1.LocPro:A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research
Yintao ZHANG ; Lingyan ZHENG ; Nanxin YOU ; Wei HU ; Wanghao JIANG ; Mingkun LU ; Hangwei XU ; Haibin DAI ; Tingting FU ; Ying ZHOU
Journal of Pharmaceutical Analysis 2025;15(8):1765-1773
Drug development encompasses multiple processes,wherein protein subcellular localization is essential.It promotes target identification,treatment development,and the design of drug delivery systems.In this research,a deep learning framework called LocPro is presented for predicting protein subcellular localization.Specifically,LocPro is unique in(a)combining protein representations from the pre-trained large language model(LLM)ESM2 and the expert-driven tool PROFEAT,(b)implementing a hybrid deep neural network architecture that integrates convolutional neural network(CNN),fully connected(FC)layer,and bidirectional long short-term memory(BiLSTM)blocks,and(c)developing a multi-label framework for predicting protein subcellular localization at multiple granularity levels.Additionally,a dataset was curated and divided using a homology-based strategy for training and validation.Compar-ative analyses show that LocPro outperforms existing methods in sequence-based multi-label protein subcellular localization prediction.The practical utility of this framework is further demonstrated through case studies on drug target subcellular localization.All in all,LocPro serves as a valuable complement to existing protein localization prediction tools.The web server is freely accessible at https://idrblab.org/LocPro/.
2.Exploration on Applying Shengyang Yiwei Decoction in Treating Summer Endogenous Fever Based on Yin-Fire Theory
Ruichen SHI ; Wanyi XIE ; Shunli ZHENG ; Chunyan XIAO ; Haibin WU
Journal of Guangzhou University of Traditional Chinese Medicine 2025;42(9):2337-2341
The prevalence of summer endogenous fever is closely related to the climate of summer.Based on Li Dongyuan's yin-fire theory,this article proposed that summer-heat,irregular diet,excessive consumption of cold foods,poor living habits,and summer damp-heat internal invasion damaging the spleen can all lead to the generation of yin-fire,thereby causing endogenous fever.The core pathogenesis of summer endogenous fever lies in spleen deficiency with yang collapse,which results into the blockage of qi movement and the production of yin-fire.The yin-fire persists throughout the entire course of the disease.Treatment of summer endogenous fever should focus on eliminating yin-fire,primarily by addressing the spleen via boosting qi and raising yang to restore the spleen's ascending and stomach's descending functions,thereby dispersing yin-fire.Clearing heat and resolving dampness can purge yin-fire and then the spleen qi's circulation is restored.By analyzing the pathological changes of dampness accumulation into phlegm,fire-heat damaging yin and liver stagnation with kidney deficiency,the disease progression can be predicted.Correspondingly,comprehensive therapy of resolving phlegm,nourishing yin,soothing liver,and tonifying kidney can be employed to prevent further deterioration.Based on Li Dongyuan's yin-fire theory,Shengyang Yiwei Decoction(mainly composed of Astragali Radix,Pinelliae Rhizoma,Ginseng Radix et Rhizoma,Glycyrrhizae Radix et Rhizoma Praeparata cum Melle,Angelicae Pubescentis Radix,Saposhnikoviae Radix,Paeoniae Radix Alba,Notopterygii Rhizoma et Radix,Citri Reticulatae Pericarpium,Poria,Bupleuri Radix,Alismatis Rhizoma,Atractylodis Macrocephalae Rhizoma,and Coptidis Rhizoma)can be used as a fundamental prescription to treat summer endogenous fever caused by yin-fire,with modifications tailored to specific clinical presentations.This theoretical exploration may provide a reference for the clinical management of summer endogenous fever.
3.Artificial intelligence in traditional Chinese medicine: from systems biological mechanism discovery, real-world clinical evidence inference to personalized clinical decision support.
