1.druglikeFilter 1.0:An AI powered filter for collectively measuring the drug-likeness of compounds
Minjie MOU ; Yintao ZHANG ; Yuntao QIAN ; Zhimeng ZHOU ; Yang LIAO ; Tianle NIU ; Wei HU ; Yuanhao CHEN ; Ruoyu JIANG ; Hongping ZHAO ; Haibin DAI ; Yang ZHANG ; Tingting FU
Journal of Pharmaceutical Analysis 2025;15(6):1370-1377
Advancements in artificial intelligence(AI)and emerging technologies are rapidly expanding the exploration of chemical space,facilitating innovative drug discovery.However,the transformation of novel compounds into safe and effective drugs remains a lengthy,high-risk,and costly process.Comprehensive early-stage evaluation is essential for reducing costs and improving the success rate of drug development.Despite this need,no comprehensive tool currently supports systematic evaluation and efficient screening.Here,we present druglikeFilter,a deep learning-based framework designed to assess drug-likeness across four critical dimensions:1)physicochemical rule evaluated by systematic determination,2)toxicity alert investigated from multiple perspectives,3)binding affinity measured by dual-path analysis,and 4)compound synthesizability assessed by retro-route prediction.By enabling automated,multidimensional filtering of compound libraries,druglikeFilter not only streamlines the drug development process but also plays a crucial role in advancing research efforts towards viable drug candidates,which can be freely accessed at https://idrblab.org/drugfilter/.
2.Combined cricopharyngeal myotomy and autologous fat injection laryngoplasty: an effective surgery for dysphagia following glossopharyngeal and vagal nerve injury
Yanyan NIU ; Wei GU ; Xiaofeng JIN ; Tingting CUI ; Hong HUO ; Jian WANG
Chinese Journal of Otorhinolaryngology Head and Neck Surgery 2025;60(11):1357-1362
Objective:To evaluate the efficacy of combined cricopharyngeal myotomy (CPM) and autologous fat injection laryngoplasty (AFIL) in the management of dysphagia secondary to glossopharyngeal and vagal nerve injury.Methods:This retrospective cohort study collected the clinical data of 18 patients with persistent dysphagia due to glossopharyngeal and vagus nerve injuries, who underwent concurrent cricopharyngeal myotomy (CPM) and autologous fat injection laryngoplasty (AFIL) at the Department of Otolaryngology, Peking Union Medical College Hospital, from January 2017 to December 2024. Pre-and postoperative assessments included electronic flexible laryngoscope, the Chinese version of Swallow Quality-of-Life Questionnaire (CSWAL-QOL), videofluoroscopic swallowing study (VFSS), body weight changes, and nasogastric tube (NGT) removal status with routine follow-up. The comparison of swallowing function before and after surgery was conducted using paired samples t-test and χ2 test. Results:The study cohort comprised 10 male and 8 female patients, with ages ranging from 33 to 70 years (mean±SD: 53.8±10.5). All surgical procedures were completed successfully without complications. During the 6-to 24-month follow-up period, 10 of the 13 patients who were initially nasogastric tube-dependent achieved successful decannulation. Compared with preoperative values, postoperative measurements demonstrated statistically significant improvements across all parameters: mean body weight increased from (56.95±9.14) kg to (59.22±8.72) kg ( t=3.689 , P<0.01), CSWAL-QOL scores improved from 91.89±17.81 to 130.83±25.42 ( t=6.921 , P<0.01), while, both VFSS scales showed marked reductions (VFSS-SWAL: 6.78±1.40 to 3.39±1.61, t=-8.001, P<0.01; PAS: 6.56±1.15 to 2.94±1.26, t=-10.114, P<0.01). Conclusions:Combined CPM and AFIL represents an effective surgical approach for dysphagia following glossopharyngeal and vagal nerve injury, thereby demonstrating significant improvements in both swallowing function and quality of life.
