目的:本研究旨在开发一种新的生物信息学方法,用于鉴定新型抗菌肽(AMPs)。它不依赖于与数据库中保存的已知AMP的序列相似性,但是在另一种抗菌化合物的结构模仿上,在这种情况下,超短,合成,阳离子脂肽(C12-OOWW-NH2)。
结果:应用于宏基因组数据集集合时,我们概述的生物信息学方法成功鉴定了几种短(8-10aa)功能性AMP,通过圆盘扩散和针对一组12种细菌菌株的最小抑制浓度(MIC)测定来验证其活性。一些肽的活性与,或在某些情况下高于使用更常规方法鉴定AMP的已发表研究。我们还探讨了修改的效果,包括肽的延伸,观察到9-12aa的活性峰值。此外,在大多数情况下,包含C末端酰胺可增强活性。我们最有希望的候选物(命名为PB2-10aa-NH2)是热稳定的,脂溶性,与乙醇具有协同作用,但不是常规抗生素(链霉素)。
结论:虽然有几种生物信息学方法可以预测AMPs,这里概述的方法简单得多,可以用于快速扫描庞大的数据集。寻找与其他抗菌化合物结构相似的肽序列可能会提供进一步的机会来鉴定具有临床相关性的新型AMP。并为紧迫的全球AMR问题做出有意义的贡献。
OBJECTIVE: This study aimed to develop a new bioinformatic approach for the identification of novel antimicrobial peptides (AMPs), which did not depend on sequence similarity to known AMPs held within databases, but on structural mimicry of another antimicrobial compound, in this case an ultrashort, synthetic, cationic lipopeptide (C12-OOWW-NH2).
RESULTS: When applied to a collection of metagenomic datasets, our outlined bioinformatic method successfully identified several short (8-10aa) functional AMPs, the activity of which was verified via disk diffusion and minimum inhibitory concentration assays against a panel of 12 bacterial strains. Some peptides had activity comparable to, or in some cases, greater than, those from published studies that identified AMPs using more conventional methods. We also explored the effects of modifications, including extension of the peptides, observing an activity peak at 9-12aa. Additionally, the inclusion of a C-terminal amide enhanced activity in most cases. Our most promising candidate (named PB2-10aa-NH2) was thermally stable, lipid-soluble, and possessed synergistic activity with ethanol but not with a conventional antibiotic (streptomycin).
CONCLUSIONS: While several bioinformatic methods exist to predict AMPs, the approach outlined here is much simpler and can be used to quickly scan huge datasets. Searching for peptide sequences bearing structural similarity to other antimicrobial compounds may present a further opportunity to identify novel AMPs with clinical relevance, and provide a meaningful contribution to the pressing global issue of AMR.