BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants w...BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants with the aim of eliminating the pathogen;however,the possibility of blocking H.pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed.This type of study is expensive and time-consuming,requiring in vitro and/or in vivo tests,which can be solved using bioinformatics.Therefore,prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein.AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H.pylori.METHODS In this in silico study,the structures of the phenolic compounds(ligands)kaempferol,myricetin,quercetin,ponciretin(flavonoids),and chlorogenic acid(phenolic acid)were selected from the PubChem database.These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H.pylori infection.The three-dimensional structure model of the CagA oncoprotein of H.pylori(receptor)was obtained through molecular modeling using computational tools from the I-Tasser platform,employing the threading methodology.The primary sequence of CagA was sourced from GenBank(BAK52797.1).A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands,utilizing the GRaSP online platform.Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4(ADT)software,and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software.Two sets of simulations were performed:One involving the central region of CagA with phenolic compounds,and another involving the carboxy-terminus region of CagA with phenolic compounds.The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software.RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality(C-score=0.09)and was validated using parameters from the MolProbity platform.The GRaSP online platform identified 24 residues(phenylalanine and leucine)as potential binding sites on the CagA oncoprotein.Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein.No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds;however,all phenolic compounds interacted with the central region of the oncoprotein.Phenolic compounds and CagA exhibited significant affinity energy(-7.9 to-9.1 kcal/mol):CagA/kaempferol formed 28 chemical bonds,CagA/myricetin formed 18 chemical bonds,CagA/quercetin formed 16 chemical bonds,CagA/ponciretin formed 13 chemical bonds,and CagA/chlorogenic acid formed 17 chemical bonds.Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif,all of them bound to residues,mostly positively or negatively charged,located near this region.CONCLUSION In silico,the tested phenolic compounds formed stable complexes with CagA.Therefore,they could be tested in vitro and/or in vivo to validate the findings,and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.展开更多
Objective To investigate whether the presence of structured CagA proteins in Western- and Eastern-type Helicobacter pylori （H. pylori） induces different incidences of gastric diseases. Methods CagA and phosphorylatd...Objective To investigate whether the presence of structured CagA proteins in Western- and Eastern-type Helicobacter pylori （H. pylori） induces different incidences of gastric diseases. Methods CagA and phosphorylatd CagA were expressed in AGS gastric epithelial cells infected with wild type and mutant strains. The ability of individual CagA was determined by immunoprecipitation and Western blot assay. Morphological changes of these cells were observed under microscope to evaluate the appearance of elongation hummingbird phenotype. Results The sizes of CagA proteins in different strains were different, and no phosphorylated CagA proteins were detected in wild-type strains. Meanwhile, the kinetics of CagA status in AGS infected with H. pylori was detected. The molecular weight of phosphorylated CagA with the same size of CagA proteins in H. pylori was different in infections with different wild-type strains. CagA and phosphorylated CagA increased in a time-dependent manner after the infection. The hummingbird phenotype with H. pylori for time-course was observed under microscope. Instead of HPK5 strain, the wild-type 26695 strain induced hummingbird phenotype in a time-dependent manner. Conclusion Translocation and phosphorylation of CagA are necessary, but not sufficient, for the induction of hummingbird phenotype in AGS cells.展开更多
