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Feature-based molecular networking and building blocks identification advance novel natural products characterization:Sesquiterpene-chromone hybrids in agarwood as an application 认领 引用
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作者 Qian Wang Han Li +5 位作者 Huiting Liu Yujie Pei Pengfei Tu Huixia Huo Jun Li Yuelin Song 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2026年第3期886-888,共3页
As important sources of new drugs,natural products(NPs)are conceptually biosynthesized from simple structural pioneers(i.e.building blocks).The traditional non-targeted purification strategy extensively suffers from t... As important sources of new drugs,natural products(NPs)are conceptually biosynthesized from simple structural pioneers(i.e.building blocks).The traditional non-targeted purification strategy extensively suffers from the time-consuming and laborious bottlenecks.Fortunately,liquid chromatography–mass spectrometry/mass spectrometry(LC–MS/MS)-guided separations widely succeed in recent decades.However,it is still challenging for LC–MS/MS to precisely capture new NPs.Efficiently extracting information from the chaotic chemical composition and confident structural annotation are two primary technical barriers for pursuing the interesting structures,particularly those exhibiting trace distributions and high-level structural complexity.Here,to provide accurate guidance for the follow-up phytochemical purification,molecular defect filtering(MDF)and feature-based molecular networking(FBMN)[1]were incorporated to explore NPs and thereafter,bottom-up structural analysis was undertaken through identifying building blocks with full exciting energy ramp(FEER)-MS 3 matching.Sesquiterpene-chromone hybrids(SCHs)structurally configured by two building blocks such as units A(chromone)and B(sesquiterpene)[2]in agarwood were characterized as a proof-of-concept.Twenty-five SCHs were captured and identified.Thereof,seven new SCHs were purified with a LC–MS/MS-guided manner and annotated using nuclear magnetic resonance(NMR)spectroscopy to justify the proposed structures.Moreover,their cell-protective and anti-inflammatory activities were evaluated.Together,the incorporation of post-acquisition data processing strategies and FEER-MS 3 spectrum matchingassisted building blocks identification facilitated novel NPs exploration and purification. 展开更多
关键词 sesquiterpene chromone hybrids agarwood liquid chromatography mass spectrometry mass spectrometry extracting information feature based molecular networking molecular defect filtering nuclear magnetic resonance spectroscopy building blocks identification
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Feature-based molecular networking(FBMN):An efficient booster for discovering novel natural products or metabolites 认领 引用 被引量：2
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作者 Meiru Han Huan Xia +4 位作者 Guiyang Xia Xiaohong Wei Jinyu Li Yuzhuo Wu Sheng Lin 《Acta Pharmaceutica Sinica B》 SCIE CAS CSCD 2025年第4期2283-2286,共4页
To the editor:The comprehensive exploration of natural products and metabolites is essential for unraveling the complexities of natural drug therapies.Inadequate tracking and separation methods result in increased res... To the editor:The comprehensive exploration of natural products and metabolites is essential for unraveling the complexities of natural drug therapies.Inadequate tracking and separation methods result in increased research costs and reduced scientific output,significantly hindering the healthy advancement of related research fields.Emerging molecular networking(MN)technologies help minimize the redundant discovery of known natural products or metabolites. 展开更多
关键词 Feature-based molecular networking Guided separation technology Natural products Metabolites Micro and trace compounds
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Modeling the chondrocyte-derived osteoblasts formation process reveals its molecular signature and regulation network 认领 引用
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作者 Raquel Ruiz-Hernández Laurie Gay +21 位作者 Verónica Moncho-Amor Pablo Martín Jhonatan A.Vergara-Arce Stefania Di Blasio Thomas Snoeks Unai Cossío Ander Matheu Maria M.Caffarel Daniela Gerovska Marcos J.Araúzo-Bravo Amaia Vilas Felipe Prosper Sergio Moya Daniel Alonso-Alconada Ana Alonso-Varona Gretel Nusspaumer Javier Lopez-Rios Karine Rizotti Robin Lovell-Badge Dominique Bonnet Ilaria Malanchi Ander Abarrategi 《Bone Research》 SCIE CAS CSCD 2026年第1期291-302,共12页
Endochondral ossification is a physiological process involving a sequential formation of cartilage and bone tissues.Classically,cartilage and bone formation have been considered independent processes at cellular level... Endochondral ossification is a physiological process involving a sequential formation of cartilage and bone tissues.Classically,cartilage and bone formation have been considered independent processes at cellular level.However,the recently described multiple cell differentiation dynamics suggest that some bone cells are indeed the progeny of cartilage cells,or chondrocyte-derived osteoblasts.We hypothesized that the cartilage-to-bone phenotype transition is triggered by specific molecular events.First,the process was assessed in mouse bone tissue,and then,it was mimicked using in vivo cell implantation and in vitro serial differentiation protocols.Data indicates that cartilage cells transition to bone cell phenotype during postnatal physiological bone formation.This process can be reproduced using cartilage precursor cells coupled to specific implantation procedures or differentiation protocols.Gene expression profiling reveals that NOTCH,BMP and MAPK signaling pathways are relevant at the phenotype-switch,while the transcription factors Mesp1,Alx1,Grhl3 and Hmx3 are the feasible driver genes for chondrocyte-derived osteoblasts formation.Altogether,this report shows that endochondral ossification can be modeled using primary cell cultures and data indicate that this process is regulated by specific molecular events,previously described at skeleton morphogenesis during embryo development,and from now on also linkable to postnatal bone development and regeneration processes. 展开更多