3.Anthocyanins from Lycium ruthenicum Murr combined with human adipose-derived pericytes/perivascular cells support proliferation of umbilical cord blood hematopoietic stem/progenitor cells
Yamei SHEN ; Yunxia NIU ; Tingting YANG ; Jie MA ; Daihong HU ; Bo ZHENG
Chinese Journal of Tissue Engineering Research 2025;29(1):58-64
BACKGROUND:Anthocyanin is one of the most important active components in Lycium ruthenicum Murr,which has antioxidant and immunomodulatory effects.CD146+human adipose-derived pericytes/perivascular cells(CD146+hAD-PCs)are the progenitors of bone marrow mesenchymal stem cells,which can promote the proliferation and differentiation of hematopoietic stem/progenitor cells in vitro.The support effect of anthocyanin in combination with CD146+hAD-PCs on umbilical cord blood hematopoietic stem/progenitor cells remains to be studied. OBJECTIVE:To investigate the supporting effect of anthocyanins in Lycium ruthenicum Murr(ALRM)combined with CD146+hAD-PCs on umbilical cord blood CD34+hematopoietic stem/progenitor cells(UCB CD34+HSPCs)in vitro. METHODS:The CCK-8 assay was used to detect the effect of different concentrations(0,200,400,600,800,1 000 mg/L)of ALRM on the proliferation of CD146+hAD-PCs.Flow cytometry was used to detect the effect of ALRM on the cell cycle of CD146+hAD-PCs.The co-culture experiments were divided into blank group,ALRM group,CD146+hAD-PCs group,and ALRM+CD146+hAD-PCs group to analyze the in vitro supporting effect of ALRM combined with CD146+hAD-PCs on UCB CD34+HSPCs.The number of expanded cells and the number of colony-forming units were compared at 1,2,and 4 weeks of co-culture.The immunophenotype of cells was detected by flow cytometry.The level of cytokines was detected by enzyme-linked immunosorbent assay. RESULTS AND CONCLUSION:(1)The cell viability of CD146+hAD-PCs was highest at an ALRM concentration of 200 mg/L,the proportion of G0/G1 phase cells decreased and the proportion of S and G2/M phase cells increased in CD146+hAD-PCs(P<0.01).(2)The change in number of UCB CD34+HSPCs cells in the ALRM+CD146+hAD-PCs group was higher than that in the ALRM group at 1,2,and 4 weeks of co-culture(all P<0.05),and higher than that in CD146+hAD-PCs group at 2 and 4 weeks of co-culture(all P<0.05).The number of cells in the ALRM group and blank group decreased gradually with the extension of co-culture time.(3)Colony forming capacity and immunophenotype analysis:The number of colony-forming units in the ALRM+CD146+hAD-PCs group was higher than that in the CD146+hAD-PCs group and ALRM group at 1 and 2 weeks of co-culture(P<0.05).The proportion of CD45+and CD34+CD33-cells in the ALRM+CD146+hAD-PCs group was higher than that in the CD146+hAD-PCs group at 1 and 2 weeks of co-culture(all P<0.01).(4)Changes in cytokines:Interleukin-2 level in the ALRM+CD146+hAD-PCs group was higher than that in the ALRM and CD146+hAD-PCs groups(P<0.05).The interleukin-3 content of the ALRM+CD146+hAD-PCs group was higher than that of the CD146+hAD-PCs group at 2 and 4 weeks(P<0.05).The expression level of granulocyte colony-stimulating factor in the ALRM+CD146+hAD-PCs group was higher than that in the CD146+hAD-PCs group at 1 week,and higher than that in the ALRM group and CD146+hAD-PCs group at 2 weeks(P<0.01).Interferon-γ content in the ALRM group and ALRM+CD146+hAD-PCs group was lower than that in the CD146+hAD-PCs group at 1,2,and 4 weeks of co-culture(P<0.01).(5)Due to the absence of stromal cells in the blank group,UCB CD34+HSPCs could not be counted after 1 week of co-culture and were not subjected to immunophenotyping,colony analysis,or cytokine assays.(6)In summary,ALRM can promote the expansion of UCB CD34+HSPCs in vitro by promoting CD146+hAD-PCs proliferation and cell cycle transformation,which is of great value in hematopoietic stem cell transplantation.
5.Identification of natural product-based drug combination (NPDC) using artificial intelligence.
Tianle NIU ; Yimiao ZHU ; Minjie MOU ; Tingting FU ; Hao YANG ; Huaicheng SUN ; Yuxuan LIU ; Feng ZHU ; Yang ZHANG ; Yanxing LIU
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1377-1390
Natural product-based drug combinations (NPDCs) present distinctive advantages in treating complex diseases. While high-throughput screening (HTS) and conventional computational methods have partially accelerated synergistic drug combination discovery, their applications remain constrained by experimental data fragmentation, high costs, and extensive combinatorial space. Recent developments in artificial intelligence (AI), encompassing traditional machine learning and deep learning algorithms, have been extensively applied in NPDC identification. Through the integration of multi-source heterogeneous data and autonomous feature extraction, prediction accuracy has markedly improved, offering a robust technical approach for novel NPDC discovery. This review comprehensively examines recent advances in AI-driven NPDC prediction, presents relevant data resources and algorithmic frameworks, and evaluates current limitations and future prospects. AI methodologies are anticipated to substantially expedite NPDC discovery and inform experimental validation.
