CAMPR4: a database of natural and synthetic antimicrobial peptides

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D377 - D383

Опубликована: Окт. 11, 2022

Abstract There has been an exponential increase in the design of synthetic antimicrobial peptides (AMPs) for its use as novel antibiotics. Synthetic AMPs are substantially enriched residues with physicochemical properties known to be critical activity; such positive charge, hydrophobicity, and higher alpha helical propensity. The current prediction algorithms have developed using AMP sequences from natural sources hence do not perform well peptides. In this version CAMP database, along updating sequence information AMPs, we created separate AMPs. CAMPR4 holds 24243 sequences, 933 structures, 2143 patents 263 family signatures. addition data on source organisms, target minimum inhibitory hemolytic concentrations, provides N C terminal modifications presence unusual amino acids, applicable. database is integrated tools rational (natural AMPs), (BLAST clustal omega), structure (VAST) analysis (PRATT, ScanProsite, CAMPSign). will aid enhance research. accessible at http://camp.bicnirrh.res.in/.

Язык: Английский

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sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure

Bioinformatics, Год журнала: 2022, Номер 39(1)

Опубликована: Ноя. 7, 2022

Abstract Motivation Antimicrobial peptides (AMPs) are essential components of therapeutic for innate immunity. Researchers have developed several computational methods to predict the potential AMPs from many candidate peptides. With development artificial intelligent techniques, protein structures can be accurately predicted, which useful sequence and function analysis. Unfortunately, predicted peptide structure information has not been applied field AMP prediction so as improve predictive performance. Results In this study, we proposed a predictor called sAMPpred-GAT identification. To best our knowledge, is first approach based on prediction. The constructs graphs structures, evolutionary information. Graph Attention Network (GAT) then performed learn discriminative features. Finally, full connection networks utilized output module whether or not. Experimental results show that outperforms other state-of-the-art in terms AUC, achieves better highly comparable performance metrics eight independent test datasets, demonstrating important Availability implementation A user-friendly webserver accessed at http://bliulab.net/sAMPpred-GAT source code available https://github.com/HongWuL/sAMPpred-GAT/. Supplementary data Bioinformatics online.

Язык: Английский

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A review on antimicrobial peptides databases and the computational tools

Database, Год журнала: 2022, Номер 2022

Опубликована: Янв. 1, 2022

Abstract Antimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has raised a global problem. The AMPs are group of natural peptides that play crucial role in the immune system various organisms features such short length and efficiency against microbes. Importantly, they represented low toxicity mammals which makes them candidates peptide-based drugs. Nevertheless, discovery is accompanied by several issues associated with labour-intensive time-consuming wet-lab experiments. During last decades, numerous studies conducted on investigation AMPs, either or synthetic type, relevant data recently available many databases. Through advancement computational methods, great number AMP obtained from publicly accessible databanks, valuable resources mining patterns to design new models prediction. However, due current flaws assessing more interrogations warranted accurate evaluation/analysis. Considering diversity newly reported ones, an improvement Machine Learning algorithms crucial. In this review, we aim provide information about different types their mechanism action landscape databases tools collect beneficial prediction model active AMPs.

Язык: Английский

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Antimicrobial Peptides: From Design to Clinical Application

Antibiotics, Год журнала: 2022, Номер 11(3), С. 349 - 349

Опубликована: Март 6, 2022

Infection of multidrug-resistant (MDR) bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant Enterobacteriaceae (CRE), and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli, brings public health issues causes economic burden. Pathogenic bacteria develop several methods to resist antibiotic killing or inhibition, mutation function sites, activation drug efflux pumps, enzyme-mediated degradation. Antibiotic resistance components can be transferred between by mobile genetic elements including plasmids, transposons, integrons, well bacteriophages. The development limits the treatment options for bacterial infection, especially MDR bacteria. Therefore, novel alternative antibacterial agents are urgently needed. Antimicrobial peptides (AMPs) display multiple mechanisms against infections, directly bactericidal activity immunomodulatory function, potential alternatives antibiotics. In this review, resistance, AMPs, especially, design, optimization, delivery AMPs reviewed. Strategies structural change, amino acid substitution, conjugation with cell-penetration peptide, terminal acetylation amidation, encapsulation nanoparticles will improve antimicrobial efficacy, reduce toxicity, accomplish local AMPs. addition, clinical trials in AMP studies applications within last five years were summarized. Overall, diverse action infection pathogenic future research investigations accelerate application.