关键词 regulation network postnatal bone development chondrocyte derived osteoblasts multiple cell differentiation dynamics molecular signature bone tissuesclassicallycartilage bone cells endochondral ossification
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Cytotoxic anthrone–cyclopentenone heterodimers from the fungus Penicillium sp.guided by molecular networking 认领 引用
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作者 Ruiyun Huo Jiayu Dong +2 位作者 Gaoran Liu Ying Shi Ling Liu 《Chinese Journal of Natural Medicines》 SCIE CAS CSCD 2025年第10期1259-1267,共9页
(±)-Penicithrones A–D(1a/1b–4a/4b),four novel pairs of anthrone–cyclopentenone heterodimers characterized by a distinctive bridged 6/6/6−5 tetracyclic core skeleton,together with three previously identified co... (±)-Penicithrones A–D(1a/1b–4a/4b),four novel pairs of anthrone–cyclopentenone heterodimers characterized by a distinctive bridged 6/6/6−5 tetracyclic core skeleton,together with three previously identified compounds(5–7),were isolated from the crude extract of the mangrove-derived fungus Penicillium sp.,guided by heteronuclear single quantum correlation(HSQC)-based small molecule accurate recognition technology(SMART 2.0)and liquid chromatography-tandem mass spectrometry(LC-MS/MS)-based molecular networking.The structural elucidation of new compounds was accomplished through comprehensive spectroscopic analysis,and their absolute configurations were determined using DP4+13C nuclear magnetic resonance(NMR)calculations and electronic circular dichroism(ECD)calculations.Compounds 1a/1b–4a/4b demonstrated moderate cytotoxicity against three human cancer cell lines HeLa,HCT116 and MCF-7 with half maximal inhibitory concentration(IC50)values ranging from 15.95±1.64 to 28.56±2.59μmol·L–1. 展开更多
关键词 Mangrove-derived fungi Molecular networking HSQC-based SMART Structure elucidation DP4+13C NMR calculation Cytotoxic activity
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Craterellus cornucopioides Water Extracts Attenuate Colitis and Explore Underlying Mechanisms via Network Pharmacology and Molecular Docking 认领 引用
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作者 XIA Juanjuan WANG Xin +5 位作者 XU Ruixiang XIA Ziwei ZHONG Weihong LIU Jing XIAO Xiong FU Xiaomei 《食品工业科技》 EI CAS 北大核心 2026年第10期425-437,共13页
Objective:The protective effects of Craterellus cornucopioides water extracts(CCWE)on rat model of UC were investigated in this study.Methods:Trinitrobenzene sulfonic acid(TNBS)was used to induce an ulcerative colitis... Objective:The protective effects of Craterellus cornucopioides water extracts(CCWE)on rat model of UC were investigated in this study.Methods:Trinitrobenzene sulfonic acid(TNBS)was used to induce an ulcerative colitis(UC)model in rats.Pathological injury was assessed by monitoring body weight changes,disease activity index(DAI)scores,and hematoxylin-eosin(HE)staining of colonic tissues.The levels of myeloperoxidase(MPO)activity,nitric oxide(NO),superoxide dismutase(SOD)activity,malondialdehyde(MDA),and pro-inflammatory cytokines(IL-1β,TNF-α,IL-6)in colon tissues were examined to evaluate the therapeutic effects of CCWE on UC.Network pharmacology was employed to screen active ingredients,targets,and pathways of CCWE against UC,followed by molecular docking validation of key interactions to elucidate its material basis and mechanism of action.Results:The DAI score of the TNBS group was significantly higher than that of the control group(P<0.05).Compared with the TNBS group,CCWE significantly reduced the DAI score(P<0.05)and improved macroscopic and histological damage.In addition,compared with the TNBS group,CCWE also significantly decreased the levels of MPO,NO,MDA,IL-1β,TNF-αand IL-6(P<0.01),while significantly increasing the level of SOD(P<0.01).The core targets of CCWE in treating UC were predicted to be STAT3,SRC,MAPK3,PIK3R1 and AKT1 by network pharmacology.The mechanisms of action encompass the HIF-1,relaxin,and PI3K/Akt signaling pathway.The main components of CCWE for treating UC might be illudin T,quercetin,4-hydroxy-4-isopropenylcyclohexanemethanol acetate,4-oxo-hex-5-enyl acetate,craterellins B,ferulic acid,craterellins A,caffeic acid,4-oxohex-1,6-diyl diacetate,and illudin M.Molecular docking results indicate that the active components of CCWE exhibit good binding affinity with these five core targets,with quercetin and 4-oxo-hex-5-enyl acetate showing the most significant docking scores.Conclusion:The active ingredients in CCWE,quercetin and 4-oxo-5-hexenyl acetate,modulate the expression of proteins including STAT3,SRC,MAPK3,PIK3R1 and AKT1,ultimately activating the HIF-1,relaxin,and PI3K/Akt signaling pathways to treat ulcerative colitis. 展开更多
关键词 Craterellus cornucopioides water extracts edible fungus colitis network pharmacology molecular docking
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Advancing Breast Cancer Molecular Subtyping:A Comparative Study of Convolutional Neural Networks and Vision Transformers on Mammograms 认领 引用
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作者 Chee Chin Lim Hui Wen Tiu +2 位作者 Qi Wei Oung Chiew Chea Lau Xiao Jian Tan 《Computers, Materials & Continua》 SCIE EI 2026年第3期1287-1308,共22页
