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Insight into the interaction of human pancreatic lipase with potential anti-obesity drug,Cetilistat,using a molecular docking and molecular dynamics simulation

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TMR pharmacology Research 2022年第3期2卷 7-11页

作者： Dnyaneshwar Nirmale Sunil S.Jalalpure KAHER’s Dr.Prabhakar Kore Basic Science Research center KLE Academy of Higher Education and ResearchNeharunagarBelagavi 590010India Principal KLE College of PharmacyBelagaviA constituent unit of KLE Academy of Higher Education and ResearchNeharunagarBelagavi 590010India

Background:Obesity is a lifestyle disease that involves an excessive amount of body fat *** is being used to treat *** mainly inhibits human pancreatic lipase,an enzyme that helps to break down the oil into small molecules of glycerol and fatty acids in the ***,pancreatic lipase inhibition is a potential therapeutic approach for obesity control and ***:cetilistat’s binding mode and interaction with human pancreatic lipase are not well *** this study,the human pancreatic lipase inhibitory activity of cetilistat was investigated by employing molecular docking and molecular dynamics *** pancreatic lipase has two states:closed state and open state which is controlled by a surface loop i.e.“lid region”which normally undergoes conformational changes only upon addition of lipids and then breakdown into glycerol and fatty *** the present study,open state conformation of the human pancreatic lipase structure was used(***).The docking study reveals that the cetilistat prefers to bind at the“lid region”of pancreatic ***,molecular dynamics simulation reveals that the cetilistat affects the structure and dynamics of human pancreatic ***,cetilistat affects the conformational changes in the“lid region”of pancreatic lipase which is important for the breakdown of ***,the radius of gyration(Rg)and solvent-accessible surface area shows that the cetilistat-bound pancreatic lipase affects the compactness of the lipase ***,our computational modeling study reveals the inhibitory action of cetilistat with human pancreatic lipase and may be further useful for the design and development of anti-obesity ***:To explore the binding mode and interaction of HPL with cetilistat,we employed molecular docking,a molecular dynamics simulation *** details of which are discussed ***:Thus,our computational modeling study reveals the inhibit

关键词： pancreatic lipase Cetilistat obesity docking molecular dynamics simulation

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Exploration of the Potential Mechanism of Gancao Yangyin Decoction on Aging Based on Network pharmacology

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Chinese Medicine and Natural Products 2021年第2期1卷 1-10页

作者： CHEN Yong CHEN Yanjuan ZHAO Li HE Hui ZHANG Siwei LIU Dongzhou Department of Rheumatology and Immunology Shenzhen People's Hospial/the Second Clinical Medical College of Jinan UniversityGuangzhouGuangdong 518020China School of Basic Medicine Jinan UniversityGuangzhouGuangdong 510632China Health Management center Shenzhen People's Hospital/the Second Clinical Medical College of Jinan UniversityGuangzhouGuangdong 518020China Chinese Medicine Department Shenzhen People's Hospital/the Second Clinical Medical College of Jinan UniversityGuangzhouGuangdong 518020China

Objective:To explore the targels and molecular mechanism of Gancao Yangyin Decoction(甘草养阴汤,GCYYD)based on network ***:The effective chemical components of 7 kinds of Chinese materia medica in GCYYD and their relevant targets were obtai ned through the traditional Chinese medicine systems pharmacology database and analysis platform(TCMSP)and the encyelopedia of traditional Chinese medicine(ETCM).The aging-related targets were obtained through GeneCards *** targets related to the effective chemical components were mapped with the aging-related targets,and the gene targets of GCY YD for intervening in aging were *** protein interaction network diagram of GCY YD interfering with aging was drawn through String database and Cytoscape 3.7.1 software,and the core target genes were *** potential targets obtained were analyzed by gene ontology(GO)biological function enrichment analysis and kyoto encyelopedia of genes and genomes(KEGG)pathway enrichment ***:Totally 130 effective chemical components of the 7 kinds of Chinese materia medica of GCYYD and 276 related targets were obtained from TCMSP and ETCM *** 216 aging-related targets were obtained through GeneCards *** were 63 target genes intervening in aging in GCYYD,with core target genes ALB,AKTI,TNF,L 6,MMP-3,VEGFA,CASP5,*** biological function and signaling pathway enrichment analyses for the target genes with R software,147 KEGG signaling pathways were found,mainly related to age-RAGE signaling pathway in diabetic complications,proteoglycans in cancer,fluid shear stress and atherosclero-sis,HIF-1 signaling pathway,human cytomegalovirus infection,celluar senescence,prostate cancer,bladder cancer,***:GCYYD can intervene in aging through"multicomponents-mulitargets-multipath-ways",which lays foundation for further experimental research.

