1.3D-EDiffMG: 3D equivariant diffusion-driven molecular generation to accelerate drug discovery.
Chao XU ; Runduo LIU ; Yufen YAO ; Wanyi HUANG ; Zhe LI ; Hai-Bin LUO
Journal of Pharmaceutical Analysis 2025;15(6):101257-101257
Structural optimization of lead compounds is a crucial step in drug discovery. One optimization strategy is to modify the molecular structure of a scaffold to improve both its biological activities and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. One of the deep molecular generative model approaches preserves the scaffold while generating drug-like molecules, thereby accelerating the molecular optimization process. Deep molecular diffusion generative models simulate a gradual process that creates novel, chemically feasible molecules from noise. However, the existing models lack direct interatomic constraint features and struggle with capturing long-range dependencies in macromolecules, leading to challenges in modifying the scaffold-based molecular structures, and creates limitations in the stability and diversity of the generated molecules. To address these challenges, we propose a deep molecular diffusion generative model, the three-dimensional (3D) equivariant diffusion-driven molecular generation (3D-EDiffMG) model. The dual strong and weak atomic interaction force-based long-range dependency capturing equivariant encoder (dual-SWLEE) is introduced to encode both the bonding and non-bonding information based on strong and weak atomic interactions. Additionally, a gate multilayer perceptron (gMLP) block with tiny attention is incorporated to explicitly model complex long-sequence feature interactions and long-range dependencies. The experimental results show that 3D-EDiffMG effectively generates unique, novel, stable, and diverse drug-like molecules, highlighting its potential for lead optimization and accelerating drug discovery.
2.Clinical features and genetic analysis of five children with epilepsies due to variants of SCN8A gene
Xin ZHANG ; Shiyan QIU ; Li YANG ; Yufen LI ; Na XU ; Xixi YU
Chinese Journal of Medical Genetics 2024;41(2):174-180
Objective:To explore the clinical and genetic characteristics of five children with epilepsies due to variants of SCN8A gene. Methods:Clinical data of five children (four males and one female) admitted to Linyi People′s Hospital due to hereditary epilepsies between August 2015 and August 2022 were collected. Whole exome sequencing was carried out for these children, and candidate variants were verified by Sanger sequencing.Results:All of the five children were found to harbor variants of the SCN8A gene. Case 1, who had benign familial infantile epilepsy, inherited a known pathogenic c. 4840A>G variant from his father with similar symptoms. Cases 2 to 4 had presented with intermediate epilepsy. Among these, case 2 has harbored a de novo c. 3967G>A variant which was rated as pathogenic (PS1+ PS2+ PM1+ PM2_Supporting+ PP3) based on the guidelines from the American College of Medical Genetics and Genomics. Cases 3 and 4 were found to respectively harbor a de novo c. 415A>T and a c. 4697C>T variant, which were both rated as likely pathogenic (PS2+ PM1+ PM2_Supporting+ PP3). Case 5, who had early-onset infantile epileptic encephalopathy transformed into Lennox Gastaut-like syndrome, has harbored a de novo c. 5615G>A variant, which was known to be pathogenic. The children had their age of onset ranging from 2 to 14 months, and all had focal seizures and generalized tonic clonic seizures. Four children (cases 1, 2, 3 and 5) had cluster seizures, four (cases 1 to 4) had become seizure-free after single or dual treatment and showed normal growth and development, whilst case 5 was drug-resistant and showed severe developmental retardation. Conclusion:The five children had new features such as cluster seizures, occasional benign seizures in adulthood, and intermediate epilepsy which are prone to relapse after discontinuation of medication, which may be attributed to the pathogenic variants of the SCN8A gene.