critical for guiding treatment and improving patient outcomes.Traditional molecular subtyping via immuno-histochemistry(IHC)test is invasive,time-consuming,and may not fully represent tumor heterogeneity.This study pr... critical for guiding treatment and improving patient outcomes.Traditional molecular subtyping via immuno-histochemistry(IHC)test is invasive,time-consuming,and may not fully represent tumor heterogeneity.This study proposes a non-invasive approach using digital mammography images and deep learning algorithm for classifying breast cancer molecular subtypes.Four pretrained models,including two Convolutional Neural Networks(MobileNet_V3_Large and VGG-16)and two Vision Transformers(ViT_B_16 and ViT_Base_Patch16_Clip_224)were fine-tuned to classify images into HER2-enriched,Luminal,Normal-like,and Triple Negative subtypes.Hyperparameter tuning,including learning rate adjustment and layer freezing strategies,was applied to optimize performance.Among the evaluated models,ViT_Base_Patch16_Clip_224 achieved the highest test accuracy(94.44%),with equally high precision,recall,and F1-score of 0.94,demonstrating excellent generalization.MobileNet_V3_Large achieved the same accuracy but showed less training stability.In contrast,VGG-16 recorded the lowest performance,indicating a limitation in its generalizability for this classification task.The study also highlighted the superior performance of the Vision Transformer models over CNNs,particularly due to their ability to capture global contextual features and the benefit of CLIP-based pretraining in ViT_Base_Patch16_Clip_224.To enhance clinical applicability,a graphical user interface(GUI)named“BCMS Dx”was developed for streamlined subtype prediction.Deep learning applied to mammography has proven effective for accurate and non-invasive molecular subtyping.The proposed Vision Transformer-based model and supporting GUI offer a promising direction for augmenting diagnostic workflows,minimizing the need for invasive procedures,and advancing personalized breast cancer management. 展开更多
关键词 Artificial intelligence breast cancer classification convolutional neural network deep learning hyperparameter tuning mammography medical imaging molecular subtypes vision transformer
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Curvularin derivatives from hydrothermal vent sediment fungus Penicillium sp.HL-50 guided by molecular networking and their antiinflammatory activity 认领 引用 被引量：2
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作者 Chunxue Yu Zixuan Xia +6 位作者 Zhipeng Xu Xiyang Tang Wenjuan Ding Jihua Wei Danmei Tian Bin Wu Jinshan Tang 《Chinese Journal of Natural Medicines》 SCIE CAS CSCD 2025年第1期119-128,共10页
Guided by molecular networking,nine novel curvularin derivatives(1-9)and 16 known analogs(10-25)were isolated from the hydrothermal vent sediment fungus Penicillium sp.HL-50.Notably,compounds 5-7 represented a hybrid ... Guided by molecular networking,nine novel curvularin derivatives(1-9)and 16 known analogs(10-25)were isolated from the hydrothermal vent sediment fungus Penicillium sp.HL-50.Notably,compounds 5-7 represented a hybrid of curvularin and purine.The structures and absolute configurations of compounds 1-9 were elucidated via nuclear magnetic resonance(NMR)spectroscopy,X-ray diffraction,electronic circular dichroism(ECD)calculations,13C NMR calculation,modified Mosher's method,and chemical derivatization.Investigation of anti-inflammatory activities revealed that compounds 7-9,11,12,14,15,and 18 exhibited significant suppressive effects against lipopolysaccharide(LPS)-induced nitric oxide(NO)production in murine macrophage RAW264.7 cells,with IC50values ranging from 0.44 to 4.40μmol·L-1.Furthermore,these bioactive compounds were found to suppress the expression of inflammation-related proteins,including inducible NO synthase(i NOS),cyclooxygenase-2(COX-2),NLR family pyrin domain-containing protein 3(NLRP3),and nuclear factor kappa-B(NF-κB).Additional studies demonstrated that the novel compound 7 possessed potent antiinflammatory activity by inhibiting the transcription of inflammation-related genes,downregulating the expression of inflammation-related proteins,and inhibiting the release of inflammatory cytokines,indicating its potential application in the treatment of inflammatory diseases. 展开更多
关键词 Penicillium sp.HL-50 Curvularin derivatives Molecular networking Anti-inflammatory activity
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Comparative cardioprotective effects of licorice-processed aconite(Zhifuzi)and Heishunpian in chronic heart failure:Integration of blood-entry component profiling,network pharmacology,and molecular docking 认领 引用
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作者 Ni-Hui Zhang Xu Liang +2 位作者 Song-Song Jing Wei-Qiang Huang Xia Li 《Traditional Medicine Research》 2026年第11期40-50,共11页
Background:Aconiti radix lateralis praeparata(Fuzi)is widely used for cardiotonic therapy in traditional Chinese medicine,but is limited by toxicity.Licorice-processed aconite(Zhifuzi,ZFZ)is classical processing inten... Background:Aconiti radix lateralis praeparata(Fuzi)is widely used for cardiotonic therapy in traditional Chinese medicine,but is limited by toxicity.Licorice-processed aconite(Zhifuzi,ZFZ)is classical processing intended to reduce toxicity while preserving efficacy,yet its comparative effects with HSP and underlying mechanisms in chronic heart failure(CHF)remain unclear.Methods:A rat CHF model was established by abdominal aortic coarctation.After model validation by echocardiography(EF≤55%),animals received HSP or ZFZ at low,medium and high doses,Shenfu Qiangxin Pills(SFQX)as a positive control,or vehicle for 4 weeks.Cardiac function,plasma biomarkers(BNP,AngII,CK),inflammatory cytokines in cardiac tissue(TNF-α,IL-6,IL-10),and histopathology(HE,Masson staining)were assessed.Blood-entry components of ZFZ were profiled by UPLC-Q Exactive-Orbitrap-MS,followed by target prediction,protein–protein interaction analysis,GO/KEGG enrichment and molecular docking.Results:Both ZFZ and HSP improved cardiac function,reduced plasma BNP,Ang II,and CK levels,alleviated inflammatory responses,and attenuated myocardial fibrosis in CHF rats.ZFZ showed relatively better effects than HSP in selected parameters,particularly in the high-dose group.Thirty-one blood-entry metabolites were detected,including 16 prototype compounds.Network pharmacology suggested that alkaloids,flavonoids and triterpenoids target multiple proteins enriched in PI3K–Akt,cAMP and calcium signaling pathways.Docking indicated that talatisamine,oleanolic acid and hetisine exhibited stable binding to MAPK1,PIK3CA and PRKACA,respectively.Conclusion:ZFZ and HSP both exerted cardioprotective effects in CHF rats,while ZFZ showed relatively better effects in selected parameters under the present experimental conditions.The integrated analysis of blood-entry component profiling,network pharmacology,and molecular docking provided preliminary mechanistic clues suggesting that the cardioprotective effects of ZFZ may be associated with multiple components,targets,and pathways.These findings provide comparative pharmacodynamic evidence and a basis for further mechanistic investigation of processed Fuzi in chronic heart failure. 展开更多
