Novel 3D Structure Based Model for Activity Prediction and Design of Antimicrobial Peptides

Liu, Shicai; Bao, Jingxiao; Lao, Xingzhen; Zheng, Heng

doi:10.1038/s41598-018-29566-5

Cited by 47 publications

(35 citation statements)

References 45 publications

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“…Homology-modeled structures can be optimized by molecular dynamics and used to visualize the interaction between AMP and biomembrane 31–33 . In this paper, we used MOE2016 (https://www.chemcomp.com/) to establish an initial molecular structure by homology modeling, and Amber14 (http://ambermd.org/) to optimize the molecular structure by molecular dynamics, as previously reported 34 . In the second version of DRAMP, 82 predicted structures were added and these structures can be downloaded in pdb format (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Such as, CAMP R3 17,52 , ADAM 53 , and AntiBP2 54 identify AMPs, BAGEL4 55 and BACTIBASE 56 mainly identify bacteriocins. We have developed a machine learning model based on 3D descriptors to predict AMPs and evaluate their antimicrobial effects by in vitro experiments 34 . The accuracy of the experimental optimal model in the training dataset is 92.59% and MCC is 0.84.…”

Section: Resultsmentioning

confidence: 99%

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DRAMP 2.0, an updated data repository of antimicrobial peptides

et al. 2019

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Data Repository of Antimicrobial Peptides (DRAMP, http://dramp.cpu-bioinfor.org/ ) is an open-access comprehensive database containing general, patent and clinical antimicrobial peptides (AMPs). Currently DRAMP has been updated to version 2.0, it contains a total of 19,899 entries (newly added 2,550 entries), including 5,084 general entries, 14,739 patent entries, and 76 clinical entries. The update covers new entries, structures, annotations, classifications and downloads. Compared with APD and CAMP, DRAMP contains 14,040 (70.56% in DRAMP) non-overlapping sequences. In order to facilitate users to trace original references, PubMed_ID of references have been contained in activity information. The data of DRAMP can be downloaded by dataset and activity, and the website source code is also available on dedicatedly designed download webpage. Although thousands of AMPs have been reported, only a few parts have entered clinical stage. In the paper, we described several AMPs in clinical trials, including their properties, indications and clinicaltrials.gov identifiers. Finally, we provide the applications of DRAMP in the development of AMPs.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

DRAMP 2.0, an updated data repository of antimicrobial peptides

et al. 2019

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“…Their amenability to mutagenesis and peptide engineering has already resulted in numerous compounds with improved bioactivities and reduced cytotoxic effects [72,79,80]. In addition, the increased power and accuracy of bioinformatics methods and molecular dynamics simulations [81] can help in the prediction of the antimicrobial activity [82] and mechanism-of-action and further aid in rational peptide analogue design [83]. Overall developments in the field over recent years provides confidence that research efforts using cyclic and disulfide-rich peptides may lead to the development of much needed novel antimicrobial agents.…”

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

The Vast Structural Diversity of Antimicrobial Peptides

Koehbach

Craik

2019

Trends in Pharmacological Sciences

194

138

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Antimicrobial peptides (AMPs) occur in all kingdoms of life and are integral to host defense. They have diverse structures and target a variety of organisms, both by non-specific membrane interactions or via specific targets. Here we discuss the structures of AMPs from the four main classes currently recognized, i.e. peptides with (i) α-helical; (ii) β-sheet; (iii) αβ; and (iv) non-αβ elements as well as the growing pool of complex topologies including various post-translational modifications. We propose to group these latter peptides into a fifth class of AMPs. Such peptides exhibit high stability and amenability to chemical engineering, making them of interest for the development of novel antimicrobial agents. Advances and challenges in the development of these peptides towards therapeutic leads are presented. AMPsa diverse, but unifying strategy for defense Antimicrobial resistance has been identified as a major threat to public health and without immediate and global action the world is headed for a dangerous post-antibiotic era [1]. Thus, there is an urgent need for the development of novel antibiotic drugs to treat infectious diseases. In contrast to the rising numbers of multi drug resistant pathogens the rate of discovery of novel drug candidates is dwindling [2]. In this regard antimicrobial peptides (AMP) are a promising class of bioactive compounds that have attracted increasing attention over recent years. Their broad spectrum of activities extends beyond the killing of bacteria and fungi, with several AMPs also exhibiting antiviral [3], antiparasitic [4] or anticancer activities [5]. Furthermore, their multifaceted mechanisms-of-action potentially reduce their susceptibility to suffer from microbial resistance [6]. Starting in the 1980s, at a time when the numbers of novel antibacterial agents started to drop, the field of AMP research gained momentum when several novel examples were independently discovered across different species. These included peptides such as the cecropins from insects [7], the magainins from amphibians [8] and the mammalian defensins [9] to name a few. Since then a plethora of AMPs has been identified from all kingdoms of life, from bacteria to fungi to plants and animals. It is not only evident that these peptides play an integral part of an organism's innate defense machinery, but their variety also makes them a rich source for the discovery of potential novel drug leads. Their distribution among virtually all living organisms is complemented by their structural variety and range of antimicrobial activities. In this review we highlight this vast structural diversity of antimicrobial peptides. As well as providing a brief overview of the structures of well-known classes of AMPs, we introduce the growing class of structurally complex AMP topologies, in particular, cyclic and cysteine-rich defense peptides. We discuss recent progress and challenges in the characterization and development of peptide-based antibacterial molecules. 3 Structural classes of antimicrobial peptides Th...

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“…Their flexible structures also may possibly induce interactions with unintended components, which could result in undesirable side-effects. Furthermore, according to the DRAMP Database, there are approximately 67% known antimicrobial peptides from all sources and particularly 78% from human source compose of more than 20 amino acid residues [ [8] , [9] , [10] , [11] , [12] ], whereas many of them including several dominant residues [ 8 ] ( Fig. 1 ).…”

Section: Introductionmentioning

confidence: 99%

Antimicrobial peptides – Advances in development of therapeutic applications

2020

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The severe infection is becoming a significant health problem which threaten the lives of patients and the safety and economy of society. In the way of finding new strategy, antimicrobial peptides (AMPs) - an important part of host defense family, emerged with tremendous potential. Up to date, huge numbers of AMPs has been investigated from both natural and synthetic sources showing not only the ability to kill microbial pathogens but also propose other benefits such as wound healing, anti-tumor, immune modulation. In this review, we describe the involvements of AMPs in biological systems and discuss the opportunity in developing AMPs for clinical applications. In the detail, their properties in antibacterial activity is followed by their application in some infection diseases and cancer. The key discussions are the approaches to improve biological activities of AMPs either by modifying chemical structure or incorporating into delivery systems. The new applications and perspectives for the future of AMPs would open the new era of their development.

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Novel 3D Structure Based Model for Activity Prediction and Design of Antimicrobial Peptides

Cited by 47 publications

References 45 publications

DRAMP 2.0, an updated data repository of antimicrobial peptides

DRAMP 2.0, an updated data repository of antimicrobial peptides

The Vast Structural Diversity of Antimicrobial Peptides

Antimicrobial peptides – Advances in development of therapeutic applications

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