Artificial Intelligence
;
Biological Products/chemistry*
;
Humans
;
Drug Combinations
;
Drug Discovery/methods*
;
Machine Learning
;
Algorithms
6.Research advancements in molecular glues derived from natural product scaffolds: Chemistry, targets, and molecular mechanisms.
Lina YIN ; Tingting NIU ; Ling LI ; Wei YU ; Bo HAN ; Asma REHMAN ; Kewu ZENG
Chinese Herbal Medicines 2025;17(2):235-245
The mechanism of action of traditional Chinese medicine (TCM) remains unclear. Historically, research on TCM has mainly focused on exploring the mechanisms of active components acting on single targets. However, it is insufficient to explain the complex mechanisms by which these active components in TCM treat diseases. In recent years, the emergence of molecular glues (MGs) theory has provided new strategies to address this issue. MGs are small molecules that can promote interactions between proteins at their interface. The characteristic of MGs is to establish connections between diverse protein structures, thereby enabling a chemically-mediated proximity effect that triggers a wide spectrum of biological functions. Natural products are the result of billions of years of evolutionary processes in the natural environment. Thus, the extensive structural diversity of natural products renders them a rich source of MGs, including polyketides, terpenoids, steroids, lignans, organic acids, alkaloids and other classes. Currently, several well-known natural MGs, including the immunosuppressants cyclosporin A (CsA) and tacrolimus (FK506), as well as the anticancer agent taxol, have been incorporated into clinical practice. Meanwhile, the advancement of new technologies is propelling the discovery of novel MGs from natural products. Thus, we primarily summarize a growing variety of MGs from natural origins reported in recent years and categorize them based on the chemical structural types. Moreover, the main sources of TCM are natural products. The discovery of natural MGs promises to provide a new perspective for the elucidation of the molecular mechanism behind the efficiency of TCM. In summary, this review aims to provide insights from the perspective of natural products that could potentially influence TCM and modern drug development.
7.Meta-synthesis of qualitative studies on the experience of bowel symptoms in patients undergoing sphincter-preserving surgery for rectal cancer
Tingting LIU ; Qiaohong NIU ; Xueping JIAO ; Jiawei WEI ; Shaoming DUAN ; Congli HU ; Rui SU
Chinese Journal of Nursing 2025;60(5):603-610
Objective To systematically evaluate and synthesize the experience and coping process of bowel symptoms in patients after sphincter-preserving surgery for rectal cancer,and to provide the evidence for the subsequent development of bowel symptom management strategies.Methods A comprehensive search was conducted across the Pubmed,Cochrane Library,CINAHL,Embase,Web of Science,CNKI,Wanfang Database,VIP Database and CBM Database for qualitative studies on the experience of bowel symptoms in post-sphincter-preserving surgery patients with rectal cancer.The search period was from database inception to October 2024.The quality of the included literature was assessed according to the Australian Joanna Briggs Institute Center for Evidence-Based Health Care Quality Assessment Criteria for Qualitative Research,and the results were synthesized through the aggregative integration method.Results 14 studies were included,yielding 52 research findings,which were grouped into 10 subcategories and further synthesized into 4 results:the physical and psychological experiences of patients with bowel symptoms;the impact of bowel symptoms on patients'daily lives;coping styles for bowel symptoms in patients;facilitators of patients bowel symptom coping.Conclusion Bowel symptoms have significant negative impacts on the lives of patients following sphincter-preserving surgery for rectal cancer,and healthcare professionals should address these patients'needs by developing effective symptom management strategies and supporting patients in enhancing self-management abilities to improve quality of life.
8.Application value analysis of X-ray digital tomosynthesis technique in urinary calculi
Cuifang YAN ; Xiaoyong DING ; Tingting NIU ; Tao NIU
Journal of Practical Radiology 2025;41(1):143-146
Objective To explore the diagnostic efficacy of digital tomosynthesis(DTS)and kidney-ureter-bladder(KUB)X-ray plain filmin for urinary calculi.Methods A total of 140 patients with urinary calculi were randomly divided into observation group and control group,with 70 cases in each.The observation group underwent bowel preparation(BP)before DTS,while the control group did not.KUB,DTS and unenhanced multidetector computed tomography(UMDCT)were performed in both groups,and the three images were assessed and compared by three physicians.Results The X-ray plain filmin detection rate of stones≤5 mm in the observation group was significantly higher than that in the control group(85.46%vs 33.33%,χ2=30.75,P<0.01),and the detec-tion rate of stones>5 mm in the observation group was also significantly higher than that in the control group(100%vs 58.44%,χ2=43.12,P<0.01).The DTS detection rate of stones≤5 mm in the observation group was significantly higher than that in the control group(90.91%vs 55.56%,χ2=17.44,P<0.01),but there was no significant difference in the detection rate of stones>5 mm between the two groups(100%vs 96.10%,P>0.05).The effective dose(ED)differed significantly among X-ray plain filmin,DTS and UMDCT(P<0.001).Except for DTS,there were significant differences in imaging sensitivity between the two groups(P<0.05).Conclusion DTS is an appropriate examination method for patients with urinary calculi,which can improve the diag-nostic rate of urinary calculi and reduce the radiation dose for patients.The detection rate of stones≤5 mm in DTS is affected by BP,but the detection rate of stones>5 mm is unaffected by BP.The diagnostic sensitivity of DTS is unaffected by BP.