关键词 chronic heart failure Aconiti radix lateralis praeparata(Fuzi) Heishunpian network pharmacology molecular docking
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The mechanism of Huangqi Guizhi Decoction in improving pulmonary embolism based on network pharmacology and molecular docking technology 认领 引用
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作者 Yiting Wang Bo Hong +4 位作者 Yanan Bao Huan Cong Jiawen Liu Dan Zeng Wenjing Li 《Asian Journal of Traditional Medicines》 CAS 2026年第1期15-30,共16页
This study explored the therapeutic targets and molecular mechanisms of Huangqi Guizhi Decoction (HGD) in alleviatingpulmonary embolism (PE) by employing network pharmacology and molecular docking techniques. Firstly,... This study explored the therapeutic targets and molecular mechanisms of Huangqi Guizhi Decoction (HGD) in alleviatingpulmonary embolism (PE) by employing network pharmacology and molecular docking techniques. Firstly, the effective activecomponents of the Chinese herbs in HGD were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database(TCMSP), and their potential therapeutic targets were predicted using the Swiss Target Prediction platform. Subsequently, PErelatedtarget genes were obtained from the Online Mendelian Inheritance in Man (OMIM) database and GeneCards database.Then, the Wei Sheng Xin tool was used to generate a Venn diagram for identifying the common targets between the herb-relatedtargets and PE-related targets. After screening these common targets, a “drug-component-target network” and a protein-proteininteraction (PPI) network were constructed. Furthermore, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia ofGenes and Genomes (KEGG) enrichment analysis were conducted on the intersecting targets, and molecular docking verificationwas performed using AutoDockTools and PyMol software. Finally, 20 active components were screened from Astragali Radix, 7from Cinnamomi Ramulus, 13 from Paeoniae Radix Alba, 5 from Zingiberis Rhizoma Recens, and 29 from Jujubae Fructus, witha total of 983 therapeutic targets. Among these targets, 134 were associated with PE, and protein kinase B1 (AKT1), mitogenactivatedprotein kinase 1 (MAPK1), and transformation-related protein 53 (TP53) served as the core targets. The results of GOand KEGG enrichment analyses indicated that the alleviation of PE by HGD is mainly related to pathways including immuneresponse, regulation of gene expression, atherosclerosis, and tumorigenesis. Molecular docking results showed that the keyactive components in HGD could bind to the core targets spontaneously and stably. This study revealed that HGD may alleviatesymptoms in PE patients by regulating signaling pathways, modulating platelet function to exert anticoagulant effects, andregulating the expression of anti-inflammatory genes, which provided a direction for subsequent experimental research. 展开更多
关键词 Huangqi Guizhi Decoction pulmonary embolism network pharmacology molecular docking
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Exploration of the Molecular Mechanisms of Codonopsis pilosula in Treating Immune Deficiency Based on Network Pharmacology,Bioinformatics,and Molecular Docking 认领 引用
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作者 Yongfei LIU Maozhao WU +2 位作者 Tao WANG Yanling REN Yanyan SONG 《Medicinal Plant》 2026年第3期47-51,58,共5页
[Objectives]To investigate the potential molecular mechanisms of Codonopsis pilosula in the treatment of immune deficiency using network pharmacology,bioinformatics analysis,and molecular docking.[Methods]Active compo... [Objectives]To investigate the potential molecular mechanisms of Codonopsis pilosula in the treatment of immune deficiency using network pharmacology,bioinformatics analysis,and molecular docking.[Methods]Active compounds of C.pilosula were retrieved from the TCMSP database using oral bioavailability(OB)≥30%and drug-likeness(DL)≥0.18 as screening criteria,followed by further optimization using SwissADME.Potential targets of the active compounds were predicted using the Prediction.charite and GeneCards databases.A protein-protein interaction(PPI)network was constructed using the STRING database and visualized with Cytoscape to identify core targets.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses were performed using the DAVID database.Molecular docking between key active compounds and core target proteins was carried out using SwissDock,and the docking results were visualized with PyMOL.[Results]A total of 21 active compounds were initially identified from the TCMSP database.After pharmacokinetic evaluation,four potential bioactive compounds were screened,namely Perlolyrine(MOL002140),7-methoxy-2-methyl isoflavone(MOL003896),Frutinone A(MOL005321),and Glycitein(MOL008400).Due to database availability and target prediction feasibility,only two compounds(7-methoxy-2-methyl isoflavone and Glycitein)were included in subsequent analyses.Therefore,the results of this study primarily reflect the potential mechanisms of these two isoflavone components.Venn analysis identified 63 overlapping targets.PPI network analysis revealed 14 core targets.GO and KEGG enrichment analyses indicated that these targets were mainly involved in inflammation-related processes,amino acid metabolism,and immune defense.Molecular docking showed that except for the Glycitein-HSP90AA1 pair(-2.253 kcal/mol),which exhibited no significant binding activity,most ligand-target pairs had binding energies lower than-5 kcal/mol.[Conclusions]This study computationally predicts that 7-methoxy-2-methyl isoflavone and Glycitein from C.pilosula may exert therapeutic effects on immune deficiency through a multi-target and multi-pathway mode of action.These findings provide a theoretical basis for further experimental validation and clinical application of C.pilosula in the prevention and treatment of immune deficiency. 展开更多
