Novel Antimicrobial Peptides Designed Using a Recurrent Neural Network Reduce Mortality in Experimental Sepsis

Deep learning for advancing peptide drug development: Tools and methods in structure prediction and design

Peptides can bind challenging disease targets with high affinity and specificity, offering enormous opportunities for addressing unmet medical needs. However, peptides' unique features, including smaller size, increased structural flexibility, and limited data availability, pose additional challenges to the design process compared to proteins. This review explores the dynamic field of peptide therapeutics, leveraging deep learning to enhance structure prediction and design. Our exploration encompasses various facets of peptide research, ranging from dataset curation handling to model development. As deep learning technologies become more refined, we channel our efforts into peptide structure prediction and design, aligning with the fundamental principles of structure-activity relationships in drug development. To guide researchers in harnessing the potential of deep learning to advance peptide drug development, our insights comprehensively explore current challenges and future directions of peptide therapeutics.

Antimicrobial peptides: An alternative to traditional antibiotics

As antibiotic-resistant bacteria and genes continue to emerge, the identification of effective alternatives to traditional antibiotics has become a pressing issue. Antimicrobial peptides are favored for their safety, low residue, and low resistance properties, and their unique antimicrobial mechanisms show significant potential in combating antibiotic resistance. However, the high production cost and weak activity of antimicrobial peptides limit their application. Moreover, traditional laboratory methods for identifying and designing new antimicrobial peptides are time-consuming and labor-intensive, hindering their development. Currently, novel technologies, such as artificial intelligence (AI) are being employed to develop and design new antimicrobial peptide resources, offering new opportunities for the advancement of antimicrobial peptides. This article summarizes the basic characteristics and antimicrobial mechanisms of antimicrobial peptides, as well as their advantages and limitations, and explores the application of AI in antimicrobial peptides prediction amd design. This highlights the crucial role of AI in enhancing the efficiency of antimicrobial peptide research and provides a reference for antimicrobial drug development.

Accelerating the Discovery and Design of Antimicrobial Peptides with Artificial Intelligence

Peptides modulate many processes of human physiology targeting ion channels, protein receptors, or enzymes. They represent valuable starting points for the development of new biologics against communicable and non-communicable disorders. However, turning native peptide ligands into druggable materials requires high selectivity and efficacy, predictable metabolism, and good safety profiles. Machine learning models have gradually emerged as cost-effective and time-saving solutions to predict and generate new proteins with optimal properties. In this chapter, we will discuss the evolution and applications of predictive modeling and generative modeling to discover and design safe and effective antimicrobial peptides. We will also present their current limitations and suggest future research directions, applicable to peptide drug design campaigns.

iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model

As a kind of small molecule protein that can fight against various microorganisms in nature, antimicrobial peptides (AMPs) play an indispensable role in maintaining the health of organisms and fortifying defenses against diseases. Nevertheless, experimental approaches for AMP identification still demand substantial allocation of human resources and material inputs. Alternatively, computing approaches can assist researchers effectively and promptly predict AMPs. In this study, we present a novel AMP predictor called iAMP-Attenpred. As far as we know, this is the first work that not only employs the popular BERT model in the field of natural language processing (NLP) for AMPs feature encoding, but also utilizes the idea of combining multiple models to discover AMPs. Firstly, we treat each amino acid from preprocessed AMPs and non-AMP sequences as a word, and then input it into BERT pre-training model for feature extraction. Moreover, the features obtained from BERT method are fed to a composite model composed of one-dimensional CNN, BiLSTM and attention mechanism for better discriminating features. Finally, a flatten layer and various fully connected layers are utilized for the final classification of AMPs. Experimental results reveal that, compared with the existing predictors, our iAMP-Attenpred predictor achieves better performance indicators, such as accuracy, precision and so on. This further demonstrates that using the BERT approach to capture effective feature information of peptide sequences and combining multiple deep learning models are effective and meaningful for predicting AMPs.

Addressing antibiotic resistance: computational answers to a biological problem?

