scholarly journals Design of a de novo aggregating antimicrobial peptide and bacterial conjugation delivery system

2018 ◽  
Author(s):  
Logan T. Collins ◽  
Peter B. Otoupal ◽  
Colleen M. Courtney ◽  
Anushree Chatterjee
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Rational Design ◽  
De Novo ◽  
Protein Aggregates ◽  
Conjugative Plasmid ◽  
Design Parameters ◽  
Bacterial Conjugation ◽  
Artificial Gene

AbstractTraditional antibiotics are reaching obsolescence as a consequence of antibiotic resistance; therefore novel antibiotic approaches are needed. A recent non-traditional approach involves formation of protein aggregates as antimicrobials to disrupt bacterial homeostasis. Previous work on protein aggregates has focused on genome mining for aggregation-prone sequences in bacterial genomes rather than on rational design of aggregating antimicrobial peptides. Here, we use a synthetic biology approach to design an artificial gene encoding the first de novo aggregating antimicrobial peptide. This artificial gene,opaL(overexpressed protein aggregator Lipophilic), disrupts bacterial homeostasis by expressing extremely hydrophobic peptides. When this hydrophobic sequence is disrupted by acidic residues, consequent aggregation and antimicrobial effect decreases. Further, to deliver this artificial gene, we developed a probiotic approach using RK2, a broad host range conjugative plasmid, to transferopaLfrom donor to recipient bacteria. We utilize RK2 to mobilize a shuttle plasmid carrying theopaLgene by adding the RK2 origin of transfer. We show thatopaLis non-toxic to the donor, allowing for maintenance and transfer since its expression is under control of a promoter with a recipient-specific T7 RNA polymerase. Upon mating of donor and recipientEscherichia coli, we observe selective growth repression in T7 polymerase expressing recipients. This technique could be used to target desired pathogens by selecting pathogen-specific promoters to controlopaLexpression. This system provides a basis for the design and delivery of novel antimicrobial peptides.ImportanceThe growing threat of antibiotic resistance necessitates new treatment options for bacterial infections that are recalcitrant to traditional antimicrobials. Existing methods usually involve small-molecule compounds which interfere with essential processes in bacterial cells. By contrast, protein aggregates operate by causing widespread disruption of bacterial homeostasis and may provide a new method for combating infections. We used rational design to create and test an aggregating de novo antimicrobial peptide, OpaL. In addition, we employed bacterial conjugation to deliver theopaLgene from donor bacteria to recipient bacteria while using a strain-specific promoter to ensure that OpaL was only expressed in targeted recipients. To the best of our knowledge, this represents the first design for a de novo peptide with aggregation-mediated antimicrobial activity. We envision that OpaL’s design parameters could be used in developing a new class of antimicrobial peptides to help treat antibiotic resistant infections.

scholarly journals Monitoring Bacterial Conjugation by Optical Microscopy

2021 ◽  
Vol 12 ◽  
Author(s):  
Gerardo Carranza ◽  
Tamara Menguiano ◽  
Fernando Valenzuela-Gómez ◽  
Yolanda García-Cazorla ◽  
Elena Cabezón ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Optical Microscopy ◽  
Resistance Genes ◽  
Fluorescent Protein ◽  
Antibiotic Resistance Genes ◽  
Conjugative Plasmid ◽  
Bacterial Conjugation ◽  
Transfer Device

Bacterial conjugation is the main mechanism for horizontal gene transfer, conferring plasticity to the genome repertoire. This process is also the major instrument for the dissemination of antibiotic resistance genes. Hence, gathering primary information of the mechanism underlying this genetic transaction is of a capital interest. By using fluorescent protein fusions to the ATPases that power conjugation, we have been able to track the localization of these proteins in the presence and absence of recipient cells. Moreover, we have found that more than one copy of the conjugative plasmid is transferred during mating. Altogether, these findings provide new insights into the mechanism of such an important gene transfer device.