关键词： Gancao Yangyin Decoction(甘草养阴汤,GCY YD) net work pharmacology aging action mechanism

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Network-pharmacology and molecular docking-based investigation of mechanism of Sophora flavescens on cancer and inflammation

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TMR Modern Herbal Medicine 2020年第4期3卷 178-191页

作者： Wenxuan Li Lijuan Deng Yuhe Lei Junshan Liu School of Traditional Chinese Medicine Southern Medical UniversityGuangzhou 510515P.R.China Formula pattern Research center School of Traditional Chinese MedicineJinan UniversityGuangzhou 510632P.R.China Department of Pharmacy Shenzhen Hospital of Guangzhou University of Chinese MedicineShenzhen518034P.R.China

Objective:In order to explore the systematical regulatory mechanism of Kushen(Sophora flavescens,SF)on inflammation and cancer,we analyzed inter-molecular interactions between herbal ingredients of SF and human inflammation and cancer through network-pharmacology and molecular docking-based ***:Firstly,ingredients and potential targets were obtained from Traditional Chinese Medicine Systems pharmacology Database and Analysis Platform,GeneCards database,Therapeutic Targets Database and Online Mendelian Inheritance in Man ***,protein-protein interaction network and medicine-ingredient-target-disease network were established and analyzed via STRING and ***-dock was performed by ***,functional enrichment and pathway enrichment were achieved by Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes ***:The results showed that 113 components of SF and 53 potential targets were related in the *** exerts anti-inflammatory and anti-cancer mechanism through key targets located in nucleus,such as JUN,MYC,RELA,NCOA,PPARG which may trigger the NF-κB pathway,the Bcl-2/Bax pathway and other pathways to effect DNA transcriptional ***:The study predicted the mechanism of SF on cancer and *** to the results,we suggest that the ingredients of SF effect on DNA bingding and transcription in nuclear receptors-like JUN,MYC,RELA,NCOA,*** receptors trigger several pathways including NF-κB pathway,the Bcl-2/Bax pathway and ***,it regulats inflammatory factors and cell proliferation,senescence and apoptosis.

关键词： Network-pharmacology molecular docking Sophora flavescens Cancer Inflammation

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One stop shop Ⅱ:taxonomic update with molecular phylogeny for important phytopathogenic genera:26–50(2019)

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Fungal Diversity 2019年第1期 41-129页

作者： Ruvishika S.Jayawardena Kevin D.Hyde Rajesh Jeewon Masoomeh Ghobad-Nejhad Dhanushka N.Wanasinghe NingGuo Liu Alan J.L.Phillips Jose Ribamar COliveira-Filho Gladstone Ada Silva Tatiana B.Gibertoni P.Abeywikrama L.M.Carris K.W.T.Chethana A.J.Dissanayake S.Hongsanan S.C.Jayasiri A.R.McTaggart R.H.Perera K.Phutthacharoen K.G.Savchenko R.G.Shivas Naritsada Thongklang Wei Dong DePing Wei Nalin NWijayawardena Ji-Chuan Kang The Engineering Research center of Southwest Biopharmaceutical Resources Ministry of EducationGuizhou UniversityGuiyang 550025People’s Republic of China center of excellence in Fungal Research Mae Fah Luang UniversityChiang RaiThailand Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Department of Biotechnology Iranian Research Organization for Science and Technology(IROST)P.O.Box 15815-3538Tehran 15819Iran World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Universidade de Lisboa Faculdade de CienciasBiosystems and Integrative Sciences Institute(BioISI)Campo Grande1749-016 LisbonPortugal Departamento de Micologia Universidade Federal de PernambucoAvenida da EngenhariaS/N-Cidade UniversitariaRecifePE 50740-600Brazil Beijing Key Laboratory of Environmet Friendly Management on Fruit Disease and Pests in North China Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Department of Plant Pathology Washington State UniversityPullmanWA 99164USA College of Life Science and Oceanography ShenZhen University1068Nanhai AvenueNanshanShenzhen 518055China Queensland Alliance for Agriculture and Food Innovation The University of QueenslandBrisbaneQLD 4001Australia Department of Biological Sciences Butler UniversityIndianapolisIN 46208USA Centre for Crop Health University of Southern QueenslandToowoombaQLD 4350Australia Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Faculty of Agriculture National Resources and EnvironmentNaresuan UniversityPhitsanulok 65000Thailand

