Zhang Heqian, Wang Yihan, Zhu Yanran, Huang Pengtao, Gao Qiandi, Li Xiaojie, Chen Zhaoying, Liu Yu, Jiang Jiakun, Gao Yuan, Huang Jiaquan, Qin Zhiwei
Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
International Academic Center of Complex Systems, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
J Adv Res. 2025 Feb;68:415-428. doi: 10.1016/j.jare.2024.02.016. Epub 2024 Mar 1.
Antimicrobial peptides (AMPs) are valuable alternatives to traditional antibiotics, possess a variety of potent biological activities and exhibit immunomodulatory effects that alleviate difficult-to-treat infections. Clarifying the structure-activity relationships of AMPs can direct the synthesis of desirable peptide therapeutics.
In this study, the lipopolysaccharide-binding domain (LBD) was identified through machine learning-guided directed evolution, which acts as a functional domain of the anti-lipopolysaccharide factor family of AMPs identified from Marsupenaeus japonicus.
LBD was identified as an output of this algorithm, in which the original LBD sequence was the input, and the three-dimensional solution structure of LBD was determined using nuclear magnetic resonance. Furthermore, our study involved a comprehensive series of experiments, including morphological studies and in vitro and in vivo antibacterial tests.
The NMR solution structure showed that LBD possesses a circular extended structure with a disulfide crosslink at the terminus and two 3-helices and exhibits a broad antimicrobial spectrum. In addition, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed that LBD induced the formation of a cluster of bacteria wrapped in a flexible coating that ruptured and consequently killed the bacteria. Finally, coinjection of LBD, Vibrio alginolyticus and Staphylococcus aureus in vivo improved the survival of M. japonicus, demonstrating the promising therapeutic role of LBD for treating infectious disease.
The findings of this study pave the way for the rational drug design of activity-enhanced peptide antibiotics.
抗菌肽（AMPs）是传统抗生素的有价值替代品，具有多种强大的生物活性，并表现出免疫调节作用，可缓解难治性感染。阐明抗菌肽的构效关系可以指导合成理想的肽类治疗药物。
在本研究中，通过机器学习引导的定向进化鉴定了脂多糖结合结构域（LBD），它是从日本对虾中鉴定出的抗菌肽抗脂多糖因子家族的一个功能结构域。
LBD被鉴定为该算法的输出结果，其中原始LBD序列为输入，利用核磁共振确定LBD的三维溶液结构。此外，我们的研究涉及一系列全面的实验，包括形态学研究以及体外和体内抗菌试验。
核磁共振溶液结构表明，LBD具有一种环状延伸结构，在末端有一个二硫键交联以及两个3-螺旋，并且具有广泛的抗菌谱。此外，扫描电子显微镜（SEM）和透射电子显微镜（TEM）显示，LBD诱导形成了包裹在柔性包膜中的细菌聚集体，该包膜破裂从而杀死细菌。最后，在体内将LBD、溶藻弧菌和金黄色葡萄球菌共同注射提高了日本对虾的存活率，证明了LBD在治疗传染病方面具有广阔的治疗前景。
本研究结果为活性增强型肽类抗生素的合理药物设计铺平了道路。