Little Antimicrobial Peptides with Big Therapeutic Roles

2019 ◽  
Vol 26 (8) ◽  
pp. 564-578 ◽  
Author(s):  
Dan Zhang ◽  
Yu He ◽  
Yang Ye ◽  
Yanni Ma ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Immune Response ◽  
Drug Resistance ◽  
Drug Discovery ◽  
Antimicrobial Peptides ◽  
Rational Design ◽  
De Novo ◽  
Biological Molecules ◽  
Action Mechanisms ◽  
New Strategies

Antimicrobial Peptides (AMPs) are short amphipathic biological molecules generally with less than 100 amino acids. AMPs not only present high bioactivities against bacteria, fungi or protists-induced infections, but also play important roles in anticancer activity, immune response and inflammation regulation. AMPs are classified as ribosomally synthesized, non-ribosomally synthesized and post-translationally modified, non-ribosomally synthesized ones and several synthetic or semisynthetic peptides according to their synthesis with or without the involvement of ribosomes. The molecular characterization and bioactivity action mechanisms are summarized for several ribosomally synthesized AMPs and main non-ribosomally synthesized members (cyclopeptides, lipopeptides, glycopeptides, lipoglycopeptides). We also analyze challenges and new strategies to overcome drug resistance and application limitations for AMP discovery. In conclusion, the growing novel small molecular AMPs have huge therapeutic potentials of antibacterial, antiviral, anticancer and immunoregulatory bioactivities through new techniquesdriven drug discovery strategy including bioinformatics prediction, de novo rational design and biosynthesis.

scholarly journals Physicochemical Features and Peculiarities of Interaction of AMP with the Membrane

2021 ◽  
Vol 14 (5) ◽  
pp. 471
Author(s):  
Malak Pirtskhalava ◽  
Boris Vishnepolsky ◽  
Maya Grigolava ◽  
Grigol Managadze
Keyword(s):  
Amino Acid ◽  
Antimicrobial Peptides ◽  
Rational Design ◽  
De Novo ◽  
Cell Envelope ◽  
Biological Membrane ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Comprehensive Understanding ◽  
Physicochemical Features

Antimicrobial peptides (AMPs) are anti-infectives that have the potential to be used as a novel and untapped class of biotherapeutics. Modes of action of antimicrobial peptides include interaction with the cell envelope (cell wall, outer- and inner-membrane). A comprehensive understanding of the peculiarities of interaction of antimicrobial peptides with the cell envelope is necessary to perform a rational design of new biotherapeutics, against which working out resistance is hard for microbes. In order to enable de novo design with low cost and high throughput, in silico predictive models have to be invoked. To develop an efficient predictive model, a comprehensive understanding of the sequence-to-function relationship is required. This knowledge will allow us to encode amino acid sequences expressively and to adequately choose the accurate AMP classifier. A shared protective layer of microbial cells is the inner, plasmatic membrane. The interaction of AMP with a biological membrane (native and/or artificial) has been comprehensively studied. We provide a review of mechanisms and results of interactions of AMP with the cell membrane, relying on the survey of physicochemical, aggregative, and structural features of AMPs. The potency and mechanism of AMP action are presented in terms of amino acid compositions and distributions of the polar and apolar residues along the chain, that is, in terms of the physicochemical features of peptides such as hydrophobicity, hydrophilicity, and amphiphilicity. The survey of current data highlights topics that should be taken into account to come up with a comprehensive explanation of the mechanisms of action of AMP and to uncover the physicochemical faces of peptides, essential to perform their function. Many different approaches have been used to classify AMPs, including machine learning. The survey of knowledge on sequences, structures, and modes of actions of AMP allows concluding that only possessing comprehensive information on physicochemical features of AMPs enables us to develop accurate classifiers and create effective methods of prediction. Consequently, this knowledge is necessary for the development of design tools for peptide-based antibiotics.

scholarly journals De Novo Design of Potent Antimicrobial Peptides

2004 ◽  
Vol 48 (9) ◽  
pp. 3349-3357 ◽  
Author(s):  
V. Frecer ◽  
B. Ho ◽  
J. L. Ding
Keyword(s):  
Antimicrobial Peptides ◽  
Rational Design ◽  
Lipid A ◽  
De Novo ◽  
Endotoxic Shock ◽  
Antimicrobial Properties ◽  
Antimicrobial Effect ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Qsar Analysis

