scholarly journals Utilizing in silico and in vitro methods to identify possible binding sites of a novel ligand against Pseudomonas aeruginosa phospholipase toxin ExoU

2022 ◽  
Vol 29 ◽  
pp. 101188
Author(s):  
Krista Chamberlain ◽  
Mya Johnson ◽  
Terry-Elinor Reid ◽  
Tzvia I. Springer
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Binding Sites ◽  
In Silico ◽  
In Vitro Methods

Design, Synthesis and In-Vitro Biological Activity of Some New 1,3-Thiazolidine-4-One Derivatives as Chemotherapeutic Agents Using Virtual Screening Strategies

2020 ◽  
Vol 16 ◽  
Author(s):  
Pragya Nayak ◽  
Monica Kachroo
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virtual Screening ◽  
In Silico ◽  
Cancer Cell Line ◽  
Inhibitory Response ◽  
Chemotherapeutic Agents ◽  
Acceptor Site ◽  
Hydrogen Bond Acceptor ◽  
Screening Strategies

: A series of new heteroaryl thiazolidine-4-one derivatives were designed and subjected to in-silico prioritization using various virtual screening strategies. Two series of thiazolidinone derivatives were synthesized and screened for their in-vitro antitubercular, anticancer, antileishmanial and antibacterial (Staphylococcus aureus; Streptococcus pneumonia; Escherichia coli; Pseudomonas aeruginosa) activities. The compounds with electronegative substitutions exhibited positive antitubercular activity, the derivatives possessing a methyl substitution exhibited good inhibitory response against breast cancer cell line MCF-7 while the compounds possessing a hydrogen bond acceptor site like hydroxyl and methoxy substitution in their structures exhibited good in-vitro antileishmanial activity. Some compounds exhibited potent activity against gram positive bacteria Pseudomonas aeruginosa as compared to the standards. Altogether, the designed compounds exhibited good in-vitro anti-infective potential which was in good agreement with the in-silico predictions and they can be developed as important lead molecules for anti-infective and chemotherapeutic drug research.

Semen Cuscutae-Fructus Lycii improves spermatogenic dysfunction by repairing the blood-testis barrier in rats according to in silico and in vitro methods

2021 ◽  
pp. 114022
Author(s):  
Yutian Zhu ◽  
Lei Dong ◽  
Jingshang Wang ◽  
Qiuning Liu ◽  
Hongxuan Tong ◽  
...  
Keyword(s):  
In Silico ◽  
In Vitro Methods ◽  
Fructus Lycii ◽  
Blood Testis Barrier

Abstract 121: Pro-inflammatory Cytokine Ifng Modulates Hepatic Sortilin Expression and Lipid Metabolism.

2015 ◽  
Vol 35 (suppl_1) ◽  
Author(s):  
John Pirault ◽  
Konstantinos Polyzos ◽  
Daniel F Ketelhuth ◽  
Göran K Hansson
Keyword(s):  
Lipid Metabolism ◽  
Binding Sites ◽  
In Silico ◽  
In Silico Analysis ◽  
Lipid Uptake ◽  
Regulatory T Lymphocytes ◽  
Inflammatory Conditions ◽  
Ldl Particles ◽  
Inflammatory Milieu

Rationale: Hypercholesterolemia and immunity are two major risk factors for cardiovascular diseases (CVDs). Yet, we reported increased atherosclerosis upon depletion of regulatory T lymphocytes (Tregs). The effect was associated with increased hepatic inflammation and reduction of Sortilin expression and lipid uptake in the liver. Objective: To define how inflammatory milieu in the liver can modulate Sortilin and lipid metabolism. Methods: To reproduce the inflammatory milieu, hepatocytes (AML-12) were treated in vitro with IFNg. Expression of genes and proteins of interest were followed by qPCR and western blot. In silico method was used to find binding sites of signal transducer and activator of transcription (STAT1) on Sortilin, confirmed later by chromatin immune precipitation assays (Chip). Lipid uptake by hepatocytes was assessed via incubation of cells with radioactive lipoproteins. Results: Culture of AML-12 cells with IFNg induced the phosphorylation of STAT1 showing an active signaling pathway. In the same inflammatory conditions, Sort1 mRNA is decreased meanwhile its inhibitor (Atf3) expression is increased. Kinetic experiments revealed the reduction of Sortilin after 12 hours of culture, suggesting a post-transcriptional regulation of Sort1 by STAT1. In silico analysis revealed putative binding sites for STAT1 on Sortilin gene which was confirmed by chromatin immunoprecipitation assay (Chip). IFNg treated hepatocytes that were incubated with radioactive lipoproteins demonstrated a reduced uptake capacity of VLDL and LDL particles compared to control cultures. Conclusion: All together, these results suggest that inflammation through production of IFNg is able to directly modulate the lipid metabolism in hepatocytes by acting on Sortilin expression.

