1.Diffusion-based generative drug-like molecular editing with chemical natural language.
Jianmin WANG ; Peng ZHOU ; Zixu WANG ; Wei LONG ; Yangyang CHEN ; Kyoung Tai NO ; Dongsheng OUYANG ; Jiashun MAO ; Xiangxiang ZENG
Journal of Pharmaceutical Analysis 2025;15(6):101137-101137
Recently, diffusion models have emerged as a promising paradigm for molecular design and optimization. However, most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geometries, with limited research on molecular sequence diffusion models. The International Union of Pure and Applied Chemistry (IUPAC) names are more akin to chemical natural language than the Simplified Molecular Input Line Entry System (SMILES) for organic compounds. In this work, we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language (SMILES) and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language. We propose DiffIUPAC, a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings. Evaluation results demonstrate that our model outperforms existing methods and successfully captures the semantic rules of both chemical languages. Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints. Additionally, to illustrate the model's applicability in drug design, we conducted case studies in functional group editing, analogue design and linker design.
2.Angiotensin Ⅱ type 1 receptor autoantibody-AT1R-Bmal1 axis promotes phenotypic transition of vascular smooth muscle cells and vascular fibrosis
Lingxia XUE ; Yaolin LONG ; Jiayan FENG ; Tian MAO ; Jiao GUO ; Zhuoxi WANG ; Yang LI ; Xiaohui WANG ; Li WANG
Journal of Army Medical University 2025;47(11):1155-1164
Objective To investigate the mechanism by which angiotensin Ⅱ type 1 receptor autoantibody(AT1-AA)promotes phenotypic switch of vascular smooth muscle cells(VSMCs)and vascular fibrosis through abnormal expression of circadian clock protein BMAL1.Methods Twelve male SD rats(6~8 weeks old,weighing 180~220 g)were randomly divided into(n=6)a control group and an AT1-AA-positive group[established by active immunization of SD rats with AT1R extracellular loop Ⅱ peptide(AT1R-ECLⅡ)].HE and Masson stainings were used to observe structural changes and fibrosis in the thoracic aorta(n=3).Western blotting was performed to detect the expression of Collagen I,phenotypic switch-related proteins(SM22,α-SMA,OPN and MMP2)in vascular tissues and primary VSMCs(n=4),as well as the expression of BMAL1 at CT0,CT4,CT8,CT12,CT16,and CT20.Transwell and scratch assays were used to assess the proliferation and migration of VSMCs(n=3).si-RNA was employed to knock down Bmal1,followed by detection of BMAL1,Collagen I,and phenotypic conversion-related protein expression(n=3).Additionally,AT1-AA-positive AT1R-knockout(AT1R-KO)rats were constructed to measure BMAL1 expression in thoracic aortic tissues(n=4).Results The AT1-AA-positive rats had significantly thickened thoracic aortic vessel wall[(140±9)%vs(120±5)%,P<0.05],badly arranged VSMCs,obvious blue Masson staining,and up-regulated Collagen I expression(P<0.05).In the thoracic aorta of AT1-AA-positive rats and AT1-AA-treated VSMCs,the expression of contractile phenotype-related proteins(α-SMA,SM22)was decreased(P<0.05),while the expression of synthetic phenotype-related proteins(OPN,MMP2)was increased(P<0.05).AT1-AA enhanced the scratch healing ability and migration ability of VSMCs.Furthermore,both mRNA and protein levels of Bmal1 were significantly up-regulated at CT12(P<0.05),and the rhythmicity of Bmal1 was lost.Knockdown of Bmal1 partially ameliorated AT1-AA-induced phenotypic switch of VSMCs.Compared with AT1-AA-positive WT rats,AT1-AA-positive AT1R-KO rats showed significantly reduced BMAL1 expression in the thoracic aorta(1.35±0.06 vs 0.86±0.07,P<0.001).At the cellular level,AT1-AA-induced phenotypic switch and high Collagen I expression in VSMCs were partially improved in AT1R-KO VSMCs.Conclusion AT1-AA promotes VSMCs phenotypic conversion and vascular fibrosis through the AT1R-Bmal1 axis.
