Host Defence Peptides: A Potent Alternative to Combat Antimicrobial Resistance in the Era of the COVID-19 Pandemic

Ali, Waqas; Elsahn, Ahmad; Ting, Darren S J; Dua, Harminder S.; Sajid, Imran

doi:10.3390/antibiotics11040475

Cited by 13 publications

(9 citation statements)

References 198 publications

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“…More information about the effect of AMPs (from PCs or not) on SARS-CoV-2 is recently discussed by Ali et al. in detail ( 163 ).…”

Section: Pcs In Covid-19mentioning

confidence: 99%

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Multifaceted involvements of Paneth cells in various diseases within intestine and systemically

Cui

Wang²,

Li³

et al. 2023

Front. Immunol.

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Serving as the guardians of small intestine, Paneth cells (PCs) play an important role in intestinal homeostasis maintenance. Although PCs uniquely exist in intestine under homeostasis, the dysfunction of PCs is involved in various diseases not only in intestine but also in extraintestinal organs, suggesting the systemic importance of PCs. The mechanisms under the participation of PCs in these diseases are multiple as well. The involvements of PCs are mostly characterized by limiting intestinal bacterial translocation in necrotizing enterocolitis, liver disease, acute pancreatitis and graft-vs-host disease. Risk genes in PCs render intestine susceptible to Crohn’s disease. In intestinal infection, different pathogens induce varied responses in PCs, and toll-like receptor ligands on bacterial surface trigger the degranulation of PCs. The increased level of bile acid dramatically impairs PCs in obesity. PCs can inhibit virus entry and promote intestinal regeneration to alleviate COVID-19. On the contrary, abundant IL-17A in PCs aggravates multi-organ injury in ischemia/reperfusion. The pro-angiogenic effect of PCs aggravates the severity of portal hypertension. Therapeutic strategies targeting PCs mainly include PC protection, PC-derived inflammatory cytokine elimination, and substituting AMP treatment. In this review, we discuss the influence and importance of Paneth cells in both intestinal and extraintestinal diseases as reported so far, as well as the potential therapeutic strategies targeting PCs.

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“…More information about the effect of AMPs (from PCs or not) on SARS-CoV-2 is recently discussed by Ali et al. in detail ( 163 ).…”

Section: Pcs In Covid-19mentioning

confidence: 99%

“…These studies suggest the beneficial role of PCs in COVID-19. More information about the effect of AMPs (from PCs or not) on SARS-CoV-2 is recently discussed by Ali et al in detail (163).…”

Section: Pcs In Covid-19mentioning

confidence: 99%

Multifaceted involvements of Paneth cells in various diseases within intestine and systemically

Cui

Wang²,

Li³

et al. 2023

Front. Immunol.

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“…In addition, they have an inherent low risk of developing antimicrobial resistance (AMR), largely attributed to their underlying rapid membrane permeabilising activity 4,7,8 . Such broad-spectrum and rapid antimicrobial activity has prompted researchers to consider AMPs as a potential remedy to the growing problem of AMR, which is a major global health threat 9,10 . Nonetheless, there has so far been a lack of success in translating AMP-based therapy to clinical use, due to challenges such as complex structure-activity relationship (SAR), drug toxicity, instability in host and infective environment, and low financial incentives 11,12 .…”

Section: Introductionmentioning

confidence: 99%

“…4,7,8 Such broad-spectrum and rapid antimicrobial activity has prompted researchers to consider AMPs as a potential remedy to the growing problem of AMR, which is a major global health threat. 9,10 Nonetheless, there has so far been a lack of success in translating AMP-based therapy to clinical use, due to challenges such as complex structure-activity relationship (SAR), drug toxicity, instability in host and infective environment, and low nancial incentives. 11,12 Owing to the complex SAR and the costly and time-consuming process of wet-lab experiments associated with AMP investigations, many researchers have proposed computational approaches, including molecular dynamics (MD) simulations and machine learning (ML) algorithms, to accelerate the discovery and development of potential AMPs for clinical use.…”

Section: Introductionmentioning

confidence: 99%

Krein support vector machine classification of antimicrobial peptides

et al. 2023

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“…In addition, they have an inherent low risk of developing antimicrobial resistance (AMR), largely attributed to their underlying rapid membrane permeabilising activity 4,7,8 . Such broad-spectrum and rapid antimicrobial activity has prompted researchers to consider AMPs as a potential remedy to the grow-ing problem of AMR, which is a major global health threat 9,10 . Nonetheless, there has so far been a lack of success in translating AMP-based therapy to clinical use, due to challenges such as complex structure-activity relationship (SAR), drug toxicity, instability in host and infective environment, and low financial incentives 11,12 .…”

Section: Introductionmentioning

confidence: 99%

Krein Support Vector Machine Classification of Antimicrobial Peptides

Redshaw

Ting

Brown

et al. 2022

Preprint

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Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and time-consuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating the discovery process. Kernel methods are a class of machine learning algorithms that utilise a kernel function to transform input data into a new representation. When appropriately normalised, the kernel function can be regarded as a notion of similarity between instances. However, many expressive notions of similarity are not valid kernel functions, meaning they cannot be used with standard kernel methods such as the support-vector machine (SVM). The Kreın-SVM represents a generalisation of the standard SVM that admits a much larger class of similarity functions. In this study, we propose and develop Kreın-SVM models for AMP classification and prediction by employing the Levenshtein distance and local alignment score as sequence similarity functions. Utilising two datasets from the literature, each containing more than 3000 peptides, we train models to predict general antimicrobial activity. Our best models achieve an AUC of 0.967 and 0.863 on the test sets of each respective dataset, outperforming the in-house and literature baselines in both cases. We also curate a dataset of experimentally validated peptides, measured against Staphylococcus aureus and Pseudomonas aeruginosa, in order to evaluate the applicability of our methodology in predicting microbe-specific activity. In this case, our best models achieve an AUC of 0.933 and 0.917, respectively. Models to predict both general and microbe-specific activities are made available as web applications.

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Host Defence Peptides: A Potent Alternative to Combat Antimicrobial Resistance in the Era of the COVID-19 Pandemic

Cited by 13 publications

References 198 publications

Multifaceted involvements of Paneth cells in various diseases within intestine and systemically

Multifaceted involvements of Paneth cells in various diseases within intestine and systemically

Krein support vector machine classification of antimicrobial peptides

Krein Support Vector Machine Classification of Antimicrobial Peptides

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