3.Genetic analysis of a family with epilepsy accompanied by developmental delay and brain deformity due to a de novo variant of TUBB2A gene
Juan ZHAO ; Na XU ; Yufen LI ; Li YANG ; Shiyan QIU ; Liping ZHU ; Xuemei SUN
Chinese Journal of Medical Genetics 2024;41(2):187-192
Objective:To explore the clinical manifestations and pathogenic variant in a family with epilepsy, developmental delay and brain deformity.Methods:Clinical data of the child and his family members who had visited the Department of Pediatrics, Linyi People's Hospital on July 2, 2022 were collected. The child, his sister and parents were subjected to high-throughput sequencing, and the result was verified by Sanger sequencing.Results:The child was a 6-year-old boy with developmentally delay and had epileptic seizures with fever sensitivity for four years. Cranial imaging showed brain dysplasia, while the video electroencephalogram showed abnormal discharge. High-throughput sequencing showed the child has harbored a heterozygous c. 5G>T (p.Arg2Leu) variant of TUBB2A gene, which was unreported previously. His sister also carried the variant and had similar clinical manifestations, whilst his parents were of the wild-type and had normal clinical phenotypes. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was classified as pathogenic (PS2+ PM2_Supporting+ PM5+ PP1+ PP2+ PP3). Conclusion:The heterozygous c. 5G>T (p.Arg2Leu) variant of the TUBB2A gene, in the form of gonadal mosaicism, probably underlay the disorders in this family.
4.Analysis of a child with SPONASTRIME dysplasia due to compound heterozygous variants of TONSL gene
Liping ZHU ; Yuzeng HAN ; Shiyan QIU ; Na XU ; Xin ZHANG ; Yufen LI ; Li YANG
Chinese Journal of Medical Genetics 2024;41(5):577-580
Objective:To explore the clinical features and genetic etiology of a child with SPONASTRIME dysplasia (SD).Methods:A 9-month-old female who had presented at the Linyi People′s Hospital in August 2022 for short stature was selected as the study subject. Clinical data of the child were collected, and whole exome sequencing (WES) was carried out. Sanger sequencing was used for validating the candidate variants.Results:The child has manifested short stature, mid-face hypoplasia, joint laxity, internal knee rotation, irregularities in the metaphysis of long bones, and flat and concave lumbar vertebrae. WES revealed that she has harbored compound heterozygous variants of the TONSL gene, namely c.3088G>T (p.Glu1030*) and c. 3053G>A (p.Arg1018His), which were inherited from her phenotypically normal parents. Neither variant was reported previously. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the c. 3088G>T variant was classified as likely pathogenic (PVS1+ PM2_Supporting), whilst the c. 3053G>A was classified as a variant of uncertain significance (PM2_Supporting+ PM3+ PP3). Conclusion:The c. 3088G>T and c. 3053G>A compound heterozygous variants of the TONSL gene probably underlay the pathogenesis in this patient. Above finding has facilitated the clinical diagnosis and genetic counseling for her family.
5.Risk Factors and a Prediction Model for Frequent Acute Exacerbations of Chronic Obstructive Pulmonary Disease
Yufen FU ; Ting MOU ; Xiang HE ; Dehong WU ; Guoping LI
Acta Academiae Medicinae Sinicae 2024;46(4):519-527
Objective To identify the risk factors of patients with frequent acute exacerbations of chro-nic obstructive pulmonary disease(AECOPD)and construct a prediction model based on the clinical data,provi-ding a theoretical basis for the clinical prevention and treatment.Methods A total of 25 638 COPD patients ad-mitted to the Department of Respiratory and Critical Care Medicine,the Third People's Hospital of Chengdu from January 1,2013 to May 1,2023 were selected.Among them,11 315 patients were included according to the inclusion and exclusion criteria,and their clinical characteristics were analyzed.Multivariate Logistic regression was carried out to identify the risk factors for frequent AECOPD.A nomogram model was utilized to quantify the risk of acute exacerbation,and the performance of the prediction model was assessed based on the area under the receiver operating characteristic(ROC)curve.Results In the patients with frequent AECOPD,male percentage(P<0.001),age(P<0.001),urban residence(P<0.001),smoking(P<0.001),length of stay(P<0.001),total cost(P<0.001),antibiotic cost(P<0.001),diabetes(P=0.003),respiratory failure(P<0.001),heart disease(P<0.001),application of systemic glucocorticoids(P<0.001),white blood cell count(P<0.001),neutrophil percentage(P<0.001),C-reactive protein(P<0.001),total cholesterol(P<0.001),and brain natriuretic peptide(BNP)(P<0.001)were all higher than those in the patients with infre-quent AECOPD.Multivariate Logistic regression analysis revealed that age,urban residence,smoking,diabe-tes,heart disease,Pseudomonas aeruginosa infection,application of systemic glucocorticoids,antibiotics,re-spiratory failure,and elevated white blood cell count,total cholesterol,and BNP were independent risk factors for hospitalization due to frequent AECOPD.A nomogram model of hospitalization due to frequent AECOPD was constructed according to risk factors.The ROC curve was established to evaluate the performance of the model,which showed the area under the ROC curve of 0.899(95%CI=0.892-0.905),the sensitivity of 85.30%,and the specificity of 79.80%.Conclusions Frequent AECOPD is associated with smoking,heart disease,ap-plication of systemic glucocorticoids,Pseudomonas aeruginosa infection,age,low body mass index,and elevat-ed BNP.Predicting the risks of hospitalization due to frequent AECOPD by the established model can provide the-oretical support for the treatment and risk factor management of the patients.