Dengying YAN ; Qiguang ZHENG ; Kai CHANG ; Rui HUA ; Yiming LIU ; Jingyan XUE ; Zixin SHU ; Yunhui HU ; Pengcheng YANG ; Yu WEI ; Jidong LANG ; Haibin YU ; Xiaodong LI ; Runshun ZHANG ; Wenjia WANG ; Baoyan LIU ; Xuezhong ZHOU
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1310-1328
Traditional Chinese medicine (TCM) represents a paradigmatic approach to personalized medicine, developed through the systematic accumulation and refinement of clinical empirical data over more than 2000 years, and now encompasses large-scale electronic medical records (EMR) and experimental molecular data. Artificial intelligence (AI) has demonstrated its utility in medicine through the development of various expert systems (e.g., MYCIN) since the 1970s. With the emergence of deep learning and large language models (LLMs), AI's potential in medicine shows considerable promise. Consequently, the integration of AI and TCM from both clinical and scientific perspectives presents a fundamental and promising research direction. This survey provides an insightful overview of TCM AI research, summarizing related research tasks from three perspectives: systems-level biological mechanism elucidation, real-world clinical evidence inference, and personalized clinical decision support. The review highlights representative AI methodologies alongside their applications in both TCM scientific inquiry and clinical practice. To critically assess the current state of the field, this work identifies major challenges and opportunities that constrain the development of robust research capabilities-particularly in the mechanistic understanding of TCM syndromes and herbal formulations, novel drug discovery, and the delivery of high-quality, patient-centered clinical care. The findings underscore that future advancements in AI-driven TCM research will rely on the development of high-quality, large-scale data repositories; the construction of comprehensive and domain-specific knowledge graphs (KGs); deeper insights into the biological mechanisms underpinning clinical efficacy; rigorous causal inference frameworks; and intelligent, personalized decision support systems.
Medicine, Chinese Traditional/methods*
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Artificial Intelligence
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Humans
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Precision Medicine
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Decision Support Systems, Clinical
4.LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research.
Yintao ZHANG ; Lingyan ZHENG ; Nanxin YOU ; Wei HU ; Wanghao JIANG ; Mingkun LU ; Hangwei XU ; Haibin DAI ; Tingting FU ; Ying ZHOU
Journal of Pharmaceutical Analysis 2025;15(8):101255-101255
Drug development encompasses multiple processes, wherein protein subcellular localization is essential. It promotes target identification, treatment development, and the design of drug delivery systems. In this research, a deep learning framework called LocPro is presented for predicting protein subcellular localization. Specifically, LocPro is unique in (a) combining protein representations from the pre-trained large language model (LLM) ESM2 and the expert-driven tool PROFEAT, (b) implementing a hybrid deep neural network architecture that integrates convolutional neural network (CNN), fully connected (FC) layer, and bidirectional long short-term memory (BiLSTM) blocks, and (c) developing a multi-label framework for predicting protein subcellular localization at multiple granularity levels. Additionally, a dataset was curated and divided using a homology-based strategy for training and validation. Comparative analyses show that LocPro outperforms existing methods in sequence-based multi-label protein subcellular localization prediction. The practical utility of this framework is further demonstrated through case studies on drug target subcellular localization. All in all, LocPro serves as a valuable complement to existing protein localization prediction tools. The web server is freely accessible at https://idrblab.org/LocPro/.