BACKGROUND Helicobacter pylori(H.pylori)colonizes the human stomach and is a major cause of peptic ulcer disease and gastric cancer.However,although the prevalence of H.pylori is high in Africa,the incidence of gastri...BACKGROUND Helicobacter pylori(H.pylori)colonizes the human stomach and is a major cause of peptic ulcer disease and gastric cancer.However,although the prevalence of H.pylori is high in Africa,the incidence of gastric cancer is low,and this phenomenon is called to be African enigma.The CagA protein produced by H.pylori is the most studied virulence factor.The carcinogenic potential of CagA is associated with the Glu-Pro-Ile-Tyr-Ala(EPIYA)patterns and CagAmultimerization(CM)motifs.AIM To better understand the EPIYA patterns and CM motifs of the cagA gene.METHODS Gastric mucosal biopsy specimens were obtained from 258 patients with dyspepsia living in the Dominican Republic,from which 120 H.pylori strains were cultured.After the bacterial DNA extraction,the EPIYA pattern and CM motif genotypes were determined using a polymerase chain reaction-based sequencing.The population structure of the Dominican Republic strains was analyzed using multilocus sequence typing(MLST).Peptic ulcer disease and gastric cancer were identified via endoscopy,and gastric cancer was confirmed by histopathology.Histological scores of the gastric mucosa were evaluated using the updated Sydney system.RESULTS All CagA-positive strains carried the Western-type CagA according to the identified EPIYA patterns.Twenty-seven kinds of CM motifs were observed.Although the typical Western CM motif(FPLKRHDKVDDLSKVG)was observed most frequently,the typical East Asian CM motif(FPLRRSAAVNDLSKVG)was not observed.However,“FPLRRSAKVEDLSKVG”,similar to the typical East Asian CM motif,was found in 21 strains.Since this type was significantly more frequent in strains classified as hpAfrica1 using MLST analysis(P=0.034),we termed it Africa1-CM(Af1-CM).A few hpEurope strains carried the Af1-CM motif,but they had a significantly higher ancestral Africa1 component than that of those without the Af1-CM motif(P=0.030).In 30 cagA-positive strains,the"GKDKGPE"motif was observed immediately upstream of the EPIYA motif in the EPIYA-A segment,and there was a significant association between strains with the hpAfrica1 population and those containing the“GKDKGPE”motif(P=0.018).In contrast,there was no significant association between the CM motif patterns and histological scores and clinical outcomes.CONCLUSION We found the unique African CM motif in Western-type CagA and termed it Africa1-CM.The less toxicity of this motif could be one reason to explain the African enigma.展开更多
文摘BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants with the aim of eliminating the pathogen;however,the possibility of blocking H.pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed.This type of study is expensive and time-consuming,requiring in vitro and/or in vivo tests,which can be solved using bioinformatics.Therefore,prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein.AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H.pylori.METHODS In this in silico study,the structures of the phenolic compounds(ligands)kaempferol,myricetin,quercetin,ponciretin(flavonoids),and chlorogenic acid(phenolic acid)were selected from the PubChem database.These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H.pylori infection.The three-dimensional structure model of the CagA oncoprotein of H.pylori(receptor)was obtained through molecular modeling using computational tools from the I-Tasser platform,employing the threading methodology.The primary sequence of CagA was sourced from GenBank(BAK52797.1).A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands,utilizing the GRaSP online platform.Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4(ADT)software,and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software.Two sets of simulations were performed:One involving the central region of CagA with phenolic compounds,and another involving the carboxy-terminus region of CagA with phenolic compounds.The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software.RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality(C-score=0.09)and was validated using parameters from the MolProbity platform.The GRaSP online platform identified 24 residues(phenylalanine and leucine)as potential binding sites on the CagA oncoprotein.Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein.No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds;however,all phenolic compounds interacted with the central region of the oncoprotein.Phenolic compounds and CagA exhibited significant affinity energy(-7.9 to-9.1 kcal/mol):CagA/kaempferol formed 28 chemical bonds,CagA/myricetin formed 18 chemical bonds,CagA/quercetin formed 16 chemical bonds,CagA/ponciretin formed 13 chemical bonds,and CagA/chlorogenic acid formed 17 chemical bonds.Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif,all of them bound to residues,mostly positively or negatively charged,located near this region.CONCLUSION In silico,the tested phenolic compounds formed stable complexes with CagA.Therefore,they could be tested in vitro and/or in vivo to validate the findings,and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.
