scholarly journals A Machine Learning Tool to Predict the Antibacterial Capacity of Nanoparticles

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1774
Author(s):  
Mahsa Mirzaei ◽  
Irini Furxhi ◽  
Finbarr Murphy ◽  
Martin Mullins
Keyword(s):  
Machine Learning ◽  
Performance Metrics ◽  
Exposure Dose ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Attribute Importance ◽  
Experimental Conditions ◽  
Wide Range ◽  
Antibacterial Capacity

The emergence and rapid spread of multidrug-resistant bacteria strains are a public health concern. This emergence is caused by the overuse and misuse of antibiotics leading to the evolution of antibiotic-resistant strains. Nanoparticles (NPs) are objects with all three external dimensions in the nanoscale that varies from 1 to 100 nm. Research on NPs with enhanced antimicrobial activity as alternatives to antibiotics has grown due to the increased incidence of nosocomial and community acquired infections caused by pathogens. Machine learning (ML) tools have been used in the field of nanoinformatics with promising results. As a consequence of evident achievements on a wide range of predictive tasks, ML techniques are attracting significant interest across a variety of stakeholders. In this article, we present an ML tool that successfully predicts the antibacterial capacity of NPs while the model’s validation demonstrates encouraging results (R2 = 0.78). The data were compiled after a literature review of 60 articles and consist of key physico-chemical (p-chem) properties and experimental conditions (exposure variables and bacterial clustering) from in vitro studies. Following data homogenization and pre-processing, we trained various regression algorithms and we validated them using diverse performance metrics. Finally, an important attribute evaluation, which ranks the attributes that are most important in predicting the outcome, was performed. The attribute importance revealed that NP core size, the exposure dose, and the species of bacterium are key variables in predicting the antibacterial effect of NPs. This tool assists various stakeholders and scientists in predicting the antibacterial effects of NPs based on their p-chem properties and diverse exposure settings. This concept also aids the safe-by-design paradigm by incorporating functionality tools.

scholarly journals Enhanced Resistance to Bacterial Infection in Protegrin-1 Transgenic Mice

2008 ◽  
Vol 52 (5) ◽  
pp. 1812-1819 ◽  
Author(s):  
Queenie C. K. Cheung ◽  
Patricia V. Turner ◽  
Cheng Song ◽  
De Wu ◽  
Hugh Y. Cai ◽  
...  
Keyword(s):  
Transgenic Mice ◽  
Bacterial Infection ◽  
Ectopic Expression ◽  
Farm Animals ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Cell Counts ◽  
Enhanced Resistance ◽  
Wide Range

ABSTRACT Antibiotic-resistant bacteria have become a public health concern. It was suggested that one source of resistant pathogens may be food-producing animals. Alternative approaches are therefore needed to enhance the resistance of farm animals to bacterial infection. Protegrin-1 (PG-1) is a neutrophil-derived antimicrobial peptide that possesses activity against a wide range of bacteria and enveloped viruses. Here we report on the production of transgenic mice that ectopically expressed PG-1 and compare their susceptibilities to Actinobacillus suis infection with those of their wild-type (WT) littermates. Of the 126 mice that were challenged with A. suis, 87% of the transgenic mice survived, whereas 31% of their WT littermates survived. The PG-1 transgenic mice had significantly lower bacterial loads in their lungs and reduced numbers of pulmonary pathological lesions. The antimicrobial function of PG-1 was confirmed in vitro by using fibroblast cells isolated from the transgenic mice but not the WT mice. Moreover, differential blood cell counts in bronchoalveolar lavage fluid indicated greater number of neutrophils in PG-1 transgenic mice than in their WT littermates after bacterial challenge. Our data suggest that the ectopic expression of PG-1 in mice confers enhanced resistance to bacterial infection, laying the foundation for the development of livestock with improved resistance to infection.

scholarly journals In Vitro Synergistic Interactions of Isavuconazole and Echinocandins against Candida auris