This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic *** focuses on 25 phytopathogenic genera:Alternaria,Bipolaris,Boeremia,Botryosphaeria,Calonectria,Coniella,Corticiaceae,Curvularia,Elsinoe,Entyloma,Erythricium,Fomitiporia,Fulviformes,Laetisaria,Limonomyces,Neofabraea,Neofusicoccum,Phaeoacremonium,Phellinotus,Phyllosticta,Plenodomus,Pseudopyricularia,Tilletia,Venturia and Waitea,using recent molecular data,up to date names and the latest taxonomic *** each genus a taxonomic background,diversity aspects,species identification and classification based on molecular phylogeny and recommended genetic markers are *** this study,varieties of the genus Boeremia have been elevated to species ***,Bipolaris,Curvularia,Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries,as many new species have been introduced to these genera.

关键词： Boeremia DNA barcodes Endophytes Plant pathology Systematics Taxonomy

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Prunus genetics and applications after de novo genome sequencing:achievements and prospects

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Horticulture Research 2019年第1期6卷 1222-1246页

作者： Maria JoséAranzana Véronique Decroocq Elisabeth Dirlewanger Iban Eduardo Zhong Shan Gao Ksenija Gasic Amy Iezzoni Sook Jung Cameron Peace Humberto Prieto Ryutaro Tao Ignazio Verde Albert G.Abbott Pere Arús IRTA Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UBCampus UABEdifici CRAGCerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain UMR 1332 BFP INRAUniversity of BordeauxA3C and Virology Teams33882 Villenave-d’Ornon CedexFrance Allergy Research center Zhejiang University310058 HangzhouChina Clemson University ClemsonSC 29634USA Department of Horticulture Michigan State University1066 Bogue StreetEast LansingMI 48824-1325USA Department of Horticulture Washington State UniversityPullmanWA 99164-6414USA Biotechnology Laboratory La Platina Research StationInstituto de Investigaciones AgropecuariasSanta Rosa11610 La PintanaSantiagoChile Laboratory of Pomology Graduate School of AgricultureKyoto UniversityKyoto 606-8502Japan Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria(CREA)-Centro di ricerca Olivicoltura Frutticoltura e Agrumicoltura(CREA-OFA)RomeItaly University of Kentucky 106 T.P.Cooper HallLexingtonKY 40546-0073USA

Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST *** public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits *** this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome *** the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs ***,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus *** include phenology,fruit quality,allergens,disease resistance,tree architecture,and ***,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop ***,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.

关键词： Prunus breeding achievements

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Study on mechanism and molecular docking verification of Angelicae Sinensis Radix and Astragali Radix in treating ischemic stroke

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TMR Modern Herbal Medicine 2023年第2期6卷 9-17页

作者： Da-Yuan Zhong Hui Cheng Hong-Sheng Luo Yi-Hui Deng Huan-Jie Li De-Liang Liu Xue-Ming Ou Ping-Wen Liu Jia-Rong Li Xiang-Bo Kong Jia-Qi Chen Department of Neurosurgery Nanhai Hospital of Traditional Chinese and Western MedicineJinan UniversityFoshan 528200China Institute of Traditional Chinese Medicine Jinan UniversityGuangzhou 510632China Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine Guangzhou University of Chinese MedicineGuangzhou 510006China College of Integrative Medicine Hunan University of Chinese MedicineChangsha 410208China Preventive Treating Disease center Foshan Hospital of Traditional Chinese MedicineFoshan 528099China.

