Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage DOI Creative Commons
Diana Lin, Darcy Sutherland,

Sambina Islam Aninta

и другие.

Antibiotics, Год журнала: 2022, Номер 11(7), С. 952 - 952

Опубликована: Июль 15, 2022

Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), family of short defense proteins, produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics. Here, we present rAMPage, scalable bioinformatics discovery platform for identifying AMP sequences from RNA sequencing (RNA-seq) datasets. In our study, demonstrate the utility scalability running it on 84 publicly available RNA-seq datasets 75 amphibian insect species-species known have rich repertoires. Across these datasets, identified 1137 putative AMPs, 1024 which were deemed novel homology search cataloged AMPs public databases. We selected 21 peptide set susceptibility testing against Escherichia coli Staphylococcus aureus observed that seven them high activity. Our study illustrates how silico methods such rAMPage can enable fast efficient an first step strenuous process drug development.

Язык: Английский

Antimicrobial peptides: Structure, mechanism, and modification DOI
Na Chen, Jiang Cheng

European Journal of Medicinal Chemistry, Год журнала: 2023, Номер 255, С. 115377 - 115377

Опубликована: Апрель 20, 2023

Язык: Английский

Процитировано

119
Recent Progress in the Discovery and Design of Antimicrobial Peptides Using Traditional Machine Learning and Deep Learning DOI Creative Commons
Jielu Yan, Jianxiu Cai, Bob Zhang

и другие.

Antibiotics, Год журнала: 2022, Номер 11(10), С. 1451 - 1451

Опубликована: Окт. 21, 2022

Antimicrobial resistance has become a critical global health problem due to the abuse of conventional antibiotics and rise multi-drug-resistant microbes. peptides (AMPs) are group natural that show promise as next-generation their low toxicity host, broad spectrum biological activity, including antibacterial, antifungal, antiviral, anti-parasitic activities, great therapeutic potential, such anticancer, anti-inflammatory, etc. Most importantly, AMPs kill bacteria by damaging cell membranes using multiple mechanisms action rather than targeting single molecule or pathway, making it difficult for bacterial drug develop. However, experimental approaches used discover design new very expensive time-consuming. In recent years, there been considerable interest in silico methods, traditional machine learning (ML) deep (DL) approaches, discovery. While few papers summarizing computational AMP prediction none them focused on DL methods. this review, we aim survey latest methods achieved approaches. First, biology background is introduced, then various feature encoding represent features peptide sequences presented. We explain most popular techniques highlight works based classify novel sequences. Finally, discuss limitations challenges prediction.

Язык: Английский

Процитировано

72
Unraveling the Role of Antimicrobial Peptides in Insects DOI Open Access
Sylwia Stączek, Małgorzata Cytryńska, Agnieszka Zdybicka‐Barabas

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(6), С. 5753 - 5753

Опубликована: Март 17, 2023

Antimicrobial peptides (AMPs) are short, mainly positively charged, amphipathic molecules. AMPs important effectors of the immune response in insects with a broad spectrum antibacterial, antifungal, and antiparasitic activity. In addition to these well-known roles, exhibit many other, often unobvious, functions host. They support elimination viral infections. participate regulation brain-controlled processes, e.g., sleep non-associative learning. By influencing neuronal health, communication, activity, they can affect functioning insect nervous system. Expansion AMP repertoire loss their specificity is connected aging process lifespan insects. Moreover, take part maintaining gut homeostasis, regulating number endosymbionts as well reducing foreign microbiota. turn, presence venom prevents spread infection social insects, where prey may be source pathogens.

Язык: Английский

Процитировано

64
Antimicrobial peptides: Opportunities and challenges in overcoming resistance DOI Creative Commons

Cezara Bucataru,

Corina Ciobănaşu

Microbiological Research, Год журнала: 2024, Номер 286, С. 127822 - 127822

Опубликована: Июнь 26, 2024

Antibiotic resistance represents a global health threat, challenging the efficacy of traditional antimicrobial agents and necessitating innovative approaches to combat infectious diseases. Among these alternatives, peptides have emerged as promising candidates against resistant pathogens. Unlike antibiotics with only one target, can use different mechanisms destroy bacteria, low toxicity mammalian cells compared many conventional antibiotics. Antimicrobial (AMPs) encouraging antibacterial properties are currently employed in clinical treatment pathogen infection, cancer, wound healing, cosmetics, or biotechnology. This review summarizes discusses drug resistance, limitations challenges AMPs peptide applications for combating drug-resistant bacterial infections, strategies enhance their capabilities.

Язык: Английский

Процитировано

53
A review on the screening methods for the discovery of natural antimicrobial peptides DOI Creative Commons
Bin Yang,

Hongyan Yang,

Jianlong Liang

и другие.

