抗菌肽的数据库辅助设计

doi:10.13560/j.cnki.biotech.bull.1985.2024-0277

摘要/Abstract

摘要：

抗菌肽（antimicrobial peptides, AMPs）是一类广泛存在于自然界，具有广谱抗菌活性的多肽类物质，其因独特的抗菌作用机制被视为传统抗生素的新型替代药物。近几十年来，研究人员在AMPs方向进行了大量工作，但AMPs的开发与应用仍然存在诸多限制，包括生物体内提取困难、生产成本高、全身细胞毒性和生理条件下的不稳定性。因此，研究者们以天然AMPs为模板进行衍生肽设计，以期开发出新的具有强效力和低毒性的AMPs药物。但试验性肽的设计及筛选过程复杂耗时、工作量大、迭代成本高。随着计算方法的不断进步，可公开访问的数据库提供了大量的AMPs数据。这些数据库为开发和构建新型抗菌药物提供了宝贵的资源。本文对现有的AMPs数据库和数据库辅助设计方法进行了综述，以期对AMPs的药物开发提供参考。

关键词: AMPs, 数据库, 数据库筛选, 肽预测, 肽设计

Abstract:

Antimicrobial peptides（AMPs）are a diverse class of peptides ubiquitously present in nature, showcasing a broad spectrum of antibacterial activity. Due to their distinctive antibacterial mechanisms, they are considered a novel alternative to conventional antibiotics. In recent decades, substantial research has been conducted on AMPs. However, challenges persist in the development and application of these peptides, including difficulties extraction in vivo, high production costs, systemic cytotoxicity, and instability in physiological conditions. Consequently, scientists employ natural AMPs as a model to generate derived peptides with the aim of creating novel peptide drugs that possess enhanced potency and reduced toxicity. The process of experimental peptide design is deep concerned by its time-consuming, labor-intensive, and costly nature. However, with the continuous advancement of computational methods, publicly accessible databases now offer substantial amounts of AMPs data. These databases serve as a valuable resource for the development and construction of novel AMPs. In this paper, the existing AMP databases and database-aided design methods are reviewed with the aim to provide reference for drug development of AMPs.

Key words: antimicrobial peptides, database, database screening, peptide prediction, peptide design

邵长轩, 张少华, 邓浩然, 于伟康, 朱永杰, 单安山. 抗菌肽的数据库辅助设计[J]. 生物技术通报, 2024, 40(12): 12-19.

SHAO Chang-xuan, ZHANG Shao-hua, DENG Hao-ran, YU Wei-kang, ZHU Yong-jie, SHAN An-shan. Database-aided Design of Antimicrobial Peptides[J]. Biotechnology Bulletin, 2024, 40(12): 12-19.

图/表 5

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数据库 Database	数据来源 Source of data	数据量 Data size	最新更新 Latest updated	预测工具 Predicting tool	网址 URL	参考文献 Reference
APD	天然、合成	3 342	2015年	Antimicrobial peptide calculator and predictor	https://aps.unmc.edu/home	[13]
dbAMP	AMPs数据库、文献	28 709	2021年	AMP predictor	http://awi.cuhk.edu.cn/dbAMP	[7]
DRAMP	天然、合成、实验验证	22 259	2022年	BHEAP prediction Stapled peptides prediction	http://dramp.cpu-bioinfor.org/	[14]
DBAASP	天然、合成	18 878	2020年	Linear AMP prediction	http://dbaasp.org/home	[15]
CAMP	天然、合成、预测	24 243	2023年	AMP prediction	http://www.camp3.bicnirrh.res.in/	[16]

数据库 Database	数据来源 Source of data	数据量 Data size	最新更新 Latest updated	预测工具 Predicting tool	网址 URL	参考文献 Reference
APD	天然、合成	3 342	2015年	Antimicrobial peptide calculator and predictor	https://aps.unmc.edu/home	[13]
dbAMP	AMPs数据库、文献	28 709	2021年	AMP predictor	http://awi.cuhk.edu.cn/dbAMP	[7]
DRAMP	天然、合成、实验验证	22 259	2022年	BHEAP prediction Stapled peptides prediction	http://dramp.cpu-bioinfor.org/	[14]
DBAASP	天然、合成	18 878	2020年	Linear AMP prediction	http://dbaasp.org/home	[15]
CAMP	天然、合成、预测	24 243	2023年	AMP prediction	http://www.camp3.bicnirrh.res.in/	[16]

数据库 Database	数据类型 Type of database	数据来源 Source of data	最新更新 Latest updated	网址 URL	参考文献 Reference
CancerPPD	抗癌肽	文献、专利、AMPs数据库	2015年	http://crdd.osdd.net/raghava/cancerppd/	[17]
ParaPep	抗寄生虫肽	天然、专利、AMPs数据库	2014年	http://webs.iiitd.edu.in/raghava/parapep/peptide.php	[18]
CyBase	环肽类	天然、预测抗菌肽	2007年	http://www.cybase.org.au/	[19]
BaAMPs	生物膜活性肽	文献	2015年	http://www.tandfonline.com/loi/gbif20	[20]
DRAVP	抗病毒肽	实验验证	2023年	http://dravp.cpu-bioinfor.org/	[21]

数据库 Database	数据类型 Type of database	数据来源 Source of data	最新更新 Latest updated	网址 URL	参考文献 Reference
CancerPPD	抗癌肽	文献、专利、AMPs数据库	2015年	http://crdd.osdd.net/raghava/cancerppd/	[17]
ParaPep	抗寄生虫肽	天然、专利、AMPs数据库	2014年	http://webs.iiitd.edu.in/raghava/parapep/peptide.php	[18]
CyBase	环肽类	天然、预测抗菌肽	2007年	http://www.cybase.org.au/	[19]
BaAMPs	生物膜活性肽	文献	2015年	http://www.tandfonline.com/loi/gbif20	[20]
DRAVP	抗病毒肽	实验验证	2023年	http://dravp.cpu-bioinfor.org/	[21]