5.Treatment of Chronic Urticaria with Traditional Chinese Medicine by Regulating PI3K/Akt Molecular Pathway: A Review
Kaifeng JI ; Haibin CAI ; Zhouwei WU ; Yuting ZHENG ; Xiaoqian XU ; Yu SONG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(17):292-298
Chronic urticaria (CU) is a common skin disease worldwide, and its incidence is increasing year by year in various regions. Clinical manifestations such as severe itching can affect normal work, sleep, and daily life and increase the negative psychological burden caused by stress, anxiety, and depression. Mast cell activation and degranulation induced by immunoglobulin(Ig)E hypersensitivity is one of the core pathogenic mechanisms of CU, and there is no cure. Antihistamines such as cetirizine and loratadine are preferred for the clinical treatment of CU. Although they can effectively improve clinical manifestations such as itchiness, long-term application can increase the risk of adverse reactions and drug resistance. The phosphatidylinositol kinase/serine-threonine protein kinase B(PI3K/Akt) signaling pathway, as a classical signaling pathway regulated by phosphatidylinositol and tyrosine kinase receptor (RTK), is a key target regulating the production and release of cytokines in macrophages and affecting the migration of leukocytes and the activation of mast cells and inflammation, and it can be involved in a variety of metabolic processes, such as mast cell activation and degranulation induced by IgE hypersensitivity and abnormal activation of the complement system so that the PI3K/Akt molecular pathway could be an important target for the future eradication of CU. However, the mechanism and potential role of the PI3K/Akt signaling pathway in the treatment of CU are less reported in China. Now, this paper reviewed the molecular mechanism of PI3K/Akt signaling pathway regulation in the treatment of CU and provided corroborative evidence and therapeutic strategy choices for the treatment of CU with traditional Chinese medicine (TCM) from the perspectives of molecular regulation and network pharmacology analysis.
6.Exploring the Mechanism of Anti-Colorectal Cancer Action of Fushao Diqin Decoction Based on the Nrf2/SLC7A11/GPX4 Signaling Pathway
Mingyue ZHENG ; Hongguang ZHOU ; Yupei ZHUANG ; Hongli ZHOU ; Yuwei LIANG ; Haibin CHEN
Journal of Nanjing University of Traditional Chinese Medicine 2024;40(5):457-468
OBJECTIVE To explore the mechanism of action of Fushao Diqin Decoction in the treatment of colorectal cancer.METHODS In vitro cell experiments were conducted using Fushao Diqin Decoction to treat colorectal cancer CT-26 cells,and the cell proliferation and migration abilities were detected.Flow cytometry was used to detect the levels of reactive oxygen species(ROS)in colorectal cancer CT-26 cells,as well as the levels of iron ions(Fe2+),malondialdehyde(MDA),and the activity of su-peroxide dismutase(SOD).PCR Array and Western blot methods were used to analyze and verify the differential gene expression of ferroptosis.Balb/c mice were randomly divided into a blank control group,a model group,an oxaliplatin group(1.5 mg·kg-1·d-1),a low-dose group of Fushao Diqin Decoction(4.49 g·kg-1·d-1),a medium dose group of Fushao Diqin Decoction(8.97 g·kg-1·d-1),and a high-dose group of Fushao Diqin Decoction(17.94 g·kg-1·d-1)for in vivo animal experi-ments.The effects of Fushao Diqin Decoction on Fe2+,ROS,MDA levels,SOD activity,and Nrf2,Keap1,SLC7A11 and GPX4 ex-pression levels in mouse tumor tissues were tested.RESULTS In vitro cell experiments showed that compared with the blank control group,Fushao Diqin Decoction significantly inhibited the proliferation and migration of colorectal cancer CT-26 cells in a dose-de-pendent manner.Fushao Diqin Decoction could increase the Fe2+content(P<0.05)and ROS level(P<0.01)in colorectal cancer CT-26 cells,increase the MDA level in CT-26 cells of colorectal cancer(P<0.01)and significantly reduce SOD activity(P<0.01).Iron death PCR array analysis found that compared with the blank control group,after intervention with Fushao Diqin Decoc-tion,the expression of genes GPX4 and SLC7A11 was significantly downregulated,while the expression of GSTA1,HMOX1,Ca9,Chac1,Keap1,Sqstm1,NOX1,FTH1,Tfr1,SAT2,Pparg,and Hamp was significantly upregulated.Western blot analysis revealed that after intervention with Fushao Diqin Decoction,the expression of Keap1 protein was upregulated(P<0.01),while the expression of Nrf2,SLC7A11,and GPX4 proteins was downregulated(P<0.01)in colorectal cancer CT-26 cells.The results of in vivo animal experiments showed that Fushao Diqin Decoction significantly inhibited the growth of subcutaneous transplanted tumors in mice(P<0.05),increased the degree of tumor tissue necrosis,and levels of Fe2+,ROS,and MDA(P<0.05,P<0.01),decreased SOD ac-tivity(P<0.01)and upregulated Keap1 protein expression(P<0.01),while downregulated Nrf2,SLC7A11,and GPX4 protein ex-pression(P<0.01).CONCLUSION Fushao Diqin Decoction has an anti-colorectal cancer effect and may promote ferroptosis in colorectal cancer cells by inhibiting the Nrf2/SLC7A11/GPX4 signaling pathway to exert its anti-colorectal cancer effect.