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 355
Author(s):  
Unai Caballero ◽  
Sarah Kim ◽  
Elena Eraso ◽  
Guillermo Quindós ◽  
Valvanera Vozmediano ◽  
...  
Keyword(s):  
Interaction Model ◽  
Antifungal Drugs ◽  
Health Concern ◽  
Candida Auris ◽  
Fungistatic Activity ◽  
Drug Concentrations ◽  
Low Concentrations ◽  
Wide Range ◽  
Time Kill

Candida auris is an emergent fungal pathogen that causes severe infectious outbreaks globally. The public health concern when dealing with this pathogen is mainly due to reduced susceptibility to current antifungal drugs. A valuable alternative to overcome this problem is to investigate the efficacy of combination therapy. The aim of this study was to determine the in vitro interactions of isavuconazole with echinocandins against C. auris. Interactions were determined using a checkerboard method, and absorbance data were analyzed with different approaches: the fractional inhibitory concentration index (FICI), Greco universal response surface approach, and Bliss interaction model. All models were in accordance and showed that combinations of isavuconazole with echinocandins resulted in an overall synergistic interaction. A wide range of concentrations within the therapeutic range were selected to perform time-kill curves. These confirmed that isavuconazole–echinocandin combinations were more effective than monotherapy regimens. Synergism and fungistatic activity were achieved with combinations that included isavuconazole in low concentrations (≥0.125 mg/L) and ≥1 mg/L of echinocandin. Time-kill curves revealed that once synergy was achieved, combinations of higher drug concentrations did not improve the antifungal activity. This work launches promising results regarding the combination of isavuconazole with echinocandins for the treatment of C. auris infections.

scholarly journals A Putative Cro-Like Repressor Contributes to Arylomycin Resistance in Staphylococcus aureus

2015 ◽  
Vol 59 (6) ◽  
pp. 3066-3074 ◽  
Author(s):  
Arryn Craney ◽  
Floyd E. Romesberg
Keyword(s):  
Staphylococcus Aureus ◽  
Ex Vivo ◽  
Transcriptional Regulator ◽  
Signal Peptidase ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Type I ◽  
Wall Teichoic Acid ◽  
Content Type ◽  
Wide Range

ABSTRACTAntibiotic-resistant bacteria are a significant public health concern and motivate efforts to develop new classes of antibiotics. One such class of antibiotics is the arylomycins, which target type I signal peptidase (SPase), the enzyme responsible for the release of secreted proteins from their N-terminal leader sequences. Despite the essentiality, conservation, and relative accessibility of SPase, the activity of the arylomycins is limited against some bacteria, including the important human pathogenStaphylococcus aureus. To understand the origins of the limited activity againstS. aureus, we characterized the susceptibility of a panel of strains to two arylomycin derivatives, arylomycin A-C16and its more potent analog arylomycin M131. We observed a wide range of susceptibilities to the two arylomycins and found that resistant strains were sensitized by cotreatment with tunicamycin, which inhibits the first step of wall teichoic acid synthesis. To further understand howS. aureusresponds to the arylomycins, we profiled the transcriptional response ofS. aureusNCTC 8325 to growth-inhibitory concentrations of arylomycin M131 and found that it upregulates the cell wall stress stimulon (CWSS) and an operon consisting of a putative transcriptional regulator and three hypothetical proteins. Interestingly, we found that mutations in the putative transcriptional regulator are correlated with resistance, and selection for resistanceex vivodemonstrated that mutations in this gene are sufficient for resistance. The results begin to elucidate howS. aureuscopes with secretion stress and how it evolves resistance to the inhibition of SPase.

scholarly journals Synthesis, In Silico, and In Vitro Evaluation of Long Chain Alkyl Amides from 2-Amino-4-Quinolone Derivatives as Biofilm Inhibitors