关键词 Network pharmacology Bioinformatics Molecular docking Codonopsis pilosula Immune deficiency
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Network Pharmacological and Molecular Mechanism Analysis of Bovine Embryonic Stem Cell Mitochondria Polypeptides(EST-Mips)in Anti-Aging 认领 引用
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作者 Junjie Hao Pengcheng Ding +1 位作者 Huoqiang Jiang Jiren Zhang 《Journal of Clinical and Nursing Research》 2026年第6期362-374,共13页
Embryonic stem cell mitochondrial peptides(EST-Mips)are a group of peptide molecules derived from bovine embryonic stem cells,closely associated with telomere maintenance and mitochondrial function.In this study,based... Embryonic stem cell mitochondrial peptides(EST-Mips)are a group of peptide molecules derived from bovine embryonic stem cells,closely associated with telomere maintenance and mitochondrial function.In this study,based on 736 EST-Mips-regulated protein targets provided by users,we employed network pharmacology and bioinformatics approaches to systematically elucidate their molecular mechanisms in delaying the aging process.By screening target-aging associations using platforms such as PubChem,GeneCards,Human Aging Genomic Resources(HAGR/GenAge),Open Genes,and AgeAnno,we identified a total of 179 shared aging-related targets(accounting for 24.3%of all targets).Key targets include hub proteins with node connectivity≥50,such as TP53,AKT1,SRC,EGFR,TNF,IL6,MAPK1,and MAPK3.GO functional enrichment analysis revealed that EST-Mips primarily participate in cell cycle regulation,apoptosis signaling,oxidative stress response,and inflammatory responses.KEGG pathway analysis demonstrated that EST-Mips exert their anti-aging effects by modulating aging-related signaling pathways,including PI3K-Akt,FoxO,p53,MAPK,JAK-STAT,and NF-κB.Comprehensive analysis indicates that EST-Mips exert their anti-aging effects through a multidimensional network involving“telomere maintenance—mitochondrial homeostasis—metabolic remodeling—immune modulation”synergistically. 展开更多
关键词 Bovine embryonic brain cells Mitochondrial polypeptides Network pharmacology Molecular docking Anti-aging
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Exploring the Mechanism of Tibetan Medicine Twenty Five Flavored Coral Pills in Treating Ischemic Stroke Based on Network Pharmacology and Molecular Docking 认领 引用
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作者 TIAN Chun-hong ZHANG Yan-ju ZHANG Lin 《神经药理学报》 CAS 2026年第1期1-11,共11页
Objective:To explore the mechanism of Twenty Five Flavored Coral Pills in the treatment of ischemic stroke(IS)based on network pharmacology and molecular docking.Methods:The active ingredients of Twenty Five Flavored ... Objective:To explore the mechanism of Twenty Five Flavored Coral Pills in the treatment of ischemic stroke(IS)based on network pharmacology and molecular docking.Methods:The active ingredients of Twenty Five Flavored Coral Pills were searched through TCMSP and Herb databases,and the target of action was screened by Pubchem database and Swiss Target Prediction database;Retrieve Ischemic Stroke disease gene targets from GeneCards database,OMIM,and TTD database;Protein interaction network analysis,KEGG and GO enrichment analysis were performed on the standardized active ingredient targets and disease target genes after crossing using String database,Cytoscape 3.9.0 software,David database and bioinformatics platform.Apply an auxiliary platform for molecular docking verification and visualize the results using PyMOL software.Results:Through network pharmacology screening,1133 effective active ingredient targets and 667 disease target genes were identified for the treatment of IS in the Twenty Five Flavored Coral Pill.A total of 177 potential target genes were identified through intersection mapping.After data topology analysis,the top 3 core components with the highest degree values were identified as TP53,SRC,and AKT1.Functional and pathway enrichment analysis indicated that the biological processes(BP)mainly involved responses to hypoxia,positive regulation of phosphatidylinositol 3-kinase/protein kinase B signaling,and negative regulation of gene expression.The cellular components(CC)mainly involved the plasma membrane,cell surface,extracellular space,and extracellular region.Molecular function(MF)involves enzyme binding,identical protein binding,protein binding,and so on.KEGG pathway enrichment involves AGE-RAGE signaling pathway in diabetic complications,Pathways in cancer,Proteoglycans in cancer,HIF-1 signaling pathway,Lipid and atherosclerosis etc.Four key components(kaempferol,beta-sitosterol,quercetin,isorhamnetin)were selected for molecular docking with the four core components(TP53,SRC,AKT1,TNF).The results showed that the key component has strong binding ability with the core target.Molecular function(MF)involves enzyme binding,identical protein binding,protein binding,and so on.KEGG pathway enrichment involves AGE-RAGE signaling pathway in diabetic complications,the Pathways in cancer,the HIF-1 signaling pathway,the lipid and atherosclerosis.Four key components(kaempferol,beta-sitosterol,quercetin,isorhamnetin)were selected for molecular docking with the four core components(TP53,SRC,AKT1,TNF).Conclusion:Network pharmacology research has preliminarily elucidated that the Tibetan medicine Twenty Five Flavored Coral Pills has multiple effective ingredients;meanwhile,the key component has a strong binding ability with the core target.and can exert synergistic therapeutic effects through multiple targets and pathways. 展开更多
关键词 network pharmacology molecular docking ischemic stroke Tibetan medicine twenty five flavored coral pills