ABSTRACT Lipopolysaccharide (LPS), shed by gram-negative bacteria during infection and antimicrobial therapy, may lead to lethal endotoxic shock syndrome. A rational design strategy based on the presumed mechanism of antibacterial effect was adopted to design cationic antimicrobial peptides capable of binding to LPS through tandemly repeated sequences of alternating cationic and nonpolar residues. The peptides were designed to achieve enhanced antimicrobial potency due to initial bacterial membrane binding with a reduced risk of endotoxic shock. The peptides designed displayed binding affinities to LPS and lipid A (LA) in the low micromolar range and by molecular modeling were predicted to form amphipathic β-hairpin-like structures when they bind to LPS or LA. They also exhibited strong effects against gram-negative bacteria, with MICs in the nanomolar range, and low cytotoxic and hemolytic activities at concentrations significantly exceeding their MICs. Quantitative structure-activity relationship (QSAR) analysis of peptide sequences and their antimicrobial, cytotoxic, and hemolytic activities revealed that site-directed substitutions of residues in the hydrophobic face of the amphipathic peptides with less lipophilic residues selectively decrease the hemolytic effect without significantly affecting the antimicrobial or cytotoxic activity. On the other hand, the antimicrobial effect can be enhanced by substitutions in the polar face with more polar residues, which increase the amphipathicity of the peptide. On the basis of the QSARs, new analogs that have strong antimicrobial effects but that lack hemolytic activity can be proposed. The findings highlight the importance of peptide amphipathicity and allow a rational method that can be used to dissociate the antimicrobial and hemolytic effects of cationic peptides, which have potent antimicrobial properties, to be proposed.

scholarly journals Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis

2016 ◽  
Vol 60 (5) ◽  
pp. 2757-2764 ◽  
Author(s):  
C. Seth Pearson ◽  
Zachary Kloos ◽  
Brian Murray ◽  
Ebot Tabe ◽  
Monica Gupta ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Antimicrobial Peptides ◽  
Rational Design ◽  
Pathogenic Bacteria ◽  
First Generation ◽  
De Novo ◽  
Specific Activity ◽  
Lung Epithelial Cells ◽  
Content Type ◽  
Low Cytotoxicity

ABSTRACTDrug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens isMycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity againstM. tuberculosisusing a combination of “database filtering” bioinformatics, protein engineering, andde novodesign. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) againstM. tuberculosisand also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of theM. tuberculosismembrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created.

scholarly journals Design of a De Novo Aggregating Antimicrobial Peptide and a Bacterial Conjugation-Based Delivery System

Biochemistry ◽  
2018 ◽  
Vol 58 (11) ◽  
pp. 1521-1526 ◽  
Author(s):  
Logan T. Collins ◽  
Peter B. Otoupal ◽  
Jocelyn K. Campos ◽  
Colleen M. Courtney ◽  
Anushree Chatterjee
Keyword(s):  
Antimicrobial Peptide ◽  
Delivery System ◽  
De Novo ◽  
Bacterial Conjugation

scholarly journals AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning

mSystems ◽  
2021 ◽  
Author(s):  
Tzu-Tang Lin ◽  
Li-Yen Yang ◽  
I-Hsuan Lu ◽  
Wen-Chih Cheng ◽  
Zhe-Ren Hsu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Deep Learning ◽  
Physicochemical Property ◽  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Innate Immune ◽  
Wet Lab ◽  
Encoding Method ◽  
Screening Approaches

Antimicrobial peptides (AMPs) are innate immune components that have aroused a great deal of interest among drug developers recently, as they may become a substitute for antibiotics. New candidates need to fight antibiotic resistance, while discovering novel AMPs through wet-lab screening approaches is inefficient and expensive.

Antimicrobial Peptides: A Promising Avenue for Human Healthcare

2020 ◽  
Vol 21 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Girish M. Bhopale
Keyword(s):  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Antimicrobial Agents ◽  
Current Status ◽  
Antimicrobial Drugs ◽  
Spectrum Activity ◽  
Low Levels ◽  
Human Healthcare ◽  
Broad Spectrum Activity ◽  
Promising Avenue

Antimicrobial drugs resistant microbes have been observed worldwide and therefore alternative development of antimicrobial peptides has gained interest in human healthcare. Enormous progress has been made in the development of antimicrobial peptide during the last decade due to major advantages of AMPs such as broad-spectrum activity and low levels of induced resistance over the current antimicrobial agents. This review briefly provides various categories of AMP, their physicochemical properties and mechanism of action which governs their penetration into microbial cell. Further, the recent information on current status of antimicrobial peptide development, their applications and perspective in human healthcare are also described.

scholarly journals A mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography

2021 ◽  
Author(s):  
Stéphane Baeriswyl ◽  
Hippolyte Personne ◽  
Ivan Di Bonaventura ◽  
Thilo Köhler ◽  
Christian van Delden ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Crystal Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
Α Helix

We report the first X-ray crystal structures of mixed chirality α-helices comprising only natural residues as the example of bicyclic and linear membrane disruptive amphiphilic antimicrobial peptides containing seven l- and four d-residues.

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