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 327 ◽  
Author(s):  
Mariana Espinosa-Valdés ◽  
Sara Borbolla-Alvarez ◽  
Ana Delgado-Espinosa ◽  
Juan Sánchez-Tejeda ◽  
Anabelle Cerón-Nava ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Biofilm Formation ◽  
Active Sites ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Biofilm Inhibition ◽  
Amide Derivatives ◽  
Long Chain

Infection from multidrug resistant bacteria has become a growing health concern worldwide, increasing the need for developing new antibacterial agents. Among the strategies that have been studied, biofilm inhibitors have acquired relevance as a potential source of drugs that could act as a complement for current and new antibacterial therapies. Based on the structure of 2-alkyl-3-hydroxy-4-quinolone and N-acylhomoserine lactone, molecules that act as mediators of quorum sensing and biofilm formation in Pseudomonas aeruginosa, we designed, prepared, and evaluated the biofilm inhibition properties of long chain amide derivatives of 2-amino-4-quinolone in Staphylococcus aureus and P. aeruginosa. All compounds had higher biofilm inhibition activity in P. aeruginosa than in S. aureus. Particularly, compounds with an alkyl chain of 12 carbons exhibited the highest inhibition of biofilm formation. Docking scores and molecular dynamics simulations of the complexes of the tested compounds within the active sites of proteins related to quorum sensing had good correlation with the experimental results, suggesting the diminution of biofilm formation induced by these compounds could be related to the inhibition of these proteins.

scholarly journals Predicting In Vitro Neurotoxicity Induced by Nanoparticles Using Machine Learning

2020 ◽  
Vol 21 (15) ◽  
pp. 5280
Author(s):  
Irini Furxhi ◽  
Finbarr Murphy
Keyword(s):  
Machine Learning ◽  
Goodness Of Fit ◽  
Information Gain ◽  
Sampling Technique ◽  
Exposure Dose ◽  
Classification Model ◽  
Machine Learning Techniques ◽  
Data Set ◽  
Tissue Specific

The practice of non-testing approaches in nanoparticles hazard assessment is necessary to identify and classify potential risks in a cost effective and timely manner. Machine learning techniques have been applied in the field of nanotoxicology with encouraging results. A neurotoxicity classification model for diverse nanoparticles is presented in this study. A data set created from multiple literature sources consisting of nanoparticles physicochemical properties, exposure conditions and in vitro characteristics is compiled to predict cell viability. Pre-processing techniques were applied such as normalization methods and two supervised instance methods, a synthetic minority over-sampling technique to address biased predictions and production of subsamples via bootstrapping. The classification model was developed using random forest and goodness-of-fit with additional robustness and predictability metrics were used to evaluate the performance. Information gain analysis identified the exposure dose and duration, toxicological assay, cell type, and zeta potential as the five most important attributes to predict neurotoxicity in vitro. This is the first tissue-specific machine learning tool for neurotoxicity prediction caused by nanoparticles in in vitro systems. The model performs better than non-tissue specific models.

scholarly journals Amyloid Beta: Multiple Mechanisms of Toxicity and Only Some Protective Effects?

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Paul Carrillo-Mora ◽  
Rogelio Luna ◽  
Laura Colín-Barenque
Keyword(s):  
Amyloid Beta ◽  
Protective Effects ◽  
Protective Mechanisms ◽  
Experimental Conditions ◽  
Mechanisms Of Toxicity ◽  
Mitochondrial Alterations ◽  
Physiological Properties ◽  
Wide Range

Amyloid beta (Aβ) is a peptide of 39–43 amino acids found in large amounts and forming deposits in the brain tissue of patients with Alzheimer’s disease (AD). For this reason, it has been implicated in the pathophysiology of damage observed in this type of dementia. However, the role of Aβin the pathophysiology of AD is not yet precisely understood. Aβhas been experimentally shown to have a wide range of toxic mechanismsin vivoandin vitro, such as excitotoxicity, mitochondrial alterations, synaptic dysfunction, altered calcium homeostasis, oxidative stress, and so forth. In contrast, Aβhas also shown some interesting neuroprotective and physiological properties under certain experimental conditions, suggesting that both physiological and pathological roles of Aβmay depend on several factors. In this paper, we reviewed both toxic and protective mechanisms of Aβto further explore what their potential roles could be in the pathophysiology of AD. The complete understanding of such apparently opposed effects will also be an important guide for the therapeutic efforts coming in the future.