3.Diffusion-based generative drug-like molecular editing with chemical natural language
Jianmin WANG ; Peng ZHOU ; Zixu WANG ; Wei LONG ; Yangyang CHEN ; Tai-No KYOUNG ; Dongsheng OUYANG ; Jiashun MAO ; Xiangxiang ZENG
Journal of Pharmaceutical Analysis 2025;15(6):1215-1225
Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited research on molecular sequence diffusion models.The International Union of Pure and Applied Chemistry(IUPAC)names are more akin to chemical natural language than the simplified molecular input line entry system(SMILES)for organic compounds.In this work,we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language(SMILES)and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language.We propose DiffIUPAC,a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings.Evaluation results demonstrate that our model out-performs existing methods and successfully captures the semantic rules of both chemical languages.Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints.Additionally,to illustrate the model's applicability in drug design,we conducted case studies in functional group editing,analogue design and linker design.
4.Tonifying kidney and activating blood therapy for the treatment of diabetic erectile dysfunction: A systematic review and meta-analysis.
Mao-Ke CHEN ; Ke-Cheng LI ; Jun-Long FENG ; Xiang-Fa LIN ; Wen-Xuan DONG ; Zi-Xiang GAO ; Hua-Nan ZHANG ; Hui CHEN ; Ji-Sheng WANG ; Bin WANG
National Journal of Andrology 2025;31(9):832-840
Objective: To systematically evaluate the clinical efficacy and safety of Tonifying kidney and activating blood therapy for the treatment of diabetic mellitus erectile dysfunction. Methods: China National Knowledge Infrastructure(CNKI), Wanfang Data, VIP, Chinese Biomedical Database(CBM), PubMed, Cochrane Library, Embase and Web of Science were searched from inception until October 20th of 2024,for randomized controlled trials of Tonifying kidney and activating blood therapy for the treatment of diabetic erectile dysfunction. Literature screening, quality evaluation, and data extraction were carried out in accordance with relevant standards. The software of RevMan5.4 was used for the analysis of publication bias. And meta-analysis was conducted to assess the impact of this therapy on IIEF-5, total effective rate, adverse reactions. The evidence levels according to the analysis results were evaluated. Results: Totally 19 RCTs were included, involving 1 612 patients. The result of meta-analysis indicated that Tonifying kidney and activating blood therapy had advantages on the improvement of IIEF-5 scores (MD=3.59,95%CI[2.14,5.03],P<0.01),total effective rate (OR=4.30,95%CI[3.29,5.32],P<0.000 01). However, there was no statistically significant difference in the incidence of adverse reactions(OR=0.98,95%CI[0.48,2.01],P=0.96) between the two groups. Conclusions: Tonifying kidney and activating blood therapy can improve the clinical efficacy and IIEF-5 score for the patients with diabetic erectile dysfunction. But considering the limited quantity of included studies, more high-quality studies still be needed to validate the therapeutic effect.
Humans
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Male
;
Erectile Dysfunction/therapy*
;
Randomized Controlled Trials as Topic
;
Kidney
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Medicine, Chinese Traditional
;
Diabetes Complications/therapy*
5.Relationship among psychological resilience, parental control, and behavioral problems in junior high school students in Guizhou Province
Chinese Journal of School Health 2024;45(5):689-692
Objective:
To investigate the relationships among psychological resilience, parental control, and behavioral problems in middle school students, aiming to provide evidencebased recommendations for the prevention and intervention of behavioral issues in middle school students, as well as for the development of related policies.
Methods:
A stratified cluster sampling method was used to select 2 745 participants from three cities in Guizhou Province with different levels of economic development from August to December 2021. The Child Behavior Checklist (CBCL), Parental Control Questionnaire, and Psychological Resilience Questionnaire were administered to junior high school students and their parents. A network analysis method was employed to construct a network analysis model of factors influencing behavioral problems.
Results:
The detection rate of behavioral problems among junior high school students in Guizhou Province was 22.62%. The scores for psychological resilience (goal focus, emotional control, positive cognition, family support, and interpersonal assistance) and proactive inquiry in behavior control were higher in the group without behavioral problems than in the group with behavioral problems. Scores for psychological control (inducing guilt, with drawing affection, and asserting authority) were higher in the group with behavioral problems than in the group without behavioral problems, with statistically significant differences (t=9.80, 17.76, 6.21, 12.20, 13.18, 6.28, 11.58, 11.10, 10.74, P<0.05). The network model showed that among the same variable factors, the strongest connection weight was between inducing guilt and withdrawing affection, with a weight of 0.79. Between different variables, there were negative correlation between behavioral problems and psychological resilience (goal focus, emotional control, positive cognition, family support, interpersonal assistance) and behavior control (proactive inquiry, behavioral restraint) with correlation coefficients (r=-0.25, -0.42, -0.16, -0.31, -0.33, -0.17, -0.03, P<0.05), respectively. There were positive correlation between psychological control factors (inducing guilt, withdrawing affection, and asserting authority) and behavioral problems (r=0.29, 0.27, 0.27), and a negative correlation between these psychological control factors and psychological resilience factors (goal focus, emotional control, positive cognition, family support, interpersonal assistance)(r=-0.53--0.13)(P<0.05). The strongest connection weight was between withdrawing affection and family support, with a connection weight of -0.53. Family support was an important bridge symptom connecting the entire behavioral problem network model, with a high centrality.