Journal of Pharmaceutical Analysis, Год журнала: 2024, Номер 15(1), С. 101046 - 101046

Опубликована: Июль 18, 2024

Natural antimicrobial peptides (AMPs) are promising candidates for the development of a new generation antimicrobials to combat antibiotic-resistant pathogens. They have found extensive applications in fields medicine, food, and agriculture. However, efficiently screening AMPs from natural sources poses several challenges, including low efficiency high antibiotic resistance. This review focuses on action mechanisms AMPs, both through membrane non-membrane routes. We thoroughly examine various highly efficient AMP methods, whole-bacterial adsorption binding, cell chromatography (CMC), phospholipid membrane-mediated capillary electrophoresis (CE), colorimetric assays, thin layer (TLC), fluorescence-based screening, genetic sequencing-based analysis, computational mining databases, virtual methods. Additionally, we discuss potential developmental enhancing discovery. provides comprehensive framework identifying within complex product systems.

Язык: Английский

Процитировано

53
CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications DOI Creative Commons
Shasha Feng, Soohyung Park, Yeol Kyo Choi

и другие.

Journal of Chemical Theory and Computation, Год журнала: 2023, Номер 19(8), С. 2161 - 2185

Опубликована: Апрель 4, 2023

Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the interface. As G protein-coupled receptors, ion channels, transporters, membrane-bound enzymes are important drug targets, understanding their binding action mechanisms in a realistic becomes critical. Advances materials science physical chemistry further demand an atomistic lipid domains interactions between membranes. Despite wide range simulation studies, generating complex assembly remains challenging. Here, we review capability CHARMM-GUI

Язык: Английский

Процитировано

45
Recent advances in antimicrobial peptide-based therapy DOI
Aditya Mulukutla,

Romi Shreshtha,

Vishal Kumar Deb

и другие.

Bioorganic Chemistry, Год журнала: 2024, Номер 145, С. 107151 - 107151

Опубликована: Янв. 27, 2024

Язык: Английский

Процитировано

26
Artificial intelligence using a latent diffusion model enables the generation of diverse and potent antimicrobial peptides DOI Creative Commons

Y. C. Wang,

Minghui Song,

Fen Liu

и другие.

Science Advances, Год журнала: 2025, Номер 11(6)

Опубликована: Фев. 5, 2025

Artificial intelligence holds great promise for the design of antimicrobial peptides (AMPs); however, current models face limitations in generating AMPs with sufficient novelty and diversity, they are rarely applied to generation antifungal peptides. Here, we develop an alternative pipeline grounded a diffusion model molecular dynamics de novo AMPs. The generated by our have lower similarity identity than those other reported methodologies. Among 40 synthesized experimental validation, 25 exhibit either antibacterial or activity. AMP-29 shows selective activity against Candida glabrata vivo efficacy murine skin infection model. AMP-24 exhibits potent vitro Gram-negative bacteria both lung Acinetobacter baumannii models. proposed approach offers designing diverse counteract threat antibiotic resistance.

Язык: Английский

Процитировано

8
AI Methods for Antimicrobial Peptides: Progress and Challenges DOI Creative Commons
Carlos A. Brizuela, Gary Liu, J Stokes

и другие.

Microbial Biotechnology, Год журнала: 2025, Номер 18(1)

Опубликована: Янв. 1, 2025

ABSTRACT Antimicrobial peptides (AMPs) are promising candidates to combat multidrug‐resistant pathogens. However, the high cost of extensive wet‐lab screening has made AI methods for identifying and designing AMPs increasingly important, with machine learning (ML) techniques playing a crucial role. approaches have recently revolutionised this field by accelerating discovery new anti‐infective activity, particularly in preclinical mouse models. Initially, classical ML dominated field, but there been shift towards deep (DL) Despite significant contributions, existing reviews not thoroughly explored potential large language models (LLMs), graph neural networks (GNNs) structure‐guided AMP design. This review aims fill that gap providing comprehensive overview latest advancements, challenges opportunities using methods, particular emphasis on LLMs, GNNs We discuss limitations current highlight most relevant topics address coming years

Язык: Английский

Процитировано

5
Glycosylation and Lipidation Strategies: Approaches for Improving Antimicrobial Peptide Efficacy DOI Creative Commons
Rosa Bellavita, Simone Braccia, Stefania Galdiero

и другие.

Pharmaceuticals, Год журнала: 2023, Номер 16(3), С. 439 - 439

Опубликована: Март 14, 2023

Antimicrobial peptides (AMPs) have recently gained attention as a viable solution for combatting antibiotic resistance due to their numerous advantages, including broad-spectrum activity, low propensity inducing resistance, and cytotoxicity. Unfortunately, clinical application is limited short half-life susceptibility proteolytic cleavage by serum proteases. Indeed, several chemical strategies, such peptide cyclization, N-methylation, PEGylation, glycosylation, lipidation, are widely used overcoming these issues. This review describes how lipidation glycosylation commonly increase AMPs’ efficacy engineer novel AMP-based delivery systems. The of AMPs, which involves the conjugation sugar moieties glucose N-acetyl galactosamine, modulates pharmacokinetic pharmacodynamic properties, improves antimicrobial reduces interaction with mammalian cells, thereby increasing selectivity toward bacterial membranes. In same way, covalent addition fatty acids, has significant impact on therapeutic index influencing physicochemical properties highlights possibility using strategies activity conventional AMPs.

Язык: Английский

Процитировано

31