scholarly journals Biochemical and Computational Studies of the Interaction between a Glucosamine Derivative, NAPA, and the IKKα Kinase

2021 ◽  
Vol 22 (4) ◽  
pp. 1643
Author(s):  
Mariangela Lopreiato ◽  
Samuele Di Cristofano ◽  
Rossana Cocchiola ◽  
Alessia Mariano ◽  
Libera Guerrizio ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Site ◽  
Kinase Activity ◽  
In Vitro Assays ◽  
Inhibition Mechanism ◽  
Atomic Interaction ◽  
Vitro Assay ◽  
Inflammatory Status ◽  
Significant Difference

The glucosamine derivative 2-(N-Acetyl)-L-phenylalanylamido-2-deoxy-β-D-glucose (NAPA), was shown to inhibit the kinase activity of IKKα, one of the two catalytic subunits of IKK complex, decreasing the inflammatory status in osteoarthritis chondrocytes. In the present work we have investigated the inhibition mechanism of IKKα by NAPA by combining computational simulations, in vitro assays and Mass Spectrometry (MS) technique. The kinase in vitro assay was conducted using a recombinant IKKα and IKKtide, a 20 amino acid peptide substrate derived from IkBα kinase protein and containing the serine residues Ser32 and Ser36. Phosphorylated peptide production was measured by Ultra Performance Liquid Chromatography coupled with Mass Spectrometry (UPLC-MS), and the atomic interaction between IKKα and NAPA has been studied by molecular docking and Molecular Dynamics (MD) approaches. Here we report that NAPA was able to inhibit the IKKα kinase activity with an IC50 of 0.5 mM, to decrease the Km value from 0.337 mM to 0.402 mM and the Vmax from 0.0257 mM·min−1 to 0.0076 mM·min−1. The computational analyses indicate the region between the KD, ULD and SDD domains of IKKα as the optimal binding site explored by NAPA. Biochemical data indicate that there is a non-significant difference between Km and Ki whereas there is a statistically significant difference between the two Vmax values. This evidence, combined with computational results, consistently indicates that the inhibition is non-competitive, and that the NAPA binding site is different than that of ATP or IKKtide.

Computational and In-Vitro Validation of Natural Molecules as Potential Acetylcholinesterase Inhibitors and Neuroprotective Agents

2019 ◽  
Vol 16 (2) ◽  
pp. 116-127 ◽  
Author(s):  
Ashwani Kumar ◽  
Vineet Mehta ◽  
Utkarsh Raj ◽  
Pritish Kumar Varadwaj ◽  
Malairaman Udayabanu ◽  
...  
Keyword(s):  
In Silico ◽  
Hippocampal Neurons ◽  
Symptomatic Relief ◽  
In Vitro Assays ◽  
Disease Modifying Drugs ◽  
In Silico Docking ◽  
Ache Inhibitors ◽  
Significant Difference ◽  
Disease Modifying

Background: Cholinesterase inhibitors are the first line of therapy for the management of Alzheimer’s disease (AD), however, it is now established that they provide only temporary and symptomatic relief, besides, having several inherited side-effects. Therefore, an alternative drug discovery method is used to identify new and safer ‘disease-modifying drugs’. Methods: Herein, we screened 646 small molecules of natural origin having reported pharmacological and functional values through in-silico docking studies to predict safer neuromodulatory molecules with potential to modulate acetylcholine metabolism. Further, the potential of the predicted molecules to inhibit acetylcholinesterase (AChE) activity and their ability to protect neurons from degeneration was determined through in-vitro assays. Results: Based on in-silico AChE interaction studies, we predicted quercetin, caffeine, ascorbic acid and gallic acid to be potential AChE inhibitors. We confirmed the AChE inhibitory potential of these molecules through in-vitro AChE inhibition assay and compared results with donepezil and begacestat. Herbal molecules significantly inhibited enzyme activity and inhibition for quercetin and caffeine did not show any significant difference from donepezil. Further, the tested molecules did not show any neurotoxicity against primary (E18) hippocampal neurons. We observed that quercetin and caffeine significantly improved neuronal survival and efficiently protected hippocampal neurons from HgCl2 induced neurodegeneration, which other molecules, including donepezil and begacestat, failed to do. Conclusion: Quercetin and caffeine have the potential as “disease-modifying drugs” and may find application in the management of neurological disorders such as AD.

scholarly journals Biofilm reduction potential of 0.02% polyhexanide irrigation solution in several types of urethral catheters

BMC Urology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Florian H. H. Brill ◽  
Julia Hambach ◽  
Christian Utpatel ◽  
Diana C. Mogrovejo ◽  
Henrik Gabriel ◽  
...  
Keyword(s):  
Membrane Filtration ◽  
Saline Solution ◽  
Bacterial Biofilm ◽  
Plate Count ◽  
Vitro Assay ◽  
Significant Difference ◽  
Irrigation Solution ◽  
Clinically Relevant Bacteria

