scholarly journals Defensins and Bioinformatics: In Silico Approaches for Novel Therapeutic Antimicrobial Peptides

2016 ◽  
Vol 01 (01) ◽  
Author(s):  
Helena C. Castro ◽  
Plínio Sathler
Keyword(s):  
Antimicrobial Peptides ◽  
In Silico ◽  
Novel Therapeutic

scholarly journals PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach

BioTech ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 8
Author(s):  
Olalekan Olanrewaju Bakare ◽  
Arun Gokul ◽  
Marshall Keyster
Keyword(s):  
Antimicrobial Peptides ◽  
Fusarium Oxysporum ◽  
In Silico ◽  
Crop Yields ◽  
Research Work ◽  
Receptor Protein ◽  
Economic Losses ◽  
Protein Receptor ◽  
Novel Biomarkers ◽  
Docking Interaction

Fusarium oxysporum remains one of the leading causes of economic losses and poor crop yields; its detection is strained due to its presentation in various morphological and physiological forms. This research work sought to identify novel biomarkers for the detection of Fusarium oxysporum using in silico approaches. Experimentally validated anti-Fusarium oxysporum antimicrobial peptides (AMPs) were used to construct a profile against Fusarium oxysporum. The performance and physicochemical parameters of these peptides were predicted. The gene for the Fusarium oxysporum receptor protein PR-1-like Protein, Fpr1, was identified and translated. The resulting protein model from the translation was then validated. The anti-Fusarium oxysporum AMPs and Fusarium oxysporum receptor protein 3-D structures were characterized, and their docking interaction analyses were carried out. The HMMER in silico tool identified novel anti-Fusarium oxysporum antimicrobial peptides with good performance in terms of accuracy, sensitivity, and specificity. These AMPs also displayed good physicochemical properties and bound with greater affinity to Fusarium oxysporum protein receptor PR-1-like Protein. The tendency of these AMPs to precisely detect Fusarium oxysporum PR-1-like Protein, Fpr1, would justify their use for the identification of the fungus. This study would enhance and facilitate the identification of Fusarium oxysporum to reduce problems associated with poor crop yield, economic losses, and decreased nutritional values of plants to keep up with the growing population.

scholarly journals EST-based in silico identification and in vitro test of antimicrobial peptides in Brassica napus

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Tao Ke ◽  
Huihui Cao ◽  
Junyan Huang ◽  
Fan Hu ◽  
Jin Huang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Antimicrobial Peptides ◽  
In Silico ◽  
In Vitro Test ◽  
Vitro Test ◽  
In Silico Identification

scholarly journals Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era

2020 ◽  
Vol 14 ◽  
pp. 117793222095273 ◽  
Author(s):  
Carlos André dos Santos-Silva ◽  
Luisa Zupin ◽  
Marx Oliveira-Lima ◽  
Lívia Maria Batista Vilela ◽  
João Pacifico Bezerra-Neto ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Small Molecules ◽  
In Silico ◽  
State Of The Art ◽  
Environmental Stresses ◽  
Gene Duplications ◽  
In Silico Prediction ◽  
Sequence Alignments ◽  
Plant Families ◽  
Simple Sequence

Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.

scholarly journals Peptide-Protein Interaction Studies of Antimicrobial Peptides Targeting Middle East Respiratory Syndrome Coronavirus Spike Protein: An In Silico Approach

2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Sabeena Mustafa ◽  
Hanan Balkhy ◽  
Musa Gabere
Keyword(s):  
Middle East ◽  
Antimicrobial Peptides ◽  
Protein Interactions ◽  
In Silico ◽  
Therapeutic Option ◽  
Binding Mode ◽  
Middle East Respiratory Syndrome ◽  
Spike Protein ◽  
In Silico Docking ◽  
Peptide Database

There is no effective therapeutic or vaccine for Middle East Respiratory Syndrome and this study attempts to find therapy using peptide by establishing a basis for the peptide-protein interactions through in silico docking studies for the spike protein of MERS-CoV. The antimicrobial peptides (AMPs) were retrieved from the antimicrobial peptide database (APD3) and shortlisted based on certain important physicochemical properties. The binding mode of the shortlisted peptides was measured based on the number of clusters which forms in a protein-peptide docking using Piper. As a result, we identified a list of putative AMPs which binds to the spike protein of MERS-CoV, which may be crucial in providing the inhibitory action. It is observed that seven putative peptides have good binding score based on cluster size cutoff of 208. We conclude that seven peptides, namely, AP00225, AP00180, AP00549, AP00744, AP00729, AP00764, and AP00223, could possibly have binding with the active site of the MERS-CoV spike protein. These seven AMPs could serve as a therapeutic option for MERS and enhance its treatment outcome.

scholarly journals Bacterial Cellulose Containing Combinations of Antimicrobial Peptides with Various QQ Enzymes as a Prototype of an “Enhanced Antibacterial” Dressing: In Silico and In Vitro Data

Pharmaceutics ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1155
Author(s):  
Aysel Aslanli ◽  
Ilya Lyagin ◽  
Nikolay Stepanov ◽  
Denis Presnov ◽  
Elena Efremenko
Keyword(s):  
Antimicrobial Peptides ◽  
Bacterial Cellulose ◽  
In Silico ◽  
Antimicrobial Agents ◽  
Penicillin Acylase ◽  
Signal Molecules ◽  
Bacterial Cells ◽  
Gram Positive ◽  
Gram Negative

To improve the action of already in use antibiotics or new antimicrobial agents against different bacteria, the development of effective combinations of antimicrobial peptides (AMPs) with enzymes that can quench the quorum (QQ) sensing of bacterial cells was undertaken. Enzymes hydrolyzing N-acyl homoserine lactones (AHLs) and peptides that are signal molecules of Gram-negative and Gram-positive bacterial cells, respectively, were estimated as “partners” for antibiotics and antimicrobial peptides in newly designed antimicrobial–enzymatic combinations. The molecular docking of six antimicrobial agents to the surface of 10 different QQ enzyme molecules was simulated in silico. This made it possible to choose the best variants among the target combinations. Further, bacterial cellulose (BC) was applied as a carrier for uploading such combinations to generally compose prototypes of effective dressing materials with morphology, providing good absorbance. The in vitro analysis of antibacterial activity of prepared BC samples confirmed the significantly enhanced efficiency of the action of AMPs (including polymyxin B and colistin, which are antibiotics of last resort) in combination with AHL-hydrolyzing enzymes (penicillin acylase and His6-tagged organophosphorus hydrolase) against both Gram-negative and Gram-positive cells.

scholarly journals Transcriptome profiling and in silico detection of the antimicrobial peptides of red king crab Paralithodes camtschaticus

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Igor A. Yakovlev ◽  
Erik Lysøe ◽  
Inger Heldal ◽  
Hege Steen ◽  
Snorre B. Hagen ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
In Silico ◽  
Transcriptome Profiling ◽  
Red King Crab ◽  
Paralithodes Camtschaticus ◽  
King Crab
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