scholarly journals Mycobacterial Esx-3 Requires Multiple Components for Iron Acquisition

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
M. Sloan Siegrist ◽  
Magnus Steigedal ◽  
Rushdy Ahmad ◽  
Alka Mehra ◽  
Marte S. Dragset ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Iron Acquisition ◽  
Multiple Reaction Monitoring ◽  
Protein Export ◽  
Secretion Systems ◽  
Experimental Conditions ◽  
Content Type ◽  
Type Vii Secretion ◽  
Wide Range

ABSTRACT The type VII secretion systems are conserved across mycobacterial species and in many Gram-positive bacteria. While the well-characterized Esx-1 pathway is required for the virulence of pathogenic mycobacteria and conjugation in the model organism Mycobacterium smegmatis, Esx-3 contributes to mycobactin-mediated iron acquisition in these bacteria. Here we show that several Esx-3 components are individually required for function under low-iron conditions but that at least one, the membrane-bound protease MycP3 of M. smegmatis, is partially expendable. All of the esx-3 mutants tested, including the ΔmycP 3ms mutant, failed to export the native Esx-3 substrates EsxH ms and EsxG ms to quantifiable levels, as determined by targeted mass spectrometry. Although we were able to restore low-iron growth to the esx-3 mutants by genetic complementation, we found a wide range of complementation levels for protein export. Indeed, minute quantities of extracellular EsxH ms and EsxG ms were sufficient for iron acquisition under our experimental conditions. The apparent separation of Esx-3 function in iron acquisition from robust EsxG ms and EsxH ms secretion in the ΔmycP 3ms mutant and in some of the complemented esx-3 mutants compels reexamination of the structure-function relationships for type VII secretion systems. IMPORTANCE Mycobacteria have several paralogous type VII secretion systems, Esx-1 through Esx-5. Whereas Esx-1 is required for pathogenic mycobacteria to grow within an infected host, Esx-3 is essential for growth in vitro. We and others have shown that Esx-3 is required for siderophore-mediated iron acquisition. In this work, we identify individual Esx-3 components that contribute to this process. As in the Esx-1 system, most mutations that abolish Esx-3 protein export also disrupt its function. Unexpectedly, however, ultrasensitive quantitation of Esx-3 secretion by multiple-reaction-monitoring mass spectrometry (MRM-MS) revealed that very low levels of export were sufficient for iron acquisition under similar conditions. Although protein export clearly contributes to type VII function, the relationship is not absolute.

scholarly journals The Pomegranate: Effects on Bacteria and Viruses That Influence Human Health

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Amy B. Howell ◽  
Doris H. D'Souza
Keyword(s):  
Antimicrobial Activity ◽  
Foodborne Pathogens ◽  
Clinical Results ◽  
Multidrug Resistant ◽  
Antimicrobial Activities ◽  
Oral Bacteria ◽  
Resistant Bacteria ◽  
Wide Range

Pomegranates have been known for hundreds of years for their multiple health benefits, including antimicrobial activity. The recent surge in multidrug-resistant bacteria and the possibility of widespread global virus pandemics necessitate the need for additional preventative and therapeutic options to conventional drugs. Research indicates that pomegranates and their extracts may serve as natural alternatives due to their potency against a wide range of bacterial and viral pathogens. Nearly every part of the pomegranate plant has been tested for antimicrobial activities, including the fruit juice, peel, arils, flowers, and bark. Many studies have utilized pomegranate peel with success. There are various phytochemical compounds in pomegranate that have demonstrated antimicrobial activity, but most of the studies have found that ellagic acid and larger hydrolyzable tannins, such as punicalagin, have the highest activities. In some cases the combination of the pomegranate constituents offers the most benefit. The positive clinical results on pomegranate and suppression of oral bacteria are intriguing and worthy of further study. Much of the evidence for pomegranates’ antibacterial and antiviral activities against foodborne pathogens and other infectious disease organisms comes fromin vitrocell-based assays, necessitating further confirmation ofin vivoefficacy through human clinical trials.

