YADAMP: yet another database of antimicrobial peptides

Piotto, Stefano; Sessa, Lucia; Concilio, Simona; Iannelli, Pio

doi:10.1016/j.ijantimicag.2011.12.003

Cited by 182 publications

(112 citation statements)

References 26 publications

(37 reference statements)

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“…The LSTM model was trained on known antimicrobial sequences from the YADAMP (yet another database of antimicrobial peptides) database (9).…”

Section: Resultsmentioning

confidence: 99%

“…Other peptides such as Novexatin (7) and Lytixar (8) are currently undergoing early-stage clinical trials (for the treatment of toenail fungal infections and MRSA respectively (6)). Currently, over 2000 natural and designed antimicrobial peptides are curated in various databases (9)(10)(11), and have displayed broad-spectrum activity against Gram positive, Gram negative, fungal, mycobacterial, and protozoal pathogens (9).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria

Nagarajan

Nagarajan²,

Roy³

et al. 2018

Journal of Biological Chemistry

112

146

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There is a pressing need for new therapeutics to combat multi-drug and carbapenem-resistant bacterial pathogens. This challenge prompted us to use a long short-term memory (LSTM) language model to understand the underlying grammar, i.e. the arrangement and frequencies of amino acid residues, in known antimicrobial peptide sequences. According to the output of our LSTM network, we synthesized 10 peptides and tested them against known bacterial pathogens. All of these peptides displayed broad-spectrum antimicrobial activity, validating our LSTM-based peptide design approach. Our two most effective antimicrobial peptides displayed activity against multidrugresistant (MDR) clinical isolates of Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and coagulase-negative staphylococci (CoNS) strains. High activity against extended-spectrum beta-lactamase (ESBL), meticillin-resistant S. aureus (MRSA), and carbapenem-resistant strains was also observed. Our peptides selectively interacted with and disrupted bacterial cell membranes and caused secondary gene-regulatory effects. Initial structural characterization revealed that our most effective peptide appeared to be well folded. We conclude that our LSTM-based peptide design approach appears to have correctly deciphered the underlying grammar of antimicrobial peptide sequences, as demonstrated by the experimentally observed efficacy of our designed peptides.Antibiotic resistance is an ever-increasing threat which is gradually rendering our current repertoire of antibiotics obsolete. If no new drugs are developed, deaths due to antimicrobial resistance are expected to exceed 10 million annually by 2050 (1). Antimicrobial peptides (AMPs) are one potential solution to this problem. Naturally occurring AMPs continue to remain an important component of the innate immune system despite their ancient evolutionary origin and widespread prevalence across many forms of life (2). Some derivatives of these such as pexiganan (3), omiganan (4), and OP-145 (5) are currently undergoing late-stage clinical trials (for diabetic foot ulcers, rosacea, and ear infections respectively (6)). Other peptides such as Novexatin (7) and Lytixar (8) are currently undergoing early-stage clinical trials (for the treatment of toenail fungal infections and MRSA respectively (6)). Currently, over 2000 natural and designed antimicrobial peptides are curated in various databases (9-11), and have displayed broad-spectrum activity against Gram positive, Gram negative, fungal, mycobacterial, and protozoal pathogens (9). Designed AMPs vs. MDR isolates.positive charge are attracted and incorporated into negatively charged bacterial membranes. Once inside the membrane, they are believed to cause disruption through three possible mechanisms: toroidal pore formation (12), carpet formation (13), and barrel stave formation (14). Although the specifics of each mechanism differ, all propose peptide-induced membrane rupture, allowing cytoplasmic leak...

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“…The LSTM model was trained on known antimicrobial sequences from the YADAMP (yet another database of antimicrobial peptides) database (9).…”

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria

Nagarajan

Nagarajan²,

Roy³

et al. 2018

Journal of Biological Chemistry

112

146

View full text Add to dashboard Cite

show abstract

“…In order to avoid inaccuracies in peptide sequences and names (for example two different sequences having the same name or vice versa), each sequence was carefully checked by comparing it with the corresponding one, if present, in public databases UniProtKB/SwissProt (Wu et al 2006), CAMP (Waghu et al 2014), and YADAMP (Piotto et al 2012).…”

Section: Data Collectionmentioning

confidence: 99%

“…The study of these key features can help in the understanding of the mechanism regulating antimicrobial activity. Peptide charge at different pH conditions is one of the most important characteristics of AMPs (Piotto et al 2012) and it is usually calculated as the sum of the contributions of each charged residue. Similarly, the isoelectric point (pI), calculated as the pH point at which a protein has no net electrical charge, is able to represent the electrostatic characteristics of peptides (Bjellqvist et al 1994).…”

Section: Database-integrated Toolsmentioning

confidence: 99%

“…To date, several databases have been created to collect AMP sequences (Novković et al 2012;Piotto et al 2012;Seshadri Sundararajan et al 2012;Zhao et al 2013;Waghu et al 2014) supporting bioinformatics in the design of optimized AMPs (Wang et al 2009;Fjell et al 2012;Maccari et al 2013). Nevertheless, all the existing databases focus on sequences exerting antimicrobial activity against microorganisms in planktonic form while, to the best of the authors' knowledge, no database fully dedicated to AMPs active on microbial biofilms has yet been developed.…”

Section: Introductionmentioning

confidence: 99%

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BaAMPs: the database of biofilm-active antimicrobial peptides

et al. 2015

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Antimicrobial peptides (AMPs) are increasingly being considered as novel agents against biofilms. The development of AMP-based anti-biofilm strategies strongly relies on the design of sequences optimized to target specific features of sessile bacterial/fungal communities. Although several AMP databases have been created and successfully exploited for AMP design, all of these use data collected on peptides tested against planktonic microorganisms. Here, an open-access, manually curated database of AMPs specifically assayed against microbial biofilms (BaAMPs) is presented for the first time. In collecting relevant data from the literature an effort was made to define a minimal standard set of essential information including, for each AMP, the microbial species and biofilm conditions against which it was tested, and the specific assay and peptide concentration used. The availability of these data in an organized framework will benefit anti-biofilm research and support the design of novel molecules active against biofilm. BaAMPs is accessible at http://www.baamps.it.

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Antimicrobial Peptides: Their History, Evolution, and Functional Promiscuity

2013

Antimicrobial Peptides

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YADAMP: yet another database of antimicrobial peptides

Cited by 182 publications

References 26 publications

Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria

Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria

BaAMPs: the database of biofilm-active antimicrobial peptides

Antimicrobial Peptides: Their History, Evolution, and Functional Promiscuity

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