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
目的:探讨原癌蛋白18(Oncoprotein 18,Op18)在肝癌侵袭转移过程中的作用机制.方法:采用R N A干扰,抑制人肝癌细胞HCCLM3中Op18的表达,RT-PCR和Westernb l o t评价干扰效率;通过细胞粘附分析、体外Transwell分析法检测Op18表达缺失后对HC...目的:探讨原癌蛋白18(Oncoprotein 18,Op18)在肝癌侵袭转移过程中的作用机制.方法:采用R N A干扰,抑制人肝癌细胞HCCLM3中Op18的表达,RT-PCR和Westernb l o t评价干扰效率;通过细胞粘附分析、体外Transwell分析法检测Op18表达缺失后对HCCLM3细胞粘附、运动和侵袭能力的改变;RT-PCR和免疫组织化学分别在48例未伴转移的肝癌组织和48例伴转移的肝癌组织中解析Op18表达与肝癌侵袭转移的关系.结果:RT-PCR和Western blot结果显示:在HCCLM3细胞中行RNAi后Op18表达被有效抑制,抑制率达到80%以上;Op18表达缺失后,在不同时间点(20、40和60 min)实验组细胞粘附能力(0.616±0.057、0.740±0.0713和1.001±0.083)较阴性对照组(0.944±0.068、1.196±0.115和1.441±0.053)明显下降(P<0.05);Transwell实验结果提示:经RNAi后实验组细胞运动、侵袭能力(运动:0.145±0.011,侵袭0.127±0.008)较阴性对照组(运动:0.206±0.008,侵袭:0.168±0.012)显著降低(P<0.01);分别在伴转移和未伴转移的肝癌组织中检测Op18的表达,RT-PCR(Op18与GAPDH相对比值:0.560±0.128vs 0.414±0.086)和IHC(积分吸光度值为:624.771±100.032 vs 413.786±71.833)实验结果均提示Op18在伴转移的肝癌组织中的表达更高(P<0.01).结论:Op18在肝癌的侵袭转移过程中发挥重要作用.展开更多
胰腺导管内乳头状粘液性肿瘤（Intraductal Papillary Mucinous Neoplasms of the Pancreas,IPMNs）是胰腺癌最重要及最常见的癌前病变之一,约占临床诊断胰腺肿瘤的7%,占偶然发现的胰腺囊肿的50%[1,2]。IPMN分型包括伴轻度不典型增生、I...胰腺导管内乳头状粘液性肿瘤（Intraductal Papillary Mucinous Neoplasms of the Pancreas,IPMNs）是胰腺癌最重要及最常见的癌前病变之一,约占临床诊断胰腺肿瘤的7%,占偶然发现的胰腺囊肿的50%[1,2]。IPMN分型包括伴轻度不典型增生、IPMN伴中度不典型增生、IPMN伴重度不典型增生及IPMN相关浸润性;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.
文摘目的:探讨原癌蛋白18(Oncoprotein 18,Op18)在肝癌侵袭转移过程中的作用机制.方法:采用R N A干扰,抑制人肝癌细胞HCCLM3中Op18的表达,RT-PCR和Westernb l o t评价干扰效率;通过细胞粘附分析、体外Transwell分析法检测Op18表达缺失后对HCCLM3细胞粘附、运动和侵袭能力的改变;RT-PCR和免疫组织化学分别在48例未伴转移的肝癌组织和48例伴转移的肝癌组织中解析Op18表达与肝癌侵袭转移的关系.结果:RT-PCR和Western blot结果显示:在HCCLM3细胞中行RNAi后Op18表达被有效抑制,抑制率达到80%以上;Op18表达缺失后,在不同时间点(20、40和60 min)实验组细胞粘附能力(0.616±0.057、0.740±0.0713和1.001±0.083)较阴性对照组(0.944±0.068、1.196±0.115和1.441±0.053)明显下降(P<0.05);Transwell实验结果提示:经RNAi后实验组细胞运动、侵袭能力(运动:0.145±0.011,侵袭0.127±0.008)较阴性对照组(运动:0.206±0.008,侵袭:0.168±0.012)显著降低(P<0.01);分别在伴转移和未伴转移的肝癌组织中检测Op18的表达,RT-PCR(Op18与GAPDH相对比值:0.560±0.128vs 0.414±0.086)和IHC(积分吸光度值为:624.771±100.032 vs 413.786±71.833)实验结果均提示Op18在伴转移的肝癌组织中的表达更高(P<0.01).结论:Op18在肝癌的侵袭转移过程中发挥重要作用.
文摘胰腺导管内乳头状粘液性肿瘤（Intraductal Papillary Mucinous Neoplasms of the Pancreas,IPMNs）是胰腺癌最重要及最常见的癌前病变之一,约占临床诊断胰腺肿瘤的7%,占偶然发现的胰腺囊肿的50%[1,2]。IPMN分型包括伴轻度不典型增生、IPMN伴中度不典型增生、IPMN伴重度不典型增生及IPMN相关浸润性;
