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

Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review DOI

Cheuk Chi Albert Ng,

Yin Zhou,

Zhongping Yao

и другие.

Analytica Chimica Acta, Год журнала: 2023, Номер 1268, С. 341330 - 341330

Опубликована: Май 8, 2023

Язык: Английский

Процитировано

24
Antimicrobial Peptides and Their Mimetics: Promising Candidates of Next‐Generation Therapeutic Agents Combating Multidrug‐Resistant Bacteria DOI Open Access
Tianyi Zhang, Qiao Jin,

Jian Ji

и другие.

Advanced Biology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 6, 2025

Abstract The increasing morbidity and mortality caused by multidrug‐resistant bacteria alerts human beings to the fact that conventional antibiotics are no longer reliable effective alternatives imperatively needed. Owing wide range of sources, diverse structures, unique mode action, antimicrobial peptides have been highly anticipated extensively studied in recent years. Besides, integration artificial intelligence helps researchers gain access vast unexplored chemical space, which opens more opportunities for optimization design novel structures. Moreover, Due advances chemistry synthetic biology, also begun focus on potential mimetics peptides. In this review, a comprehensive discussion about natural synthesized as well their is made, so provide summary field inspire follow‐up research.

Язык: Английский

Процитировано

2
Latex of medicinal plants: a reservoir of antimicrobial peptides, proteins, and enzymes for drug discovery DOI Creative Commons

Zainab Abiodun Molik,

Temitayo O. Ajayi, Queeneth A. Ogunniyi

и другие.

Deleted Journal, Год журнала: 2025, Номер 2(1)

Опубликована: Янв. 13, 2025

The exploration of latex from medicinal plants has unveiled a promising source antimicrobial peptides (AMPs), proteins and enzymes with significant therapeutic potentials. Despite their value, these sources remain underutilized. Latex, complex, viscous fluid secreted by specific plants, in the Euphorbiaceae, Apocynaceae, Moraceae, Papaveraceae, Asclepiadaceae families, serves multiple functions, including wound healing, protection against herbivores, most importantly, as defense microbial pathogens This review provides an overview latex-producing emphasizing role discovery molecules. Notable among is Hevea brasiliensis, hevein hevein-like peptides, which have demonstrated antifungal antibacterial activities. Other key AMPs are cysteine-rich lectins that exhibit potent properties. Additionally, peptidases proteases obtained garnered attention for potential both activity enhancement peptide stability efficacy. These molecules act through unique mechanisms, disrupting cell membranes, making them valuable candidates fight multidrug-resistant pathogens. They underscore contribution to modern research. While discoveries hold great promises, some challenges still exist. Interestingly, biotechnology advancements synthesis genetic engineering improved latex-derived biomolecules enabling large-scale production modification, enhancing stability, potency, effectiveness use. Also, integration genomic proteomic tools will further unlock full potentials, paving way novel agents capable addressing antibiotic resistance.

Язык: Английский

Процитировано

1
Accelerating the Discovery and Design of Antimicrobial Peptides with Artificial Intelligence DOI
Mariana del Carmen Aguilera‐Puga, Natalia L. Cancelarich, Mariela M. Marani

и другие.

Methods in molecular biology, Год журнала: 2023, Номер unknown, С. 329 - 352

Опубликована: Сен. 7, 2023

Язык: Английский

Процитировано

19
Design strategies for positively charged endolysins: Insights into Artilysin development DOI Creative Commons
José Vicente Carratalá, Anna Arı́s, Elena García‐Fruitós

и другие.

Biotechnology Advances, Год журнала: 2023, Номер 69, С. 108250 - 108250

Опубликована: Сен. 6, 2023

Endolysins are bacteriophage-encoded enzymes that can specifically degrade the peptidoglycan layer of bacterial cell wall, making them an attractive tool for development novel antibacterial agents. The use genetic engineering techniques production and modification endolysins offers opportunity to customize their properties activity against specific targets, paving way personalized therapies infections. Gram-negative bacteria possess outer membrane hinder action recombinantly produced endolysins. However, certain capable crossing by virtue segments share resembling those cationic peptides. These regions increase affinity endolysin towards surface assist in permeabilization membrane. In order improve bactericidal effectiveness endolysins, approaches have been implemented net charge, including Artilysins containing positively charged amino acids at one end. At present, there no guidelines outlining steps implementing these modifications. There is ongoing debate surrounding optimal location positive need a linker region, acid composition peptides modifying aim this study provide clarity on topics analyzing comparing most effective modifications found previous literature.

Язык: Английский

Процитировано

18
Challenges in computational discovery of bioactive peptides in ’omics data DOI Creative Commons
Luís Pedro Coelho, Célio Dias Santos Júnior, César de la Fuente‐Núñez

и другие.

