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人工智能驱动的抗菌肽发现:挖掘与生成

AI-Driven Antimicrobial Peptide Discovery: Mining and Generation.

作者信息

Szymczak Paulina, Zarzecki Wojciech, Wang Jiejing, Duan Yiqian, Wang Jun, Coelho Luis Pedro, de la Fuente-Nunez Cesar, Szczurek Ewa

机构信息

Institute of AI for Health, Helmholtz Zentrum Munich, Neuherberg 85764, Germany.

Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland.

出版信息

Acc Chem Res. 2025 Jun 17;58(12):1831-1846. doi: 10.1021/acs.accounts.0c00594. Epub 2025 Jun 3.


DOI:10.1021/acs.accounts.0c00594
PMID:40459283
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12177927/
Abstract

ConspectusThe escalating threat of antimicrobial resistance (AMR) poses a significant global health crisis, potentially surpassing cancer as a leading cause of death by 2050. Traditional antibiotic discovery methods have not kept pace with the rapidly evolving resistance mechanisms of pathogens, highlighting the urgent need for novel therapeutic strategies. In this context, antimicrobial peptides (AMPs) represent a promising class of therapeutics due to their selectivity toward bacteria and slower induction of resistance compared to classical, small molecule antibiotics. However, designing effective AMPs remains challenging because of the vast combinatorial sequence space and the need to balance efficacy with low toxicity. Addressing this issue is of paramount importance for chemists and researchers dedicated to developing next-generation antimicrobial agents.Artificial intelligence (AI) presents a powerful tool to revolutionize AMP discovery. By leveraging AI, we can navigate the immense sequence space more efficiently, identifying peptides with optimal therapeutic properties. This Account explores the emerging application of AI in AMP discovery, focusing on two primary strategies: AMP mining, and AMP generation, as well as the use of discriminative methods as a valuable toolbox.AMP mining involves scanning biological sequences to identify potential AMPs. Discriminative models are then used to predict the activity and toxicity of these peptides. This approach has successfully identified numerous promising candidates, which were subsequently validated experimentally, demonstrating the potential of AI in AMP design and discovery.AMP generation, on the other hand, creates novel peptide sequences by learning from existing data through generative modeling. This class of models optimizes for desired properties, such as increased activity and reduced toxicity, potentially producing synthetic peptides that surpass naturally occurring ones. Despite the risk of generating unrealistic sequences, generative models hold the promise of accelerating the discovery of highly effective and highly novel and diverse AMPs.In this Account, we describe the technical challenges and advancements in these AI-based approaches. We discuss the importance of integrating various data sources and the role of advanced algorithms in refining peptide predictions. Additionally, we highlight the future potential of AI to not only expedite the discovery process but also to uncover peptides with unprecedented properties, paving the way for next-generation antimicrobial therapies.In conclusion, the synergy between AI and AMP discovery opens new frontiers in the fight against AMR. By harnessing the power of AI, we can design novel peptides that are both highly effective and safe, offering hope for a future where AMR is no longer a looming threat. Our paper underscores the transformative potential of AI in drug discovery, advocating for its continued integration into biomedical research.

摘要

综述 抗微生物药物耐药性(AMR)威胁的不断升级构成了重大的全球健康危机,到2050年,其可能超过癌症成为主要死因。传统的抗生素发现方法已无法跟上病原体快速演变的耐药机制,凸显了对新型治疗策略的迫切需求。在此背景下,抗菌肽(AMPs)作为一类有前景的治疗药物,因其对细菌的选择性以及与传统小分子抗生素相比更慢的耐药性诱导而备受关注。然而,由于巨大的组合序列空间以及需要在疗效和低毒性之间取得平衡,设计有效的抗菌肽仍然具有挑战性。解决这个问题对于致力于开发下一代抗菌药物的化学家和研究人员来说至关重要。 人工智能(AI)为抗菌肽的发现带来了变革性的强大工具。通过利用人工智能,我们可以更有效地在巨大的序列空间中探索,识别具有最佳治疗特性的肽。本综述探讨了人工智能在抗菌肽发现中的新兴应用,重点关注两种主要策略:抗菌肽挖掘和抗菌肽生成,以及将判别方法作为一个有价值的工具集。 抗菌肽挖掘涉及扫描生物序列以识别潜在的抗菌肽。然后使用判别模型预测这些肽的活性和毒性。这种方法已成功识别出许多有前景的候选物,随后通过实验进行了验证,证明了人工智能在抗菌肽设计和发现中的潜力。 另一方面,抗菌肽生成通过生成式建模从现有数据中学习来创建新的肽序列。这类模型针对所需特性进行优化,例如提高活性和降低毒性,有可能产生超越天然存在的合成肽。尽管存在生成不切实际序列的风险,但生成式模型有望加速发现高效、新颖且多样的抗菌肽。 在本综述中,我们描述了这些基于人工智能的方法中的技术挑战和进展。我们讨论了整合各种数据源的重要性以及先进算法在优化肽预测方面的作用。此外,我们强调了人工智能未来的潜力,不仅可以加快发现过程,还能发现具有前所未有的特性的肽,为下一代抗菌疗法铺平道路。 总之,人工智能与抗菌肽发现之间的协同作用为对抗AMR开辟了新的前沿。通过利用人工智能的力量,我们可以设计出既高效又安全的新型肽,为AMR不再是迫在眉睫的威胁的未来带来希望。我们的论文强调了人工智能在药物发现中的变革潜力,倡导将其持续整合到生物医学研究中。

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本文引用的文献

[1]
FGeneBERT: function-driven pre-trained gene language model for metagenomics.

Brief Bioinform. 2025-3-4

[2]
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Elife. 2025-3-13

[3]
Machine learning for antimicrobial peptide identification and design.

Nat Rev Bioeng. 2024-5

[4]
Mining biology for antibiotic discovery.

PLoS Biol. 2024-11-26

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Peptides from non-immune proteins target infections through antimicrobial and immunomodulatory properties.

Trends Biotechnol. 2025-1

[6]
In-silico and in-vitro study of novel antimicrobial peptide AM1 from Aegle marmelos against drug-resistant Staphylococcus aureus.

Sci Rep. 2024-10-28

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Adv Sci (Weinh). 2024-11

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Can large language models predict antimicrobial peptide activity and toxicity?

RSC Med Chem. 2024-4-23

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