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Exploring Potential Mechanisms of Atractylodes lancea in Chronic Pancreatitis by Network Pharmacology and Molecular Docking 认领 引用
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作者 Hui WANG Mengyun WANG +1 位作者 Yanzhen ZUO Yuhong LI 《Asian Agricultural Research》 2026年第7期63-68,共6页
[Objectives]To explore the mechanism of Atractylodes lancea in the treatment of chronic pancreatitis(CP).[Methods]The network pharmacology and molecular docking techniques were applied.The active components of A.lance... [Objectives]To explore the mechanism of Atractylodes lancea in the treatment of chronic pancreatitis(CP).[Methods]The network pharmacology and molecular docking techniques were applied.The active components of A.lancea were screened through the TCMSP database,and the potential targets of A.lancea were predicted using the SwissTargetPrediction database.Disease-related targets of chronic pancreatitis were collected from the GeneCards and OMIM databases.Cytoscape software was used to construct and analyse the"drug component-target"network.The intersecting targets between the active component targets of A.lancea and CP-related targets were identified,and a protein-protein interaction(PPI)network was constructed and analysed using the STRING database and Cytoscape software to obtain the core targets.GO functional enrichment analysis and KEGG pathway enrichment analysis of the intersecting targets were performed using RStudio software.Finally,AutoDock Tools software was employed to validate the molecular docking between the major active components and the core targets.[Results]A total of 9 active components of A.lancea,279 component-related targets,1160 disease-related targets,and 94 intersecting drug-disease targets were identified.The core genes involved in the treatment of CP by A.lancea mainly included IL6,TNF,STAT3,TP53,and EGFR.The major signalling pathways included the PI3K-Akt signalling pathway,lipid and atherosclerosis,and proteoglycans in cancer.The intervention of A.lancea in CP involves a complex biological process with multiple targets and pathways.[Conclusions]This study elucidates the mechanism of A.lancea against CP from the perspectives of multi-component and multi-target actions,and provides a theoretical basis as well as directions for subsequent molecular biological experiments. 展开更多
关键词 Atractylodes lancea Chronic pancreatitis(CP) Network pharmacology Molecular docking
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Fingerprint-enhanced hierarchical molecular graph neural networks for property prediction 认领 引用 被引量：1
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作者 Shuo Liu Mengyun Chen +1 位作者 Xiaojun Yao Huanxiang Liu 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2025年第6期1311-1320,共10页
Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based me... Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates. 展开更多
关键词 Deep learning Hierarchical molecular graph Molecular fingerprint Molecular property prediction Directed message-passing neural network
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Dual Self-attention Fusion Message Neural Network for Virtual Screening in Drug Discovery by Molecular Property Prediction 认领 引用
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作者 Jingjing Wang Kangming Hou +2 位作者 Hao Chen Jing Fang Hongzhen Li 《Journal of Bionic Engineering》 SCIE EI CSCD 2025年第1期354-369,共16页
The development of deep learning has made non-biochemical methods for molecular property prediction screening a reality,which can increase the experimental speed and reduce the experimental cost of relevant experiment... The development of deep learning has made non-biochemical methods for molecular property prediction screening a reality,which can increase the experimental speed and reduce the experimental cost of relevant experiments.There are currently two main approaches to representing molecules:(a)representing molecules by fixing molecular descriptors,and(b)representing molecules by graph convolutional neural networks.Currently,both of these Representative methods have achieved some results in their respective experiments.Based on past efforts,we propose a Dual Self-attention Fusion Message Neural Network(DSFMNN).DSFMNN uses a combination of dual self-attention mechanism and graph convolutional neural network.Advantages of DSFMNN:(1)The dual self-attention mechanism focuses not only on the relationship between individual subunits in a molecule but also on the relationship between the atoms and chemical bonds contained in each subunit.(2)On the directed molecular graph,a message delivery approach centered on directed molecular bonds is used.We test the performance of the model on eight publicly available datasets and compare the performance with several models.Based on the current experimental results,DSFMNN has superior performance compared to previous models on the datasets applied in this paper. 展开更多
关键词 Directed message passing network Deep learning Molecular property prediction Self-attention mechanism
Deciphering bioactive compounds of complex natural products by tandem mass spectral molecular networking combined with an aggregation-induced emission based probe 认领 引用 被引量：5
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作者 Zhenzhong Yang Jun Li +2 位作者 Xuechun Chen Xiaoping Zhao Yi Wang 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2022年第1期129-135,共7页