6.Mechanism of miR-483-3p regulating autophagy to reduce myocardial fibrosis in rats
Liqin CHEN ; Xiangwei LÜ ; Weikun ZHAO ; Qiuyu QIN ; Zifeng HE ; Yuechang LI ; Yufen LU
Chinese Journal of Geriatric Heart Brain and Vessel Diseases 2024;26(6):683-687
Objective To study the role of microRNA(miR)-483-3p in reducing myocardial fibrosis in rats,and explore the relationship between its mechanism and autophagy.Methods A total of 24 male SD rats were randomly divided into sham operation group,model group,blank transfec-tion group and high expression group,with 6 rats in each group.The blank transfection group and the high-expression group were pretreated with a single injection of adeno-associated virus(AAV)-blank transfection and AAV-miR-483-3p(5×1011 vg)in the tail vein,respectively.In 14 d later,the sham group was injected with 2.5 ml/(kg·d)normal saline for 14 d,and rat model of myocardial fibrosis was established by 2 mg/ml isoproterenol[2.5 ml/(kg·d)]injection through tail vein for 14 consecutive days.Myocardial pathological damage,severity of myocardial fibrosis,and expression levels of collagen-Ⅰ,microtubule-associated protein light chain 3(LC3),autoph-agy-related protein 5(Atg5)and autophagy degradation substrate(P62)in cardiomyocytes were evaluated and measured.Results Compared with the sham operation group,the model group had obviously larger myocardial fibrosis area,higher positive expression of Collagen-Ⅰ,and increased protein levels of Atg5 and LC3-Ⅱ/LC3-Ⅰ,and decreased expression level of P62 protein(P<0.05).The myocardial fibrosis area,positive expression of Collagen-Ⅰ,the expression levels of Atg5 and LC3-Ⅱ/LC3-Ⅰ protein[(13.64±1.51)%vs(27.47±1.55)%,(13.48±3.07)%vs(30.91±2.45)%,0.98±0.17 vs 1.24±0.28,0.66±0.05 vs 1.26±0.09,P<0.05]were significant-ly decreased,and the expression level of P62 was notably increased(0.91±0.11 vs 0.74±0.06,P<0.05)in the high expression group than the model group.Conclusion MiR-483-3p attenuates myocardial fibrosis in rats,and the mechanism may be related to the inhibition of cardiomyocyte autophagy.
7.Summary of the best evidence in prevention and management of center venous catheter dysfunction in hemodialysis patients
Luxia WEI ; Yuling LI ; Guang ZHANG ; Yufen ZHAO ; Wenfang ZHAO
Chinese Journal of Modern Nursing 2024;30(2):215-221
Objective:To retrieve, summarize, evaluate and integrate the best evidence for the prevention and management of center venous catheter dysfunction in hemodialysis patients.Methods:The relevant literature on prevention of center venous catheter dysfunction in hemodialysis patients was systematically searched in UpToDate, BMJ Best Practice, Cochrane Library, National Guideline Clearinghouse, Guidelines International Network, National Kidney Foundation, PubMed, CNKI and other databases, including guidelines, clinical decision-making, evidence summary, systematic evaluation and expert consensus. The search period was from January 1st, 2013 to March 1st, 2023. Two researchers independently evaluated the quality of the literature, evaluated the quality of the included literature and extracted evidence.Results:A total of 15 articles were included, including three guidelines, three clinical decision-making, five expert consensus, two systematic evaluations, one evidence summary and one government document. Ultimately, seven themes and 32 best evidence were formed, including personnel training and management, evaluation and monitoring, catheter insertion, catheter maintenance, drug prevention, catheter dysfunction management and health education.Conclusions:This study summarizes the best evidence for the prevention and management of center venous catheter dysfunction in hemodialysis patients. Medical staff can choose and apply this evidence-based basis based on clinical situations and patient preferences, thereby reducing the incidence of catheter dysfunction.
