related risk factors
Chao WEN ; Xiaoxia TANG ; Jinfeng ZHANG ; Man DUAN ; Gang CHEN ; Wenwen ZHU ; Ya WANG
Adverse Drug Reactions Journal 2024;26(7):412-416
Objective:To investigate the differences in the incidence of QT interval prolongation between moxifloxacin and levofloxacin in anti-infective therapy among cardiology intensive care unit (CCU) patients, and to analyze the risk factors for QT interval prolongation.Methods:The data of patients who received anti-infective treatments with moxifloxacin and levofloxacin in CCU of Xiaogan Central Hospital from January 2020 to December 2022 were collected and analyzed retrospectively. The clinical characteristics in the 2 groups were compared. Potential influencing factors of QT interval prolongation were analyzed using univariate regression analysis. Variables with P<0.2 were included in a logistic regression model for multivariate analysis. The effect values were expressed as odds ratio ( OR) and its 95% confidence interval ( CI). Results:A total of 146 patients were included in the study, with 76 patients in the moxifloxacin group and 70 patients in the levofloxacin group. In the moxifloxacin group, 18 out of 76 patients (23.68%) experienced QT interval prolongation, while in the levofloxacin group, 6 out of 70 patients (8.57%) experienced QT interval prolongation; the difference between the 2 groups was statistically significant ( P=0.025). There were no statistically significant differences in other factors between the 2 groups. Univariate regression analysis showed that female ( OR=2.958, 95% CI: 1.144-7.647, P=0.025), myocardial infarction ( OR=2.958, 95% CI: 1.144-7.647, P=0.025), concomitant use of amiodarone ( OR=2.569, 95% CI: 1.042-6.337, P=0.040) and escitalopram were influencing factors of QT interval prolongation. Factors with P<0.2 were entered in the multivariate logistic regression analysis, and the results showed that female ( OR=3.616, 95% CI: 1.240-10.538, P=0.019), hypokalemia ( OR=2.953, 95% CI: 1.263-6.905, P=0.012), and myocardial infarction ( OR=3.026, 95% CI: 1.057-8.666, P=0.039) were independent risk factors for QT interval prolongation. Conclusions:Moxifloxacin is associated with a higher incidence of QT interval prolongation compared to levofloxacin. Female and patients with hypokalemia and myocardial infarction have high risks for QT interval prolongation.
10.2,3-Seco and 3-nor guaianolides fromAchillea alpina with antidiabetic activity.
Guimin XUE ; Chenguang ZHAO ; Jinfeng XUE ; Jiangjing DUAN ; Hao PAN ; Xuan ZHAO ; Zhikang YANG ; Hui CHEN ; Yanjun SUN ; Weisheng FENG
Chinese Journal of Natural Medicines (English Ed.) 2023;21(8):610-618
In this study, we presented the isolation and characterization of eight novel seco-guaianolide sesquiterpenoids (1-8) and two known guaianolide derivatives (9 and 10), from the aerial part of Achillea alpina L.. Compounds 1-3 were identified as guaianolides bearing an oxygen insertion at the 2, 3 position, while compounds 4-8 belonged to a group of special 3-nor guaianolide sesquiterpenoids. The structural elucidation of 1-8, including their absolute configurations, were accomplished by a combination of spectroscopic data analysis and quantum electronic circular dichroism (ECD) calculations. To evaluate the potential antidiabetic activity of compounds 1-10, we investigated their effects on glucose consumption in palmitic acid (PA)-mediated HepG2-insulin resistance (IR) cells. Among the tested compounds, compound 7 demonstrated the most pronounced ability to reverse IR. Moreover, a mechanistic investigation revealed that compound 7 exerted its antidiabetic effect by reducing the production of the pro-inflammatory cytokine IL-1β, which was achieved through the suppression of the NLRP3 pathway.
Humans
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Hypoglycemic Agents/pharmacology*
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Circular Dichroism
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Cytokines
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Glucose
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Hep G2 Cells
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Insulin Resistance

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