Evaluation of toxicological aspects of three new benzoxazole compounds with sunscreen photophysical properties using in silico and in vitro methods

2021 ◽  
pp. 105300
Author(s):  
Jâmeson Ferreira da Silva ◽  
Dione Silva Corrêa ◽  
Érico Leite Campos ◽  
Giovana Zamprônio Leite ◽  
João Denis Medeiros de Oliveira ◽  
...  
Keyword(s):  
In Silico ◽  
Photophysical Properties ◽  
In Vitro Methods

scholarly journals Molecular Mechanism of Switching of TrkA/p75NTR Signaling in Monocrotophos Induced Neurotoxicity

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Vivek Kumar ◽  
Amit Kumar Gupta ◽  
Rajendra Kumar Shukla ◽  
Vinay Kumar Tripathi ◽  
Sadaf Jahan ◽  
...  
Keyword(s):  
Binding Sites ◽  
In Silico ◽  
Cholinergic Neurons ◽  
Behavioral Changes ◽  
Organophosphate Pesticide ◽  
Molecular Switching ◽  
Downstream Signaling ◽  
Potential Therapeutic Intervention

Abstract We demonstrate the role of molecular switching of TrkA/p75NTR signaling cascade in organophosphate pesticide-Monocrotophos (MCP) induced neurotoxicity in stem cell derived cholinergic neurons and in rat brain. Our in-silico studies reveal that MCP followed the similar pattern of binding as staurosporine and AG-879 (known inhibitors of TrkA) with TrkA protein (PDB ID: 4AOJ) at the ATP binding sites. This binding of MCP to TrkA led to the conformational change in this protein and triggers the cell death cascades. The in-silico findings are validated by observing the down regulated levels of phosphorylated TrkA and its downstream molecules viz., pERK1/2, pAkt and pCREB in MCP-exposed cells. We observe that these MCP induced alterations in pTrkA and downstream signaling molecules are found to be associated with apoptosis and injury to neurons. The down-regulation of TrkA could be linked to increased p75NTR. The in-vitro studies could be correlated in the rat model. The switching of TrkA/p75NTR signaling plays a central role in MCP-induced neural injury in rBNSCs and behavioral changes in exposed rats. Our studies significantly advance the understanding of the switching of TrkA/p75NTR that may pave the way for the application of TrkA inducer/p75NTR inhibitor for potential therapeutic intervention in various neurodegenerative disorders.

scholarly journals Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism

2015 ◽  
Vol 8 (3) ◽  
pp. 95-105 ◽  
Author(s):  
Sivakumar Prasanth Kumar ◽  
Vilas R. Parmar ◽  
Yogesh T. Jasrai ◽  
Himanshu A. Pandya
Keyword(s):  
Seed Germination ◽  
In Silico ◽  
Protein Targets ◽  
In Vitro Methods

scholarly journals Pseudomonas aeruginosa reverse diauxie is an optimized, resource utilization strategy

2020 ◽  
Author(s):  
S. Lee McGill ◽  
Yeni Yung ◽  
Kristopher A. Hunt ◽  
Michael A. Henson ◽  
Luke Hanley ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Systems Biology ◽  
In Silico ◽  
Carbon Sources ◽  
Opportunistic Pathogen ◽  
Metabolic Model ◽  
Wide Distribution ◽  
Overflow Metabolism ◽  
A Genome

AbstractPseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an ‘overflow’ metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as ‘reverse diauxie’. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence.

scholarly journals Berberine Derivatives as Pseudomonas aeruginosa MexXY-OprM Inhibitors: Activity and In Silico Insights

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6644
Author(s):  
Giorgia Giorgini ◽  
Gianmarco Mangiaterra ◽  
Nicholas Cedraro ◽  
Emiliano Laudadio ◽  
Giulia Sabbatini ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
In Silico ◽  
Rational Design ◽  
Specific Binding ◽  
In Silico Analysis ◽  
In Vitro Assays ◽  
Binding Modes ◽  
Starting Point ◽  
Berberine Derivatives

The natural alkaloid berberine has been demonstrated to inhibit the Pseudomonas aeruginosa multidrug efflux system MexXY-OprM, which is responsible for tobramycin extrusion by binding the inner membrane transporter MexY. To find a structure with improved inhibitory activity, we compared by molecular dynamics investigations the binding affinity of berberine and three aromatic substituents towards the three polymorphic sequences of MexY found in P. aeruginosa (PAO1, PA7, and PA14). The synergy of the combinations of berberine or berberine derivatives/tobramycin against the same strains was then evaluated by checkerboard and time-kill assays. The in silico analysis evidenced different binding modes depending on both the structure of the berberine derivative and the specific MexY polymorphism. In vitro assays showed an evident MIC reduction (32-fold and 16-fold, respectively) and a 2–3 log greater killing effect after 2 h of exposure to the combinations of 13-(2-methylbenzyl)- and 13-(4-methylbenzyl)-berberine with tobramycin against the tobramycin-resistant strain PA7, a milder synergy (a 4-fold MIC reduction) against PAO1 and PA14, and no synergy against the ΔmexXY strain K1525, confirming the MexY-specific binding and the computational results. These berberine derivatives could thus be considered new hit compounds to select more effective berberine substitutions and their common path of interaction with MexY as the starting point for the rational design of novel MexXY-OprM inhibitors.

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