PROTEOMICS, Год журнала: 2024, Номер 24(12-13)

Опубликована: Март 8, 2024

Peptides have a plethora of activities in biological systems that can potentially be exploited biotechnologically. Several peptides are used clinically, as well industry and agriculture. The increase available 'omics data has recently provided large opportunity for mining novel enzymes, biosynthetic gene clusters, molecules. While these primarily consist DNA sequences, other types provide important complementary information. Due to their size, the approaches proven successful at discovering proteins canonical size cannot naïvely applied discovery peptides. encoded directly genome short open reading frames (smORFs), or they derived from larger by proteolysis. Both peptide classes pose challenges simple methods prediction result numbers false positives. Similarly, functional annotation proteins, traditionally based on sequence similarity infer orthology then transferring functions between characterized uncharacterized ones, sequences. use techniques is much more limited alternative machine learning instead. Here, we review limitations traditional been developed bioactive with focus prokaryotic genomes metagenomes.

Язык: Английский

Процитировано

8
PLMACPred prediction of anticancer peptides based on protein language model and wavelet denoising transformation DOI Creative Commons
Muhammad Arif, Saleh Musleh,

Huma Fida

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Июль 23, 2024

Anticancer peptides (ACPs) perform a promising role in discovering anti-cancer drugs. The growing research on ACPs as therapeutic agent is increasing due to its minimal side effects. However, identifying novel using wet-lab experiments are generally time-consuming, labor-intensive, and expensive. Leveraging computational methods for fast accurate prediction of would harness the drug discovery process. Herein, machine learning-based predictor, called PLMACPred, developed from peptide sequence only. PLMACPred adopted set encoding schemes representing evolutionary-property, composition-property, protein language model (PLM), i.e., evolutionary scale modeling (ESM-2)- ProtT5-based embedding encode peptides. Then, two-dimensional (2D) wavelet denoising (WD) was employed remove noise extracted features. Finally, ensemble-based cascade deep forest (CDF) identify ACP. attained superior performance all three benchmark datasets, namely, ACPmain, ACPAlter, ACP740 over tenfold cross validation independent dataset. outperformed existing models improved accuracy by 18.53%, 2.4%, 7.59% ACPalter, dataset, respectively. We showed that ProtT5 ESM-2 capable capturing better contextual information entire than other ACP prediction. For explainability proposed model, SHAP (SHapley Additive exPlanations) method used analyze feature effect A list motifs MEME suites. believe, will support accelerating well activities microbial

Язык: Английский

Процитировано

7
Antimicrobial peptides and proteins against drug-resistant pathogens DOI Creative Commons

Y. C. Wang,

Minghui Song,

Wenqiang Chang

и другие.

The Cell Surface, Год журнала: 2024, Номер 12, С. 100135 - 100135

Опубликована: Ноя. 27, 2024

Язык: Английский

Процитировано

7
Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens DOI Creative Commons
Leandro Pereira-Dias, Paulo R. Oliveira-Pinto, Juliana Oliveira-Fernandes

и другие.

Biotechnology Advances, Год журнала: 2023, Номер 68, С. 108223 - 108223

Опубликована: Авг. 1, 2023

Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family linear, membrane-active, amphipathic polypeptides, have been shown exhibit antibacterial, antifungal, antiviral activity, be inducers plant resistance against wide range phytopathogens. Peptaibiotics belong the new generation alternatives agrochemicals, aligned with United Nations Sustainable Development Goals One Health approach toward ensuring global food security safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially agriculture, where only small number has tested reduced This lack adoption stems peptaibiotics' poor water solubility difficulty synthesize purify them vitro, which compromises their delivery inclusion formulations. In this review, we offer comprehensive analysis classification, biosynthesis, relevance protection, mode action phytopathogens, along techniques enabling researchers extract, purify, elucidate structure, databases holding such valuable data. It is also discussed how chemical synthesis ionic liquids could increase solubility, genetic engineering epigenetics boost vitro production, omics can reduce screenings' workload through silico selection best candidates. These strategies turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.

Язык: Английский

Процитировано

17
Membrane-Active Peptides and Their Potential Biomedical Application DOI Creative Commons

Andreea Gostaviceanu,

Simona Gavrilaș, Lucian Copolovici

и другие.

Pharmaceutics, Год журнала: 2023, Номер 15(8), С. 2091 - 2091

Опубликована: Авг. 6, 2023

Membrane-active peptides (MAPs) possess unique properties that make them valuable tools for studying membrane structure and function promising candidates therapeutic applications. This review paper provides an overview of the fundamental aspects MAPs, focusing on their interaction mechanisms potential MAPs exhibit various structural features, including amphipathic structures specific amino acid residues, enabling selective with multiple membranes. Their action involve disrupting lipid bilayers through different pathways, depending peptide composition. The is significant. They have demonstrated antimicrobial activity against bacteria fungi, making alternatives to conventional antibiotics. can selectively target cancer cells induce apoptosis, opening new avenues in therapeutics. Additionally, serve as drug delivery vectors, facilitating transport cargoes across cell represent a fascinating class biomolecules significant basic research clinical Understanding designing enhanced selectivity efficacy will further expand utility diverse fields. Exploring holds promise developing novel strategies infections, cancer, challenges.

Язык: Английский

Процитировано

14