8.Intermediate and long-term outcomes of transcatheter closure of congenital coronary cameral fistulas in 66 children
Yifan LI ; Yufen LI ; Junjie LI ; Yumei XIE ; Shushui WANG ; Zhiwei ZHANG
Chinese Journal of Pediatrics 2024;62(2):145-152
Objective:To evaluate the intermediate and long-term outcomes and technical aspects of transcatheter closure (TCC) of coronary cameral fistulas (CCF) in pediatric patients.Methods:This was a case-control study. All pediatric patients with CCF who underwent TCC between January 2005 and December 2019 were retrospectively reviewed. Data was collected from medical records, including demographic characteristics, procedural details, intraoperative and postoperative serious adverse events, follow-up results and prognosis. Patients with serious adverse events and without serious adverse events were compared regarding their clinical features and CCF characteristics. Comparisons between groups were performed with independent sample t test, chi-square test or Fisher exact test. Results:A total of 66 CCF patients (34 boys, 32 girls, 3.9 (1.9, 6.2) years old, 15 (11, 20) kg) underwent attempted TCC. All of the CCF were all medium or large fistulas including 55 proximal fistulas (83%) and 11 distal fistulas (17%). The CCF originated more frequently from the right coronary artery (38 cases (58%)), followed by the left coronary artery (28 cases (42%)). The incidence of coronary artery aneurysms (CAA) was 61% (40/66).Procedural treatment was achieved in 64 patients and procedural success was achieved in 59 patients (92%). Six (9%) serious adverse events occurred in 5 patients during the perioperative period. Acute complications included procedure-related death in one patient and acute myocardial infarction in one patient. Periprocedural complications occurred in 3 patients at one day postoperatively including acute myocardial infarction (2 cases), occluder detachment (1 case), and tricuspid chordae tendinae rupture (1 case). Clinical follow-up data were available in 58 of the 62 patients who underwent initial successful TCC with a follow-up period of 9.3 (6.5, 13.4) years. Ten adverse events occurred in 9 patients including 5 complications consisted of aortic valve perforation (1 case), coronary thrombosis (1 case), progressive aneurysmal dilation after reintervention (1 case), and new-onset tricuspid valve prolapse with significant regurgitation (2 cases) and large residual shunts due to fistula recanalization (5 cases). Therefore, the incidence of intermediate and long-term adverse events was 17% (10/58). During the periprocedural and follow-up period, 16 adverse events occurred in 13 patients, whereas no adverse events occurred in 51 patients. Patients with seriovs adverse events presented with larger proportion of large CCF (11/13 vs. 39% (20/51), P=0.005), giant CAA (10/13 vs.14% (7/51), P=0.030), and higher mean pulmonary artery pressure ((20±9) vs.(16±6) mmHg, 1 mmHg=0.133 kPa, t=2.02, P=0.048) compared to patients without serious adverse events. Conclusions:TCC in CCF children appears to be effective with favorable intermediate and long-term outcomes. Strict indication of TCC is mandatory.