基金supported by China Postdoctoral Science Foundation (Grant No. 20070420277)
文摘Objective To investigate whether the presence of structured CagA proteins in Western- and Eastern-type Helicobacter pylori （H. pylori） induces different incidences of gastric diseases. Methods CagA and phosphorylatd CagA were expressed in AGS gastric epithelial cells infected with wild type and mutant strains. The ability of individual CagA was determined by immunoprecipitation and Western blot assay. Morphological changes of these cells were observed under microscope to evaluate the appearance of elongation hummingbird phenotype. Results The sizes of CagA proteins in different strains were different, and no phosphorylated CagA proteins were detected in wild-type strains. Meanwhile, the kinetics of CagA status in AGS infected with H. pylori was detected. The molecular weight of phosphorylated CagA with the same size of CagA proteins in H. pylori was different in infections with different wild-type strains. CagA and phosphorylated CagA increased in a time-dependent manner after the infection. The hummingbird phenotype with H. pylori for time-course was observed under microscope. Instead of HPK5 strain, the wild-type 26695 strain induced hummingbird phenotype in a time-dependent manner. Conclusion Translocation and phosphorylation of CagA are necessary, but not sufficient, for the induction of hummingbird phenotype in AGS cells.
基金Supported by The Grants-in-aid for Scientific Research from the Ministry of Education,Culture,Sports,Science,and Technology of Japan,No.16H05191,No.221S0002,No.16H06279,No.18KK0266 and No.19H03473(partly)the National Fund for Innovation and Development of Science and Technology from the Ministry of Higher Education Science and Technology of the Dominican Republic,No.2012-2013-2A1-65 and No.2015-3A1-182(MC).
文摘BACKGROUND Helicobacter pylori(H.pylori)colonizes the human stomach and is a major cause of peptic ulcer disease and gastric cancer.However,although the prevalence of H.pylori is high in Africa,the incidence of gastric cancer is low,and this phenomenon is called to be African enigma.The CagA protein produced by H.pylori is the most studied virulence factor.The carcinogenic potential of CagA is associated with the Glu-Pro-Ile-Tyr-Ala(EPIYA)patterns and CagAmultimerization(CM)motifs.AIM To better understand the EPIYA patterns and CM motifs of the cagA gene.METHODS Gastric mucosal biopsy specimens were obtained from 258 patients with dyspepsia living in the Dominican Republic,from which 120 H.pylori strains were cultured.After the bacterial DNA extraction,the EPIYA pattern and CM motif genotypes were determined using a polymerase chain reaction-based sequencing.The population structure of the Dominican Republic strains was analyzed using multilocus sequence typing(MLST).Peptic ulcer disease and gastric cancer were identified via endoscopy,and gastric cancer was confirmed by histopathology.Histological scores of the gastric mucosa were evaluated using the updated Sydney system.RESULTS All CagA-positive strains carried the Western-type CagA according to the identified EPIYA patterns.Twenty-seven kinds of CM motifs were observed.Although the typical Western CM motif(FPLKRHDKVDDLSKVG)was observed most frequently,the typical East Asian CM motif(FPLRRSAAVNDLSKVG)was not observed.However,“FPLRRSAKVEDLSKVG”,similar to the typical East Asian CM motif,was found in 21 strains.Since this type was significantly more frequent in strains classified as hpAfrica1 using MLST analysis(P=0.034),we termed it Africa1-CM(Af1-CM).A few hpEurope strains carried the Af1-CM motif,but they had a significantly higher ancestral Africa1 component than that of those without the Af1-CM motif(P=0.030).In 30 cagA-positive strains,the"GKDKGPE"motif was observed immediately upstream of the EPIYA motif in the EPIYA-A segment,and there was a significant association between strains with the hpAfrica1 population and those containing the“GKDKGPE”motif(P=0.018).In contrast,there was no significant association between the CM motif patterns and histological scores and clinical outcomes.CONCLUSION We found the unique African CM motif in Western-type CagA and termed it Africa1-CM.The less toxicity of this motif could be one reason to explain the African enigma.
