Abstract：
The main issue with clinical infections is multidrug resistance to traditional antibiotics. As they are essential to innate immunity, shielding hosts from pathogenic microbes, traditional herbal remedies are an excellent supplier of antimicrobial peptides (AMPs), vital parts of defensive systems. Nevertheless, little is known about the bioactive peptide components of most ethnobotanical species. Our goal in this study was to find new, likely AMPs from Portulaca oleracea (P. oleracea) using in silico studies. The P. oleracea transcriptome was gained from Sequence Read Archive (SRA) and quality controlled, then adapters and other low-quality reads were trimmed. Afterward, de novo assembled and translated open reading frames (ORFs) were determined. Next, the ORFs were filtered based on AMP physiochemical criteria and deep learning methods. Finally, the five selected putative AMPs docked with E. coli and S. aureus membranes that showed penetration in bilayers. In this step, PO2 was chosen as a candidate AMP to analyze with molecular dynamics (MD) simulations. Our data demonstrated that PO2 is more stable in E. coli than in S. aureus. Moreover, these predicted AMPs can be good candidates for in vitro and in vivo analysis.
摘要：
临床感染的主要问题是对传统抗生素的多药耐药性。因为它们对先天免疫至关重要，保护宿主免受病原微生物的侵害，传统草药是抗菌肽（AMP）的优秀供应商，防御系统的重要组成部分。然而，对大多数民族植物学物种的生物活性肽成分知之甚少。我们在这项研究中的目标是找到新的，可能来自马齿轮轴(P.oleracea)使用计算机模拟研究。从序列阅读存档（SRA）获得了P.oleracea转录组，并进行了质量控制，然后修剪适配器和其他低质量读数。之后,确定从头组装和翻译的开放阅读框(ORF)。接下来,根据AMP理化标准和深度学习方法筛选ORF.最后,五个选定的推定AMP与大肠杆菌和金黄色葡萄球菌膜对接,其显示在双层中的渗透。在这一步,选择PO2作为候选AMP进行分子动力学(MD)模拟分析。我们的数据表明PO2在大肠杆菌中比在金黄色葡萄球菌中更稳定。此外，这些预测的AMPs可以是体外和体内分析的良好候选者。