Natural products are great treasure troves for the discovery of bioactive components.Current bioassay guided fractionation for identification of bioactive components is time-and workload-consuming.In this study,we pro... Natural products are great treasure troves for the discovery of bioactive components.Current bioassay guided fractionation for identification of bioactive components is time-and workload-consuming.In this study,we proposed a robust and convenient strategy for deciphering the bioactive profile of natural products by mass spectral molecular networking combined with rapid bioassay.As a proof-of-concept,the strategy was applied to identify angiotensin converting enzyme(ACE)inhibitors of Fangjihuangqi decoction(FJHQD),a traditional medicine clinically used for the treatment of heart failure.The chemical profile of FJHQD was comprehensively revealed with the assistance of tandem mass spectral molecular networking,and a total of 165 compounds were identified.With characterized constituents,potential clinical applications of FJHQD were predicted by Bioinformatics Analysis Tool for Molecular mech ANism of Traditional Chinese Medicine,and a range of cardiovascular related diseases were significantly enriched.ACE inhibitory activities of FJHQD and its constituents were then investigated with an aggregation-induced emission based fluorescent probe.FJHQD exhibited excellent ACE inhibitory effects,and a bioactive molecular network was established to elucidate the ACE inhibitory profile of constituents in FJHQD.This bioactive molecular network provided a panoramic view of FJHQD’s ACE inhibitory activities,which demonstrated that flavones from Astragali Radix and Glycyrrhizae Radix et Rhizoma,saponins from Astragali Radix,and sesquiterpenoids from Atractylodis Macrocephalae Rhizoma were principal components responsible for this effect of FJHQD.Among them,four novel ACE inhibitors were the first to be reported.Our study indicated that the proposed strategy offers a useful approach to uncover the bioactive profile of traditional medicines and provides a pragmatic workflow for exploring bioactive components. 展开更多
关键词 Bioactive profile Bioactive molecular network Fangjihuangqi decoction Angiotensin converting enzyme inhibitors
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Potential mechanism of Camellia luteoflora against colon adenocarcinoma:An integration of network pharmacology and molecular docking 认领 引用
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作者 Yu-Di Dong Xi-Ming Wu +4 位作者 Wan-Qing Liu You-Wu Hu Hong Zhang Wan-Di Fang Qing Luo 《World Journal of Gastrointestinal Oncology》 SCIE 2025年第6期372-391,共20页
BACKGROUND Camellia luteoflora is a unique variety of Camellia in China which is only distributes in Chishui City,Guizhou Province and Luzhou City,Sichuan Province.Its dried leaves are used by local residents as tea t... BACKGROUND Camellia luteoflora is a unique variety of Camellia in China which is only distributes in Chishui City,Guizhou Province and Luzhou City,Sichuan Province.Its dried leaves are used by local residents as tea to drink with light yellow and special aroma for health care.It has high potential economic medicinal value.Colon adenocarcinoma(COAD)is the third most frequent malignancy and its incidence and mortality is increasing.However,the current common treatments for COAD bring great side effects.In recent years,natural products and their various de-rivatives have shown significant potential to supplement conventional therapies and to reduce associated toxicity while improving efficacy.In order to overcome the limitations of traditional treatment methods,the global demand and development of natural anti-COAD drugs were increasingly hindered.AIM To investigate the potential targets and mechanisms of Camellia luteoflora anti-COAD.METHODS Nuclear magnetic resonance and mass spectrometry was used to identified the compounds of Camellia luteoflora.Network pharmacology analysis and survival analysis was used in this study to investigate the anti-COAD effect and mechanism of Camellia luteoflora.RESULTS Firstly,a total of 13 compounds were identified.Secondly,10 active ingredients for 204 potential targets were screened and protein-protein interaction analysis showed that TP53,STAT3,ESR1,MAPK8,AKR1C3,RELA,CYP19A1,CYP1A1,JUN and CYP17A1 were hub targets.GO and KEGG enrichment analyses revealed that Camellia luteoflora exerted anti-COAD effect through multiple functions and pathways.Then,the analysis of survival and stage indicated that TP53 was highly expressed in COAD and the overall survival of high-TP53 and high-CYP19A1 COAD patients was significantly shorter than the low group and there was significant difference in MAPK and RELA expression between different stages.Finally,the molecular docking results demonstrated the binding affinities and sites between active ingredients and TP53,STAT3,ESR1.CONCLUSION Our study systematically demonstrated the potential anti-COAD mechanism of Camellia luteoflora and provided a theoretical basis for its further application in the COAD treatment. 展开更多
关键词 Camellia luteoflora Tea Colon adenocarcinoma Natural product Network pharmacology Molecular docking
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Rapid discovery of two unprecedented meroterpenoids from Daphne altaica Pall.using molecular networking integrated with MolNetEnhancer and Network Annotation Propagation 认领 引用 被引量：1
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作者 Wei-Yu Zhou Zi-Han Xi +7 位作者 Ning-Ning Du Li Ye Ming-Hao Jiang Jin-Le Hao Bin Lin Guo-Dong Yao Xiao-Xiao Huang Shao-Jiang Song 《Chinese Chemical Letters》 SCIE CAS CSCD 2024年第8期294-298,共5页
Under the guidance of the approach which integrates molecular networking,MolNetEnhancer and Net-work Annotation Propagation(NAP),daphnaltaicanoids A and B(1 and 2)with unprecedented 9-oxa-tetracyclo[6.6.1.02,6.0^(8... Under the guidance of the approach which integrates molecular networking,MolNetEnhancer and Net-work Annotation Propagation(NAP),daphnaltaicanoids A and B(1 and 2)with unprecedented 9-oxa-tetracyclo[6.6.1.02,6.08,13]pentadecane and tetracyclo[5.3.0.12,5.24,11]tridecane central frameworks were iso-lated from Daphne altaica Pall.,representing two types of unparalleled meroterpenoid cores.Their struc-tures were elucidated by extensive spectroscopic analysis,nuclear magnetic resonance(NMR)calcula-tions,DP4+analysis and electronic circular dichroism(ECD)calculations.The plausible biosynthetic path-ways for 1 and 2 were postulated.Biologically,2 exerted potent neuroprotective activities which were su-perior to trolox at 12.5 and 25μmol/L.Moreover,1 and 2 exhibited more noticeable acetylcholinesterase inhibitory activities than donepezil.Molecular docking simulations were performed to explore the inter-molecular interaction of compounds 1 and 2 with acetylcholinesterase.The bioactivity evaluation results highlight the prospects of 1 and 2 as a novel category of neurological agents. 展开更多