7.Effect of salidroside on bone loss in rats with obstructive sleep apnea syndrome by regulating the OPG/RANKL pathway
Haibin MA ; Zhaoxu YAO ; Chuanjun WU ; Lin LIU ; Kaili SUN ; Hui GONG ; Wenyan ZHENG
Chinese Archives of Otolaryngology-Head and Neck Surgery 2024;31(8):526-530,533
OBJECTIVE To investigate the effect of salidroside (Sal) on bone loss in obstructive sleep apnea syndrome(OSAS) rats by regulating the osteoprotegerin(OPG)/receptor activator of nuclear factor kappa-B ligand(RANKL) pathway. METHODS Rats were randomly divided into(12 rats/group) control group,OSAS group,Sal-L,Sal-M,and Sal-H groups(17.5,35,70 mg/kg). Except for the control group,all other groups were used to replicate the OSAS rat model through hypoxia and reoxygenation cycles. Bone density meters,three-point bending experiments,and Micro CT were applied to measure the bone density,biomechanics,and microstructural changes of the femur in rats. ELISA method was applied to detect serum levels of osteocalcin(BGP),alkaline phosphatase(ALP),and cross-linked carboxy-terminal telopeptide of type Ⅰ collagen(CTX-I). RT-PCR was applied to detect OPG and RANKL mRNA levels in the femur. Western blotting was applied to detect the expression of OPG/RANKL pathway proteins in the femur. RESULTS Compared with the control group,the bone density,maximum intensity,maximum load,trabecular bone volume fraction(Tb.BV/TV),trabecular number(Tb.N),trabecular thickness(Tb.Th),BGP,ALP,OPG mRNA and protein expression,OPG/RANKL ratio of rats in the OSAS group were decreased,the mRNA and protein expression of CTX-I and RANKL were increased(P<0.05). Compared with the OSAS group,the bone density,maximum intensity,maximum load,Tb.BV/TV,Tb.N,Tb.Th,BGP,ALP,OPG mRNA and protein expression,OPG/RANKL ratio of rats in the Sal-L,Sal-M,and Sal-H groups were increased sequentially,the mRNA and protein expression of CTX-I and RANKL were decreased sequentially,the above changes were most great in the Sal-H group(P<0.05). CONCLUSION Salidroside promotes bone formation and inhibits bone resorption by increasing OPG expression and decreasing RANKL expression,thereby reducing bone loss in OSAS rats.