scholarly journals Electrical impulse characterization along actin filaments in pathological conditions

2021 ◽  
Author(s):  
Christian Hunley ◽  
Md Mohsin ◽  
Marcelo Marucho
Keyword(s):  
Actin Filaments ◽  
High Performance ◽  
Original Research ◽  
Experimental Conditions ◽  
Theoretical Formulation ◽  
Pathological Conditions ◽  
Wide Range ◽  
Biological Environment ◽  
Electrical Impulses

We present an interactive Mathematica notebook that characterizes the electrical impulses along actin filaments in both muscle and non-muscle cells for a wide range of physiological and pathological conditions. The program is based on a multi-scale (atomic → monomer → filament) approach capable of accounting for the atomistic details of a protein molecular structure, its biological environment, and their impact on the travel distance, velocity, and attenuation of monovalent ionic wave packets propagating along microfilaments. The interactive component allows investigators to conduct original research by choosing the experimental conditions (intracellular Vs in vitro), nucleotide state (ATP Vs ADP), actin isoform (alpha, gamma, beta, and muscle or non-muscle cell), as well as, a conformation model that covers a variety of mutants and wild-type (the control) actin filament. The simplicity of the theoretical formulation and the high performance of the Mathematica software enable the analysis of multiple conditions without computational restrictions. These studies may provide an unprecedented molecular understanding of why and how age, inheritance, and disease conditions induce dysfunctions in the biophysical mechanisms underlying the propagation of electrical signals along actin filaments.

scholarly journals In Vitro Anticancer Potential of Berberis lycium Royle Extracts against Human Hepatocarcinoma (HepG2) Cells

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Kiren Mustafa ◽  
Hassan Mohamed ◽  
Aabid Manzoor Shah ◽  
Shaoxuan Yu ◽  
Muhammad Akhlaq ◽  
...  
Keyword(s):  
Liver Cancer ◽  
Hepg2 Cells ◽  
Apoptotic Cell ◽  
Cancer Cell Line ◽  
Ethanolic Extract ◽  
Health Concern ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Wide Range

Human liver cancer has emerged as a serious health concern in the world, associated with poorly available therapies. The Berberis genus contains vital medicinal plants with miraculous healing properties and a wide range of bioactivities. In this study, different crude extracts of B. lycium Royle were prepared and screened against Human Hepatocarcinoma (HepG2) cell lines. The water/ethanolic extract of B. lycium Royle (BLE) exhibited significant antiproliferative activity against the HepG2 cancer cell line with an IC50 value of 47 μg/mL. The extract decreased the clonogenic potential of HepG2 cells in a dose-dependent manner. It induced apoptotic cell death in HepG2 cells that were confirmed by cytometric analysis and microscopic examination of cellular morphology through DAPI-stained cells. Biochemical evidence of apoptosis came from elevating the intracellular ROS level that was accompanied by the loss of mitochondrial membrane potential. The mechanism of apoptosis was further confirmed by gene expression analysis using RT-qPCR that revealed the decline in Bcl-2 independent of p53 mRNA and a rise in CDK1 while downregulating CDK5, CDK9, and CDK10 mRNA levels at 48 h of BLE treatment. The most active fraction was subjected to HPLC which indicated the presence of berberine (48 μg/mL) and benzoic acid (15.8 μg/mL) as major compounds in BLE and a trace amount of luteolin, rutin, and gallic acid. Our study highlighted the importance of the most active BLE extract as an excellent source of nutraceuticals against Human Hepatocarcinoma that can serve as an herbal natural cure against liver cancer.

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