关键词 Daphne altaica Pall. Molecular networking MolNetEnhancer NAP Unprecedented meroterpenoid frameworks Neuroprotective activities Acetylcholinesterase inhibitors
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Network pharmacology and molecular docking reveal the potential inner mechanism between sensitive skin and hyperpigmentation 认领 引用
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作者 Jianhua Zhang Shichao Liu +2 位作者 Wenjiao Guo Zhiyun Du Li Lin 《Journal of Dermatologic Science and Cosmetic Technology》 2025年第1期11-23,共13页
Background:Sensitive skin affects a substantial portion of the global population and has significant implications for skin health and well-being.In addition to unpleasant sensory effects,individuals with sensitive ski... Background:Sensitive skin affects a substantial portion of the global population and has significant implications for skin health and well-being.In addition to unpleasant sensory effects,individuals with sensitive skin were likely to be more susceptible to hyperpigmentation.However,the association between sensitive skin and hyperpigmentation,as well as the underlying molecular mechanisms,remain unclear.Objective:This study aims to investigate the correlation and intrinsic mechanisms between sensitive skin and hyperpigmentation through network pharmacology combined with molecular docking.Materials and Methods:The targets associated with sensitive skin and hyperpigmentation were collected from the human gene database,GeneCards.Subsequently,the protein-protein interaction(PPI)network,Kyoto Encyclopedia of Genes and Genomes(KEGG),and Gene Ontology(GO)enrichment analysis were performed to explore the biological connections between sensitive skin and hyperpigmentation.Additionally,the targets of 15 active compounds with reported lightening effects were collected from TCMSP,BATMAN and SymMap databases.Target analysis and molecular docking were performed to identify potential candidates for addressing hyperpigmentation on sensitive skin.The anti-melanogenesis effect of the identified candidate was verified in B16F10 cells.Results:A total of 16971 sensitive skin targets and 11382 hyperpigmentation targets were screened,and 9693 overlapping targets were identified,with a core set comprising 164 targets.The combination of PPI network,KEGG and GO analysis revealed the key role of tyrosinase and immune-mediated inflammation in pigmentation on sensitive skin.Among the 15 active compounds,oxyresveratrol was identified as having a high correlation with the core set targets and predicted strong inhibition of Tyrosine-protein Kinase Kit.The application of oxyresveratrol exhibited a dose-dependent suppression of melanin production in B16F10 cells.Conclusion:This study suggested the crucial roles of immune-mediated inflammation in sensitive skin and hyperpigmentation,as well as highlighted the potential of oxyresveratrol in addressing hyperpigmentation on sensitive skin.These comprehensive findings provide a deeper understanding of the connection mechanism between sensitive skin and hyperpigmentation,offering new insights for the development of targeted treatments and interventions. 展开更多
关键词 Sensitive skin Hyperpigmentation Oxyresveratrol Network pharmacology Molecular docking
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Exploring the material basis and mechanisms of the action of Hibiscus mutabilis L. for its anti-inflammatory effects based on network pharmacology and cell experiments 认领 引用
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作者 Wenyuan Chen Xiaolan Chen +2 位作者 Jing Wan Qin Deng Yong Gao 《日用化学工业（中英文）》 CAS 北大核心 2026年第1期55-64,共10页
To explore the material basis and mechanisms of the anti-inflammatory effects of Hibiscus mutabilis L..The active ingredients and potential targets of Hibiscus mutabilis L.were obtained through the literature review a... To explore the material basis and mechanisms of the anti-inflammatory effects of Hibiscus mutabilis L..The active ingredients and potential targets of Hibiscus mutabilis L.were obtained through the literature review and SwissADME platform.Genes related to the inflammation were collected using Genecards and OMIM databases,and the intersection genes were submitted on STRING and DAVID websites.Then,the protein interaction network(PPI),gene ontology(GO)and pathway(KEGG)were analyzed.Cytoscape 3.7.2 software was used to construct the“Hibiscus mutabilis L.-active ingredient-target-inflammation”network diagram,and AutoDockTools-1.5.6 software was used for the molecular docking verification.The antiinflammatory effect of Hibiscus mutabilis L.active ingredient was verified by the RAW264.7 inflammatory cell model.The results showed that 11 active components and 94 potential targets,1029 inflammatory targets and 24 intersection targets were obtained from Hibiscus mutabilis L..The key anti-inflammatory active ingredients of Hibiscus mutabilis L.are quercetin,apigenin and luteolin.Its action pathway is mainly related to NF-κB,cancer pathway and TNF signaling pathway.Cell experiments showed that total flavonoids of Hibiscus mutabilis L.could effectively inhibit the expression of tumor necrosis factor(TNF-α),interleukin 8(IL-8)and epidermal growth factor receptor(EGFR)in LPS-induced RAW 264.7 inflammatory cells.It also downregulates the phosphorylation of human nuclear factor ĸB inhibitory protein α(IĸBα)and NF-κB p65 subunit protein(p65).Overall,the anti-inflammatory effect of Hibiscus mutabilis L.is related to many active components,many signal pathways and targets,which provides a theoretical basis for its further development and application. 展开更多
关键词 Hibiscus mutabilis L. inflammation network pharmacology molecular docking cell validation
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