Al-Omari Ahmad M, Akkam Yazan H, Zyout Ala'a, Younis Shayma'a, Tawalbeh Shefa M, Al-Sawalmeh Khaled, Al Fahoum Amjed, Arnold Jonathan
Biomedical Systems and Informatics Engineering Department, College of Engineering, Yarmouk University, Irbid, Jordan.
Medicinal Chemistry and Pharmacognosy Department, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan.
PLoS One. 2024 Dec 20;19(12):e0315477. doi: 10.1371/journal.pone.0315477. eCollection 2024.
Antimicrobial peptides (AMPs) are excellent at fighting many different infections. This demonstrates how important it is to make new AMPs that are even better at eliminating infections. The fundamental transformation in a variety of scientific disciplines, which led to the emergence of machine learning techniques, has presented significant opportunities for the development of antimicrobial peptides. Machine learning and deep learning are used to predict antimicrobial peptide efficacy in the study. The main purpose is to overcome traditional experimental method constraints. Gram-negative bacterium Escherichia coli is the model organism in this study. The investigation assesses 1,360 peptide sequences that exhibit anti- E. coli activity. These peptides' minimal inhibitory concentrations have been observed to be correlated with a set of 34 physicochemical characteristics. Two distinct methodologies are implemented. The initial method involves utilizing the pre-computed physicochemical attributes of peptides as the fundamental input data for a machine-learning classification approach. In the second method, these fundamental peptide features are converted into signal images, which are then transmitted to a deep learning neural network. The first and second methods have accuracy of 74% and 92.9%, respectively. The proposed methods were developed to target a single microorganism (gram negative E.coli), however, they offered a framework that could potentially be adapted for other types of antimicrobial, antiviral, and anticancer peptides with further validation. Furthermore, they have the potential to result in significant time and cost reductions, as well as the development of innovative AMP-based treatments. This research contributes to the advancement of deep learning-based AMP drug discovery methodologies by generating potent peptides for drug development and application. This discovery has significant implications for the processing of biological data and the computation of pharmacology.
抗菌肽(AMPs)在对抗多种不同感染方面表现出色。这表明制造出在消除感染方面更出色的新型抗菌肽是多么重要。各种科学学科的根本性变革催生了机器学习技术,这为抗菌肽的开发带来了重大机遇。在该研究中,机器学习和深度学习被用于预测抗菌肽的功效。主要目的是克服传统实验方法的局限性。革兰氏阴性菌大肠杆菌是本研究中的模式生物。该调查评估了1360个具有抗大肠杆菌活性的肽序列。已观察到这些肽的最小抑菌浓度与一组34种理化特性相关。实施了两种不同的方法。第一种方法是利用预先计算的肽的理化属性作为机器学习分类方法的基本输入数据。在第二种方法中,这些基本的肽特征被转换为信号图像,然后传输到深度学习神经网络。第一种和第二种方法的准确率分别为74%和92.9%。所提出的方法是针对单一微生物(革兰氏阴性大肠杆菌)开发的,然而,它们提供了一个框架,经过进一步验证后可能适用于其他类型的抗菌、抗病毒和抗癌肽。此外,它们有可能显著减少时间和成本,并开发出基于抗菌肽的创新疗法。这项研究通过生成用于药物开发和应用的有效肽,为基于深度学习的抗菌肽药物发现方法的发展做出了贡献。这一发现对生物数据处理和药理学计算具有重要意义。