背景:幽门螺杆菌定植(H.幽门螺杆菌)与胃癌有很强的相关性,毒力因子CagA与致癌作用有关。已经使用药用植物进行了研究,目的是消除病原体;但是,阻断幽门螺杆菌诱导的细胞分化以防止肿瘤发生和/或进展的可能性尚未得到解决.这类研究既昂贵又费时,需要体外和/或体内测试,这可以用生物信息学来解决。因此,进行了前瞻性计算分析,以评估药用植物酚类化合物与CagA癌蛋白之间相互作用的可行性。
目的:对药用植物的酚类化合物与幽门螺杆菌的CagA癌蛋白之间的相互作用进行计算研究。
方法:在这项计算机模拟研究中,酚类化合物(配体)山奈酚的结构,杨梅素,槲皮素,ponciretin(类黄酮),从PubChem数据库中选择绿原酸(酚酸)。这些酚类化合物是基于先前的研究选择的,这些研究建议药用植物作为消除幽门螺杆菌感染的非药物治疗。利用I-Tasser平台的计算工具,通过分子建模获得幽门螺杆菌(受体)CagA癌蛋白的三维结构模型,采用线程方法。CagA的一级序列来源于GenBank(BAK52797.1)。进行筛选以鉴定CagA癌蛋白结构中可能与配体相互作用的结合位点,利用GRaSP在线平台。配体和受体均使用AutoDockTools4(ADT)软件进行分子对接。并使用ADT和AutoDockVinav.1.2.0软件组合进行模拟。进行了两组模拟:一组涉及具有酚类化合物的CagA中心区域,和另一个涉及具有酚类化合物的CagA的羧基末端区域。然后使用PyMol和BIOVIADiscoveryStudio软件分析受体-配体复合物。
结果:获得的CagA癌蛋白的结构模型显示出高质量(C分数=0.09),并使用MolProbity平台的参数进行了验证。GRaSP在线平台鉴定了24个残基(苯丙氨酸和亮氨酸)作为CagA癌蛋白上的潜在结合位点。用CagA癌蛋白的三维模型进行分子对接模拟。在CagA的羧基末端区域和酚类化合物之间的模拟中未观察到复合物;然而,所有酚类化合物都与癌蛋白的中心区域相互作用。酚类化合物和CagA表现出显着的亲和能(-7.9至-9.1kcal/mol):CagA/山奈酚形成28个化学键,CagA/杨梅素形成18个化学键,CagA/槲皮素形成16个化学键,CagA/ponciretin形成了13个化学键,与CagA/绿原酸形成17个化学键。尽管没有酚类化合物直接与K-Xn-R-X-R膜结合基序的氨基酸残基结合,它们都与残留物结合,主要带正电荷或负电荷,位于这个地区附近。
结论:在计算机上,测试的酚类化合物与CagA形成稳定的络合物。因此,它们可以在体外和/或体内进行测试以验证发现,并评估对CagA/细胞靶标相互作用和胃细胞致癌分化的干扰。
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.
OBJECTIVE: 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.
CONCLUSIONS: 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.