Conclusions
The detection rate of behavioral problems among junior high school students in Guizhou Province is relatively high. Assisting adolescents in establishing a supportive family environment facilitates the cultivation of their psychological resilience, thereby mitigating the occurrence of behavioral problems.
6.A comparative study of short-term clinical outcomes of total laparoscopic and laparoscopic- assisted radical resection of distal gastric cancer: a propensity score-matched analysis
Shenxiang LONG ; Xinning WANG ; Xubin WANG ; Xuehui MAO ; Shubo TIAN ; Leping LI ; Xiaobo GUO
Chinese Journal of General Surgery 2024;39(2):86-91
Objective:To analyze the short-term clinical outcomes of total laparoscopic distal gastrectomy (TLDG) and laparoscopic-assisted distal gastrectomy (LADG) combined with Billroth-Ⅱ+Braun anastomosis.Methods:Clinical characteristics of patients undergoing laparoscopic distal gastrectomy combined with Billroth-Ⅱ+Braun anastomosis at Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University from Jan 2020 to Oct 2022 were analyzed. Patients were divided into TLDG group ( n=62) and LADG group ( n=62) according to the surgical approach. Results:There were significant differences in the preoperative clinical data section between the two groups, and 124 patients (62 in each group) were enrolled after using propensity score matching to balance significant variables. Compared with the LADG group, the TLDG group showed statistically differences in time to first venting [(2.9±1.3) vs. (2.3±0.8) d, Z=-3.072, P=0.002], time to first fluid diet [(5.9±1.3) vs. (5.4±1.4) d, Z=-2.031, P=0.042] and incision length [(7.1±1.4) vs. (4.8±0.8) cm, Z=-6.331, P=0.000]. Total postoperative complication rate in the TLDG group and the LADG group (29% vs. 37%, χ2=0.911, P=0.340) was not statistically significant. Incidence of postoperative pneumonia was lower in the TLDG group than in the LADG group (3% vs. 13%, χ2=3.916, P=0.048), and incidence of all remaining postoperative complications were not statistically significant. There was no statistically significant difference in the incidence of serious postoperative complications between the TLDG and LADG groups ( P=1.000). Multifactorial analysis revealed that male ( P=0.023) and age ≥65 years ( P=0.001) were independent risk factors for postoperative complications. Conclusion:TLDG is safe and feasible and has better short-term clinical efficacy than LADG.