The increasing prevalence of infections caused by antibiotic-resistant bacteria is a global healthcare crisis. Understanding the spread of resistance is predicated on the surveillance of antibiotic resistance genes within an environment. Bioinformatics and artificial intelligence (AI) methods applied to metagenomic sequencing data offer the capacity to detect known and infer yet-unknown resistance mechanisms, and predict future outbreaks of antibiotic-resistant infections. Machine learning methods, in particular, could revive the waning antibiotic discovery pipeline by helping to predict the molecular structure and function of antibiotic resistance compounds, and optimising their interactions with target proteins. Consequently, AI has the capacity to play a central role in guiding antibiotic stewardship and future clinical decision-making around antibiotic resistance.

A Systematic Review of Deep Learning Methodologies Used in the Drug Discovery Process with Emphasis on In Vivo Validation

The discovery and development of new drugs are extremely long and costly processes. Recent progress in artificial intelligence has made a positive impact on the drug development pipeline. Numerous challenges have been addressed with the growing exploitation of drug-related data and the advancement of deep learning technology. Several model frameworks have been proposed to enhance the performance of deep learning algorithms in molecular design. However, only a few have had an immediate impact on drug development since computational results may not be confirmed experimentally. This systematic review aims to summarize the different deep learning architectures used in the drug discovery process and are validated with further in vivo experiments. For each presented study, the proposed molecule or peptide that has been generated or identified by the deep learning model has been biologically evaluated in animal models. These state-of-the-art studies highlight that even if artificial intelligence in drug discovery is still in its infancy, it has great potential to accelerate the drug discovery cycle, reduce the required costs, and contribute to the integration of the 3R (Replacement, Reduction, Refinement) principles. Out of all the reviewed scientific articles, seven algorithms were identified: recurrent neural networks, specifically, long short-term memory (LSTM-RNNs), Autoencoders (AEs) and their Wasserstein Autoencoders (WAEs) and Variational Autoencoders (VAEs) variants; Convolutional Neural Networks (CNNs); Direct Message Passing Neural Networks (D-MPNNs); and Multitask Deep Neural Networks (MTDNNs). LSTM-RNNs were the most used architectures with molecules or peptide sequences as inputs.

Andrographolide and 4-Phenylbutyric Acid Administration Increase the Expression of Antimicrobial Peptides Beta-Defensin-1 and Cathelicidin and Reduce Mortality in Murine Sepsis

Antibiotic resistance is a global threat and requires the search for new treatment strategies. Natural antimicrobial peptides (AMPs) have pronounced antibacterial, antiviral, antifungal, and antitumor activity. AMPs’ clinical use is complicated by the high synthesis costs and rapid proteolytic degradation. The search for small molecules, inducers of endogenous AMP expression, could become a new approach. Here, we investigated for the first time the effect of seven small molecules (andrographolide, levofloxacin, azithromycin, montelukast, 4-phenylbutyric acid, rosuvastatin and valsartan) on AMP (beta-defensin-1, hBD-1 and cathelicidin, LL-37) serum levels in rats. In control groups, the level of hBD-1 was 295.0 (292.9–315.4) pg/mL, and for LL-37, it was 223.8 (213.3–233.6) pg/mL. Andrographolide (ANDR) and 4-phenylbutyric acid (4-PHBA) administration significantly enhanced the level of both AMPs. The hBD-1 level was 581.5 (476.3–607.7) pg/mL for ANDR and 436.9 (399.0–531.6) pg/mL for 4-PHBA. The LL-37 level was 415.4 (376.2–453.8) pg/mL for ANDR and 398.9 (355.7–410.1) pg/mL for 4-PHBA. Moreover, we have shown that these compounds reduce mortality in a murine model of sepsis caused by a carbapenem-resistant Klebsiella aerogenes isolate. From our point of view, these small molecules are promising candidates for further study as potent AMP inducers. The data obtained allow the development of new strategies to combat antibiotic resistance and infectious diseases.