深度学习揭示古菌蛋白质组中的抗生素

Deep learning reveals antibiotics in the archaeal proteome.

作者信息

Torres Marcelo D T, Wan Fangping, de la Fuente-Nunez Cesar

机构信息

Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.

出版信息

Nat Microbiol. 2025 Aug 12. doi: 10.1038/s41564-025-02061-0.

Abstract

Antimicrobial resistance is one of the greatest threats facing humanity, making the need for new antibiotics more critical than ever. While most antibiotics originate from bacteria and fungi, archaea offer a largely untapped reservoir for antibiotic discovery. In this study, we leveraged deep learning to systematically explore the archaeome, uncovering promising candidates for combating antimicrobial resistance. By mining 233 archaeal proteomes, we identified 12,623 molecules with potential antimicrobial activity. These peptide compounds, termed archaeasins, have unique compositional features that differentiate them from traditional antimicrobial peptides, including a distinct amino acid profile. We synthesized 80 archaeasins, 93% of which showed antimicrobial activity in vitro against Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus and Enterococcus spp. Notably, in vivo validation identified archaeasin-73 as a lead candidate, significantly reducing A. baumannii loads in mouse infection models, with effectiveness comparable to that of established antibiotics such as polymyxin B. Our findings highlight the potential of archaea as a resource for developing next-generation antibiotics.

摘要

抗生素耐药性是人类面临的最大威胁之一,这使得新型抗生素的需求比以往任何时候都更加迫切。虽然大多数抗生素来源于细菌和真菌,但古菌在很大程度上是尚未开发利用的抗生素发现资源库。在本研究中,我们利用深度学习系统地探索古菌组,发现了对抗生素耐药性有前景的候选物。通过挖掘233个古菌蛋白质组,我们鉴定出12623种具有潜在抗菌活性的分子。这些肽化合物被称为古菌素,具有独特的组成特征,使其有别于传统抗菌肽,包括独特的氨基酸谱。我们合成了80种古菌素,其中93%在体外对鲍曼不动杆菌、大肠杆菌、肺炎克雷伯菌、铜绿假单胞菌、金黄色葡萄球菌和肠球菌属表现出抗菌活性。值得注意的是,体内验证确定古菌素-73为主要候选物,可显著降低小鼠感染模型中鲍曼不动杆菌的载量,其有效性与多粘菌素B等已确立的抗生素相当。我们的研究结果突出了古菌作为开发下一代抗生素资源的潜力。

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