9.Effects of the various herbs and different proportions of the herbs in Huidu Yinhua powder on methicillin-resistant Staphylococcus aureus
Yufen LI ; Shuang JIANG ; Wu SONG ; Tao JIANG ; Chang LIU ; Haofang ZHOU ; Yating TANG ; Lin WEI ; Xin SU
Chinese Journal of Comparative Medicine 2024;34(2):63-71
Objective To study the inhibitory effect of Huidu Yinhua powder from the Orthodox Manual of External Medicine on methicillin-resistant Staphylococcus aureus(MRSA),virulence factor α-hemolysin(Hla)activity,and biofilm formation,and to explore the optimal ratios of Huidu Yinhua powder and provide experimental support for its use.Methods The inhibitory effects of Huidu Yinhua powder and the herbs in the formula on USA300 were analyzed by the minimum inhibitory concentration(MIC),minimum bactericidal concentration(MBC),and disk diffusion assay(K-B method).Hemolysis,neutralization,oligomerization,and Western blot assays were used to verify in which form the drug inhibits the activity of virulence factor α-hemolysin(Hla).A biofilm assay was performed to evaluate the inhibitory effect of Huidu Yinhua powder on biofilm.Orthogonal experiments were performed to explore the optimal ratio of Huidu Yinhua powder.Results Huidu Yinhua powder inhibited the MRSA strain with a MIC90 of 64 mg/mL and an MBC of 256 mg/mL with antibacterial circle diameter of(7.50±0.50)mm.Huidu Yinhua powder inhibited Hla activity by inhibiting Hla secretion.The minimum effective concentration(MEC)was 16 mg/mL,and the MEC of biofilm was 8 mg/mL.In Huidu Yinhua powder,honeysuckle and astragalus only affected the hemolytic activity of MRSA and biofilm formation without inhibiting bacterial growth.The hemolytic activity and biofilm of MEC were both 32 mg/mL.Glycyrrhiza had a strong bacterial inhibitory capacity with a MIC90 of 8 mg/mL and biofilm MEC of 1 mg/mL without showing inhibitory hemolytic activity at subinhibitory concentrations.The orthogonal experiment showed that,at a ratio of honeysuckle,astragalus,and glycyrrhiza in Huidu Yinhua powder of 1∶2∶4,the MIC90 was 16 mg/mL,MEC of hemolytic activity was 8 mg/mL and that of biofilm was 4 mg/mL,both of which were the lowest among the nine groups.Conclusions Huidu Yinhua powder affects the hemolytic activity and biofilm formation of MRSA at subinhibitory concentrations with the optimal ratio of honeysuckle,astragalus,and glycyrrhiza being 1∶2∶4.
10.Scoping review of pharmaceutical service provided by community pharmacists for patients with chronic diseases in China
Yuanhui HU ; Guolin LI ; Chang FENG ; Yuyao PEI ; Yufen ZHENG
China Pharmacy 2024;35(20):2559-2564
OBJECTIVE To summarize and analyze the profile of the implementation of pharmaceutical service by community pharmacists for patients with chronic diseases in China. METHODS Literature was searched from CNKI, Wanfang database, PubMed (Medline), Embase, and Scopus to collect studies about community pharmacists providing pharmaceutical services for patients with chronic diseases. The ways and contents of the implementation of pharmaceutical services for chronic diseases by community pharmacists were summarized descriptively. RESULTS A total of 75 studies were included, involving 49 trial studies and 26 cross-sectional studies. The study sites were mainly located in the developed regions of China, and the types of disease involved in the studies were mainly diabetes mellitus (n=30) and hypertension (n=28); most studies used the following indexes to evaluate pharmaceutical services, such as changes in disease symptoms and related indicators(n=35), improvement of patient compliance(n=34), and the occurrence of adverse drug reactions (irrational drug use) (n=25). The pharmaceutical service provided by community pharmacists included medication education (84.0%), monitoring and follow-up (64.0%), and identifying and solving medication-related problems (58.7%). Thirty-eight studies mentioned that pharmaceutical services were achieved through teamwork, 16 of which mentioned healthcare alliances. A few studies investigated stratified healthcare systems (n=15) and internet-based pharmaceutical services (n=10). CONCLUSIONS In China, pharmaceutical services provided by community pharmacies for patients with chronic diseases are still mainly confined to economically developed areas, and the scope of services is limited to a few diseases and basic pharmaceutical practices. In the future, the implementation of precise pharmaceutical services for different diseases and patients’ disease status, the establishment of medical alliances, and the development of internet-based pharmaceutical services should become the focus of pharmaceutical services.

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