Background:Traditional Chinese medicine(TCM)has been shown to be effective in treating ischemic stroke(IS),and the combination of Angelicae Sinensis Radix(ASR)and Astragali Radix(AR)is a core TCM prescription that is widely acknowledged for its efficacy in IS *** study utilized network pharmacology methods to explore the molecular mechanisms underlying the therapeutic effects of Angelicae Sinensis Radix and Astragali Radix in IS treatment,with preliminary validation conducted through molecular ***:Information on the structure,targets,main biological functions,and pathways of the active components in Angelicae Sinensis Radix and Astragali Radix was collected using databases such as PubChem,PharmMapper,UniProt,and *** results were visualized using software such as Cytoscape 3.6.1,Ledock,and ***:We retrieved 20 active components and 149 targets associated with the compatibility of Angelicae Sinensis Radix and Astragali Radix from various databases,and GeneCards database was used to search 3350 IS-related gene targets,including 78 key targets of Angelicae Sinensis Radix and Astragali Radix for the treatment of *** analysis of these 78 targets using gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)revealed the involvement of 48 GO terms in the treatment of IS,mainly in biological processes such as metabolism,biological regulation,and stress *** composition of biological devices such as supercavitary membrane,cell fluid,and extracellular space was also *** biological functions mainly included protein binding,ion binding,hydrolytic enzyme activity,and *** identified pathways were estrogen signaling pathway,mitogen-activated protein kinase(MAPK)signaling pathway,PI3K-AKT signaling pathway,RAP1 signaling pathway,P53 signaling pathway,PPAR signaling pathway,FOXO signaling pathway,RAS signaling pathway,prolactin signaling pathway,HIF-1 signaling pathway,and TNF signaling ***

关键词： Angelicae Sinensis Radix Astragali Radix ischemic stroke network pharmacology molecular docking

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Study on mechanisms and molecular verification of Buyang Huanwu decoction in treating ischemic stroke from the perspective of cuproptosis

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TMR Integrative Medicine 2023年第13期7卷 1-10页

作者： Da-Yuan Zhong Hui Cheng Hong-Sheng Luo Quan Li Lan Li Huan-Jie Li Chun-Guang Guan De-Liang Liu Ping-Wen Liu Jia-Rong Li Xiang-Bo Kong Jia-Qi Chen Yi-Hui Deng Xue-Ming Ou Department of Neurosurgery Guangdong Provincial Hospital of Integrated Traditional Chinese and Western MedicineFoshan 528200China Institute of Traditional Chinese Medicine Jinan UniversityGuangzhou 510000China Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine Guangzhou University of Chinese MedicineGuangzhou 510006China College of Integrative Medicine Hunan University of Chinese MedicineChangsha 410208China Preventive Treating Disease center Foshan Hospital of Chinese MedicineFoshan 528099China Department of Geriatrics Dongguan Eastern Central HospitalDongguan 523560China

Background:Ischemic stroke(IS)is a global health issue and the current treatment options for IS are *** Huanwu decoction(BHD)has demonstrated effectiveness in treating ***,the mechanisms by which BHD treats IS remain unclear,and no studies have been conducted to analyze these mechanisms from the perspective of *** order to investigate the potential of BHD to intervene in IS through Cuproptosis,this study employed a systematic pharmacological approach and molecular docking ***:To investigate the mechanism of BHD in treating IS through Cuproptosis,relevant information on the structure,targets,and major biological functions and pathways of compounds related to BHD was collected from databases such as PubChem,PharmMapper,UniProt,and *** results were then visualized using Cytoscape3.6.1,Ledock,and pymol ***:BHD is composed of 7 Chinese medicines,which contain 82 compounds,including 10 core *** compounds are associated with 241 genes,of which 97 are common to BHD,IS,and *** 97 common genes,including 10 core genes,are involved in biological processes such as proteolysis,regulation of apoptosis and cholesterol storage,as well as cellular components and molecular *** common genes among BHD,IS,and Cuproptosis,including 10 core genes,participate mainly in Kyoto Encyclopedia of Genes and Genomes pathways such as pathways in cancer,PI3K-Akt signaling pathway,and Estrogen signaling *** to molecular docking results,linolenic acid showed good docking scores with 9 out of 10 core genes,except for SRC.13-hydroxy-9,11-octadecadienoic acid also demonstrated good docking scores with EGFR,MAPK14,and ***,senkyunone also had good docking scores with EGFR,MAPK14,and F2,all of which had docking energy greater than−5 ***:In this study,the potential of BHD for treating IS through Cuproptosis and its underlying mechanisms were explored and partially valida

关键词： Buyang Huanwu decoction ischemic stroke network pharmacology molecular docking

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