8.Robot-assisted laparoscopic surgery for urachal remnant anomalies in children
Wenhai LI ; Haibin WANG ; Kai ZHENG ; Huan LI ; Wu WANG ; Jun YANG ; Hongqiang BIAN
Journal of Clinical Surgery 2024;32(12):1305-1308
Objective To explore the experience of robot-assisted laparoscopic surgery in the treatment of residual malformation of urachus with children.Methods The clinical date of 10 children with urachal remnants malformation treated by Da Vinci Robot Assisted Laparoscopic Surgery in Wuhan Children's Hospital from July 2021 to July 2023 were retrospectively analyzed.Robot-assisted laparoscopic surgery was used to analyze the intraoperative situation,postoperative complications,surgical effect and pathological results.Results All 10 cases were treated by Da Vinci Robot Assisted Laparoscopic Surgery without Laparotomy and complete excision,while maintain the umbilical integrality,8 cases with symptoms were resected after preoperative imaging diagnosis,1 case was asymptomatic and resected due to continuous enlargement of the cyst,and 1 case was found to be resected during other operations.The average operation time was(140.70±17.66)min,the median blood loss was 7.5(4.5,27.5)ml,the postoperative urethral catheterization was(6.2±1.26)d,the hospital stay was(9.9±0.94)d and the average cost was(46378.92±2777.13)yuan.All the urachal remnants were confirmed by Pathology as 9 cases of urachal cysts and 1 case of urachal fistula.Conclusion Robot-assisted laparoscopic surgery is safe and effective in the treatment of urachal remnants malformation in children,the surgical procedure for resected repair of the anterior abdominal wall has unique advantages.
9.Robot-assisted laparoscopic surgery for urachal remnant anomalies in children
Wenhai LI ; Haibin WANG ; Kai ZHENG ; Huan LI ; Wu WANG ; Jun YANG ; Hongqiang BIAN
Journal of Clinical Surgery 2024;32(12):1305-1308
Objective To explore the experience of robot-assisted laparoscopic surgery in the treatment of residual malformation of urachus with children.Methods The clinical date of 10 children with urachal remnants malformation treated by Da Vinci Robot Assisted Laparoscopic Surgery in Wuhan Children's Hospital from July 2021 to July 2023 were retrospectively analyzed.Robot-assisted laparoscopic surgery was used to analyze the intraoperative situation,postoperative complications,surgical effect and pathological results.Results All 10 cases were treated by Da Vinci Robot Assisted Laparoscopic Surgery without Laparotomy and complete excision,while maintain the umbilical integrality,8 cases with symptoms were resected after preoperative imaging diagnosis,1 case was asymptomatic and resected due to continuous enlargement of the cyst,and 1 case was found to be resected during other operations.The average operation time was(140.70±17.66)min,the median blood loss was 7.5(4.5,27.5)ml,the postoperative urethral catheterization was(6.2±1.26)d,the hospital stay was(9.9±0.94)d and the average cost was(46378.92±2777.13)yuan.All the urachal remnants were confirmed by Pathology as 9 cases of urachal cysts and 1 case of urachal fistula.Conclusion Robot-assisted laparoscopic surgery is safe and effective in the treatment of urachal remnants malformation in children,the surgical procedure for resected repair of the anterior abdominal wall has unique advantages.
10.Microbial production of S-adenosyl-l-methionine: a review.
Meijing LI ; Zheyan MI ; Jinhao WANG ; Zhongce HU ; Haibin QIN ; Yuanshan WANG ; Yuguo ZHENG
Chinese Journal of Biotechnology 2023;39(6):2248-2264
S-adenosyl-l-methionine (SAM) is ubiquitous in living organisms and plays important roles in transmethylation, transsulfuration and transamination in organisms. Due to its important physiological functions, production of SAM has attracted increasing attentions. Currently, researches on SAM production mainly focus on microbial fermentation, which is more cost-effective than that of the chemical synthesis and the enzyme catalysis, thus easier to achieve commercial production. With the rapid growth in SAM demand, interests in improving SAM production by developing SAM hyper-producing microorganisms aroused. The main strategies for improving SAM productivity of microorganisms include conventional breeding and metabolic engineering. This review summarizes the recent research progress in improving microbial SAM productivity to facilitate further improving SAM productivity. The bottlenecks in SAM biosynthesis and the solutions were also addressed.
S-Adenosylmethionine/metabolism*
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Plant Breeding
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Fermentation
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Metabolic Engineering

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