9.druglikeFilter 1.0: An AI powered filter for collectively measuring the drug-likeness of compounds.
Minjie MOU ; Yintao ZHANG ; Yuntao QIAN ; Zhimeng ZHOU ; Yang LIAO ; Tianle NIU ; Wei HU ; Yuanhao CHEN ; Ruoyu JIANG ; Hongping ZHAO ; Haibin DAI ; Yang ZHANG ; Tingting FU
Journal of Pharmaceutical Analysis 2025;15(6):101298-101298
Advancements in artificial intelligence (AI) and emerging technologies are rapidly expanding the exploration of chemical space, facilitating innovative drug discovery. However, the transformation of novel compounds into safe and effective drugs remains a lengthy, high-risk, and costly process. Comprehensive early-stage evaluation is essential for reducing costs and improving the success rate of drug development. Despite this need, no comprehensive tool currently supports systematic evaluation and efficient screening. Here, we present druglikeFilter, a deep learning-based framework designed to assess drug-likeness across four critical dimensions: 1) physicochemical rule evaluated by systematic determination, 2) toxicity alert investigated from multiple perspectives, 3) binding affinity measured by dual-path analysis, and 4) compound synthesizability assessed by retro-route prediction. By enabling automated, multidimensional filtering of compound libraries, druglikeFilter not only streamlines the drug development process but also plays a crucial role in advancing research efforts towards viable drug candidates, which can be freely accessed at https://idrblab.org/drugfilter/.
10.Genome sequencing and biological characteristics analysis of a Streptococcus dys-galactiae from yak
Wenjing CHENG ; Tian NIU ; Shuai YANG ; Tingting LIU ; Hongcai MA ; Jiangyong ZENG ; Lihong ZHANG ; Junjie HU
Chinese Journal of Veterinary Science 2025;45(7):1426-1436
This study aims to understand the biological characteristics of Streptococcus dysgalacti-ae of yak origin.Bacterial isolation and identification,drug susceptibility test,virulence gene test and pathogenicity test were carried out on milk samples of yaks from Naqu City to evaluate the bi-ological characteristics of the isolated strains.Meanwhile,molecular biological information such as virulence factors and drug resistance genes were analyzed by whole genome sequencing,and viru-lence genes were verified by PCR.The results showed that a strain of Streptococcus dysgalactiae was isolated from the milk of yak,and its colony morphology was pinpoint size,smooth edge and milky white.This strain is sensitive to many antibiotics(penicillin G,cephalosporin,ciprofloxacin,tetracycline,erythromycin,etc.).Virulence gene test results showed that the strain carries six key virulence genes(cyl,eno,scpB,bca,bac and napr),which may be closely related to its pathoge-nicity.In the pathogenicity test,the mice were listless and less active after infection,but no death occurred during the observation period.The pathological changes of spleen,kidney,liver and lung tissue were found,suggesting that the strain had certain pathogenic potential but not high lethali-ty.Whole genome sequencing data showed that the gene length of this strain was 4 079 280 bp,the GC content was 39.41%,3 964 coding genes were predicted,604 of which were annotated as viru-lence factors,and another 28 gene mutations may enhance its pathogenic ability.Through annota-tion of CARD database,two Pat A resistance genes and two lmrp resistance genes were found,re-vealing their potential resistance mechanism.Through whole genome sequencing technology and bioinformatics analysis method,this study revealed the genomic characteristics,drug resistance and pathogenicity mechanism of Streptococcus dysgalactiae of yak origin.The findings provide impor-tant scientific evidence for further exploration of the pathogenicity,drug resistance mechanisms,and molecular evolution of yak-derived Streptococcus agalactiae.

Result Analysis
Print
Save
E-mail