7.Synthesis and anti-tumor activity of pyrazole pyrimidine PI3Kγ /δ inhibitors
Mao-qing DENG ; Feng-ming ZOU ; Zi-ping QI ; Chun WANG ; Kai-li LONG ; Qing-wang LIU ; Ao-li WANG ; Jing LIU ; Xiao-fei LIANG
Acta Pharmaceutica Sinica 2024;59(7):2041-2052
PI3K
8.Protective mechanism of rhubarb decoction against inflammatory damage of brain tissue in rats with mild hepatic encephalopathy: A study based on the PI3K/AKT/mTOR signaling pathway
Guangfa ZHANG ; Yingying CAI ; Long LIN ; Lei FU ; Fan YAO ; Meng WANG ; Rongzhen ZHANG ; Yueqiao CHEN ; Liangjiang HUANG ; Han WANG ; Yun SU ; Yanmei LAN ; Yingyu LE ; Dewen MAO ; Chun YAO
Journal of Clinical Hepatology 2024;40(2):312-318
ObjectiveTo investigate the role and possible mechanism of action of rhubarb decoction (RD) retention enema in improving inflammatory damage of brain tissue in a rat model of mild hepatic encephalopathy (MHE). MethodsA total of 60 male Sprague-Dawley rats were divided into blank group (CON group with 6 rats) and chronic liver cirrhosis modeling group with 54 rats using the complete randomization method. After 12 weeks, 40 rats with successful modeling which were confirmed to meet the requirements for MHE model by the Morris water maze test were randomly divided into model group (MOD group), lactulose group (LT group), low-dose RD group (RD1 group), middle-dose RD group (RD2 group), and high-dose RD group (RD3 group), with 8 rats in each group. The rats in the CON group and the MOD group were given retention enema with 2 mL of normal saline once a day; the rats in the LT group were given retention enema with 2 mL of lactulose at a dose of 22.5% once a day; the rats in the RD1, RD2, and RD3 groups were given retention enema with 2 mL RD at a dose of 2.5, 5.0, and 7.5 g/kg, respectively, once a day. After 10 days of treatment, the Morris water maze test was performed to analyze the spatial learning and memory abilities of rats. The rats were analyzed from the following aspects: behavioral status; the serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) and the level of blood ammonia; pathological changes of liver tissue and brain tissue; the mRNA and protein expression levels of phosphatidylinositol 3-kinase (PI3K), protein kinase B (AKT), and mammalian target of rapamycin (mTOR) in brain tissue. A one-way analysis of variance was used for comparison of continuous data between multiple groups, and the least significant difference t-test was used for further comparison between two groups. ResultsCompared with the MOD group, the RD1, RD2, and RD3 groups had a significantly shorter escape latency (all P<0.01), significant reductions in the levels of ALT, AST, IL-1β, IL-6, TNF-α, and blood ammonia (all P<0.05), significant alleviation of the degeneration, necrosis, and inflammation of hepatocytes and brain cells, and significant reductions in the mRNA and protein expression levels of PI3K, AKT, and mTOR in brain tissue (all P<0.05), and the RD3 group had a better treatment outcome than the RD1 and RD2 groups. ConclusionRetention enema with RD can improve cognitive function and inflammatory damage of brain tissue in MHE rats, possibly by regulating the PI3K/AKT/mTOR signaling pathway.
9.Application of Intestinal Organoids in The Study of Intestinal Disease Mechanism
Long-Zheng QIANG ; Hai-Guang MAO ; Meng-Ting WANG ; Li-Li QI ; Jin-Bo WANG
Progress in Biochemistry and Biophysics 2024;51(2):394-403
Intestinal organoids are constructed by crypts or stem cells from the intestine under the 3D support of the culture matrix. They contain all mature cells of the intestine, and have become a new and efficient platform for studying the mechanism of intestinal diseases. Compared with 2D cell culture, organoids can not only more effectively simulate the physiological structure and function of the intestine, but also better restore the true ecology of the intestine in different external environments. Therefore, it is more widely used in the study of pathogenesis of different intestinal diseases. This article reviewed the new progress of intestinal organoids culture, and the application and progress of intestinal organoids in the pathogenesis of inflammatory bowel diseases, colorectal cancer and celiac disease in recent years, and also discussed the application of intestinal organoids in drug research and development and screening.
10.Role of neuroimmune communication via the gut-brain axis in the pathogenesis of hepatic encephalopathy
Yong LIN ; Jiongfen LI ; Feiyan LI ; Yuanqin DU ; Meiyan LIU ; Minggang WANG ; Fuli LONG ; Na WANG ; Dewen MAO
Journal of Clinical Hepatology 2024;40(12):2518-2523
Hepatic encephalopathy (HE) is a common severe liver disease syndrome in clinical practice and is one of the critical and severe diseases in internal medicine, and more than half of liver failure patients diagnosed with overt HE have a survival time of less than 1 year. A comprehensive analysis of the complex pathogenesis of HE and the development of diagnosis and treatment regimens based on evidence-based medicine are of great importance for alleviating high medical resource consumption, high medical expenses, and high incidence and mortality rates in clinical practice. The latest studies have shown that the intestinal tract and the central nervous system can perform bidirectional continuous interaction and signal transmission and regulate the function of inflammation signals, molecules, cells, and organs, which is known as neuroimmune communication and is highly consistent with the main pathological features of HE. With a focus on the mechanism of neuroimmune communication in HE, this article reviews the association between inflammation signal transduction via the gut-brain axis and neurotransmitter regulation and its role in neuroimmune communication in HE, which provides new ideas for the clinical diagnosis and treatment of HE and the research and development of related drugs.


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