Язык: Английский

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Immunomodulatory and Allergenic Properties of Antimicrobial Peptides

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(5), С. 2499 - 2499

Опубликована: Фев. 24, 2022

With the growing problem of emergence antibiotic-resistant bacteria, search for alternative ways to combat bacterial infections is extremely urgent. While analyzing effect antimicrobial peptides (AMPs) on immunocompetent cells, their all parts immune system, and humoral cellular immunity, revealed. AMPs have direct effects neutrophils, monocytes, dendritic T-lymphocytes, mast participating in innate immunity. They act B-lymphocytes indirectly, enhancing induction antigen-specific which ultimately leads activation adaptive The adjuvant activity relation viral antigens was reason inclusion vaccines made it possible formulate concept a “defensin vaccine” as an innovative basis constructing vaccines. immunomodulatory function involves influence cells nearest microenvironment, recruitment other supporting response pathogenic microorganisms completing inflammatory process, thus exhibiting systemic effect. For successful use medical practice, necessary study detail, taking into account pleiotropy. degree maturity system microenvironment can contribute prevention complications increase effectiveness therapy, since suppress inflammation some circumstances, but aggravate damage organism others. It should also be taken that real functions one or another AMP depend types total regulatory target cell, not only properties individual peptide. A wide spectrum biological activity, including pathogens, inactivation toxins has attracted attention researchers, however, cytostatic against normal well allergenic low stability host proteases, are serious limitations AMPs. In this connection, tasks searching compounds selectively affect development appropriate method application become critically important. scope review summarize current concepts newest advances research natural synthetic AMPs, examine prospects use.

Язык: Английский

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A review on the screening methods for the discovery of natural antimicrobial peptides

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

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ToxinPred 3.0: An improved method for predicting the toxicity of peptides

Computers in Biology and Medicine, Год журнала: 2024, Номер 179, С. 108926 - 108926

Опубликована: Июль 21, 2024

Язык: Английский

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iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities

Briefings in Bioinformatics, Год журнала: 2023, Номер 24(4)

Опубликована: Июнь 27, 2023

Antimicrobial peptides (AMPs) are short that play crucial roles in diverse biological processes and have various functional activities against target organisms. Due to the abuse of chemical antibiotics microbial pathogens' increasing resistance antibiotics, AMPs potential be alternatives antibiotics. As such, identification has become a widely discussed topic. A variety computational approaches been developed identify based on machine learning algorithms. However, most them not capable predicting AMPs, those predictors can specify only focus few them. In this study, we first surveyed 10 their terms features they employed algorithms utilized. Then, constructed comprehensive AMP datasets proposed new deep learning-based framework, iAMPCN (identification CNNs), related 22 activities. Our experiments demonstrate significantly improved prediction performance corresponding four types sequence features. Benchmarking independent test showed outperformed number state-of-the-art for Furthermore, analyzed amino acid preferences different evaluated model varying redundancy thresholds. To facilitate community-wide types, made source codes publicly available at https://github.com/joy50706/iAMPCN/tree/master. We anticipate explored as valuable tool identifying with specific further experimental validation.

Язык: Английский

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Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization

Briefings in Bioinformatics, Год журнала: 2024, Номер 25(2)

Опубликована: Янв. 22, 2024

Abstract Antimicrobial peptides (AMPs), short with diverse functions, effectively target and combat various organisms. The widespread misuse of chemical antibiotics has led to increasing microbial resistance. Due their low drug resistance toxicity, AMPs are considered promising substitutes for traditional antibiotics. While existing deep learning technology enhances AMP generation, it also presents certain challenges. Firstly, generation overlooks the complex interdependencies among amino acids. Secondly, current models fail integrate crucial tasks like screening, attribute prediction iterative optimization. Consequently, we develop a integrated framework, Diff-AMP, that automates identification, We innovatively kinetic diffusion attention mechanisms into reinforcement framework efficient generation. Additionally, our module incorporates pre-training transfer strategies precise identification screening. employ convolutional neural network multi-attribute learning-based optimization strategy produce AMPs. This molecule optimization, thereby advancing research. have deployed Diff-AMP on web server, code, data server details available in Data Availability section.

Язык: Английский

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

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

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