DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides

Shi, Guobang; Kang, Xinyue; Dong, Fang; Liu, Yanchao; Zhu, Ning; Hu, Yuxuan; Xu, Hong‐Xi; Lao, Xingzhen; Zheng, Heng

doi:10.1093/nar/gkab651

Cited by 176 publications

(124 citation statements)

References 46 publications

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“…Hence, AMPs could be potentially useful in medicine [ 5 , 6 , 7 ]. So far, over 4000 peptides have been identified in the database of The Data Repository of Antimicrobial Peptides (DRAMP) [ 8 ]. Five subgroups can be distinguished in the AMPs: anionic peptides; short helical cationic peptides without cysteine residues; peptides rich in amino acids such as proline, arginine, phenylalanine, or tryptophan; and anionic as well as cationic peptides containing disulfide bonds capable of forming stable β-sheets [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Cationic Peptides and Their Cu(II) and Ni(II) Complexes: Coordination and Biological Characteristics

Kotynia

Wiatrak

Kamysz

et al. 2021

IJMS

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Antimicrobial peptides are a promising group of compounds used for the treatment of infections. In some cases, metal ions are essential to activate these molecules. Examples of metalloantibiotics are, for instance, bleomycin and dermcidin. This study is focused on three new pseudopeptides with potential biological activity. The coordination behavior of all ligands with Cu(II) and Ni(II) ions has been examined. Various analytical methods such as potentiometric titration, UV-Vis and CD spectroscopies, and mass spectrometry were used. All compounds are convenient chelators for metal ion-binding. Two of the ligands tested have histidine residues. Surprisingly, imidazole nitrogen is not involved in the coordination of the metal ion. The N-terminal amino group, Dab side chains, and amide nitrogen atoms of the peptide bonds coordinated Cu(II) and Ni(II) in all the complexes formed. The cytotoxicity of three pseudopeptides and their complexes was evaluated. Moreover, their other model allowed for assessing the attenuation of LPS-induced cytotoxicity and anti-inflammatory activities were also evaluated, the results of which revealed to be very promising.

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Section: Introductionmentioning

confidence: 99%

Cationic Peptides and Their Cu(II) and Ni(II) Complexes: Coordination and Biological Characteristics

Kotynia

Wiatrak

Kamysz

et al. 2021

IJMS

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“…The Infectious Diseases Society of America (IDSA) identified a group of particularly problematic pathogens, termed ESKAPE pathogens ( E. faecium , S. aureus , K. pneumoniae , A. baumannii , P. aeruginosa , Enterobacter spp. ), requiring urgent effective treatments [ 596 ]. These pathogens are known to ‘escape’ the bactericidal effects of many antibiotics via multiple drug resistance mechanisms, rendering them almost totally resistant to existing antibiotics [ 597 ].…”

Section: Discussionmentioning

confidence: 99%

Antimicrobial Peptides: An Update on Classifications and Databases

Hafeez

Jiang

Bergen

et al. 2021

IJMS

180

142

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Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

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“…Further, currently, the B-AMP database has relatively more AMPs with reported anti-Gram positive activity (2534 B-AMPs) than anti-Gram negative activity (2389 B-AMPs), which is a reflection of the AMP sequences in the DRAMP database. To overcome this, we plan to integrate AMP sequences from additional databases and build and host their 3D structural models in B-AMP ( 3D Structure of Antimicrobial Peptides ; dPABBs: A webserver for Designing of Peptides Against Bacterial Biofilms ; Wang et al., 2016 ; Kang et al., 2019 ; Pirtskhalava et al., 2021 ; Shi et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…From DRAMP V3.0 ( Kang et al., 2019 ; Shi et al., 2021 ), we downloaded a dataset of 5562 AMP sequences, with known antibacterial, antifungal and antibiofilm activities. These AMPs were listed as Pep2 to Pep5563, where Pep1 is the LPXTG motif of the pilin subunit of C. striatum (GenPept ID: WP_170219081.1) ( SpaH/EbpB family LPXTG-anchored major pilin [Corynebacterium striatum] - Protein - NCBI ).…”

Section: Methodsmentioning

confidence: 99%

“…AMPs with annotated anti-Gram positive activity (based on information in DRAMP; ( Kang et al., 2019 ; Shi et al., 2021 ) were filtered from B-AMP using an in-house developed Python script ( ). The Python script employs a conditional statement to automatically scan the.csv file for the term “Anti-Gram+” from the activity column in the sheet.…”

Section: Methodsmentioning

confidence: 99%

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AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to Corynebacterium striatum, an Emerging Pathogen

Mhade¹,

Panse²,

Tendulkar³

et al. 2021

Front. Cell. Infect. Microbiol.

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Antimicrobial peptides (AMPs) have been recognized for their ability to target processes important for biofilm formation. Given the vast array of AMPs, identifying potential anti-biofilm candidates remains a significant challenge, and prompts the need for preliminary in silico investigations prior to extensive in vitro and in vivo studies. We have developed Biofilm-AMP (B-AMP), a curated 3D structural and functional repository of AMPs relevant to biofilm studies. In its current version, B-AMP contains predicted 3D structural models of 5544 AMPs (from the DRAMP database) developed using a suite of molecular modeling tools. The repository supports a user-friendly search, using source, name, DRAMP ID, and PepID (unique to B-AMP). Further, AMPs are annotated to existing biofilm literature, consisting of a vast library of over 10,000 articles, enhancing the functional capabilities of B-AMP. To provide an example of the usability of B-AMP, we use the sortase C biofilm target of the emerging pathogen Corynebacterium striatum as a case study. For this, 100 structural AMP models from B-AMP were subject to in silico protein-peptide molecular docking against the catalytic site residues of the C. striatum sortase C protein. Based on docking scores and interacting residues, we suggest a preference scale using which candidate AMPs could be taken up for further in silico, in vitro and in vivo testing. The 3D protein-peptide interaction models and preference scale are available in B-AMP. B-AMP is a comprehensive structural and functional repository of AMPs, and will serve as a starting point for future studies exploring AMPs for biofilm studies. B-AMP is freely available to the community at https://b-amp.karishmakaushiklab.com and will be regularly updated with AMP structures, interaction models with potential biofilm targets, and annotations to biofilm literature.

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DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides

Cited by 176 publications

References 46 publications

Cationic Peptides and Their Cu(II) and Ni(II) Complexes: Coordination and Biological Characteristics

Cationic Peptides and Their Cu(II) and Ni(II) Complexes: Coordination and Biological Characteristics

Antimicrobial Peptides: An Update on Classifications and Databases

AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to Corynebacterium striatum, an Emerging Pathogen

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