Abstract Background Long-term use of urethral catheters is associated with high risk of urinary tract infection (UTI) and blockage. Microbial biofilms are a common cause of catheter blockage, reducing their lifetime and significantly increasing morbidity of UTIs. A 0.02% polyhexanide irrigation solution developed for routine mechanical rinsing shows potential for bacterial decolonization of urethral catheters and has the potential to reduce or prevent biofilm formation. Methods Using an in vitro assay with standard market-leading types of catheters artificially contaminated with clinically relevant bacteria, assays were carried out to evaluate the biofilm reduction and prevention potential of a 0.02% polyhexanide solution versus no intervention (standard approach) and irrigation with saline solution (NaCl 0.9%). The efficiency of decolonization was measured through microbial plate count and membrane filtration. Results Irrigation using a 0.02% polyhexanide solution is suitable for the decolonization of a variety of transurethral catheters. The effect observed is significant compared to irrigation with 0.9% saline solution (p = 0.002) or no treatment (p = 0.011). No significant difference was found between irrigation with 0.9% saline solution and no treatment (p = 0.74). Conclusions A 0.02% polyhexanide solution is able to reduce bacterial biofilm from catheters artificially contaminated with clinically relevant bacteria in vitro. The data shows a reduction of the viability of thick bacterial biofilms in a variety of commercially available urinary catheters made from silicone, latex-free silicone, hydrogel-coated silicone and PVC. Further research is required to evaluate the long-term tolerability and efficacy of polyhexanide in clinical practice.

Curcumin: Natural Antimicrobial and Anti Inflammatory Agent

2021 ◽  
pp. 1-8
Author(s):  
Pehlivanović Belma ◽  
Čaklovica Kenan ◽  
Lagumdžija Dina ◽  
Omerović Naida ◽  
Žiga Smajić Nermina ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Protein Denaturation ◽  
Dose Range ◽  
In Vitro Assays ◽  
Natural Antimicrobial ◽  
In Vivo Models ◽  
Vitro Assay ◽  
Inflammatory Agent ◽  
Anti Inflammatory

The pursuance of novel antimicrobial and anti-inflammatory agents has been expanding due to a significant need for more efficient pharmacotherapy of various infections and chronic diseases. During the last decade, pharmacokinetics, pharmacodynamics and pharmacological properties of curcumin have been extensively studied. The aim of the present study was to evaluate the antibacterial activity of curcumin against both Gram-positive and Gram-negative bacteria as well as its antifungal activity by using in vitro agar well diffusion assay. Moreover, the anti-inflammatory activity of curcumin was determined with in vitro assay of inhibition of protein denaturation. Results demonstrated wide antimicrobial activity of curcumin upon all of the test bacteria and fungi. The strongest activity of curcumin was observed at a concentration of 0.50 mg/ml against S. aureus, L. monocytogenes, E. coli, P. aeruginosa and C. albicans, resulting in a maximum zone of inhibition of 14.7 mm, 14.3 mm, 13.7 mm, 10.7 mm and 10.7 mm, respectively. Findings suggested that the antimicrobial activity of curcuminis dependent upon the concentrations. Furthermore, results demonstrated high effectiveness of curcumin compared to standard acetylsalicylic acid in inhibiting heat-induced protein denaturation, which activity is also depended upon the concentrations. The present study emphasises the potential application of curcumin as a natural antimicrobial and anti-inflammatory agent. However, findings of this study are restricted to in vitro assays and consideration should be given to conducting a study involving wider dose range test substances as well as including further research on in vivo models.

scholarly journals An In Vitro Assessment of Immunostimulatory Responses to Ten Model Innate Immune Response Modulating Impurities (IIRMIs) and Peptide Drug Product, Teriparatide

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7461
Author(s):  
Claire K. Holley ◽  
Edward Cedrone ◽  
Duncan Donohue ◽  
Barry W. Neun ◽  
Daniela Verthelyi ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Innate Immune Response ◽  
Innate Immune ◽  
Cytokine Secretion ◽  
Poly I:C ◽  
In Vitro Assays ◽  
Innate Immune Responses ◽  
Vitro Assay

Understanding, predicting, and minimizing the immunogenicity of peptide-based therapeutics are of paramount importance for ensuring the safety and efficacy of these products. The so-called anti-drug antibodies (ADA) may have various clinical consequences, including but not limited to the alteration in the product’s distribution, biological activity, and clearance profiles. The immunogenicity of biotherapeutics can be influenced by immunostimulation triggered by the presence of innate immune response modulating impurities (IIRMIs) inadvertently introduced during the manufacturing process. Herein, we evaluate the applicability of several in vitro assays (i.e., complement activation, leukocyte proliferation, and cytokine secretion) for the screening of innate immune responses induced by ten common IIRMIs (Bacillus subtilis flagellin, FSL-1, zymosan, ODN2006, poly(I:C) HMW, poly(I:C) LMW, CLO75, MDP, ODN2216, and Escherichia coli O111:B4 LPS), and a model biotherapeutic Forteo™ (teriparatide). Our study identifies cytokine secretion from healthy human donor peripheral blood mononuclear cells (PBMC) as a sensitive method for the in vitro monitoring of innate immune responses to individual IIRMIs and teriparatide (TP). We identify signature cytokines, evaluate both broad and narrow multiplex cytokine panels, and discuss how the assay logistics influence the performance of this in vitro assay.

scholarly journals Protein polyglutamylation catalyzed by the bacterial calmodulin-dependent pseudokinase SidJ

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Alan Sulpizio ◽  
Marena E Minelli ◽  
Min Wan ◽  
Paul D Burrowes ◽  
Xiaochun Wu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mass Spectrometry ◽  
Ubiquitin Ligase ◽  
Legionella Pneumophila ◽  
Kinase Activity ◽  
Effector Protein ◽  
Dependent Manner ◽  
Biochemical Analyses ◽  
Human And Mouse

Pseudokinases are considered to be the inactive counterparts of conventional protein kinases and comprise approximately 10% of the human and mouse kinomes. Here, we report the crystal structure of the Legionella pneumophila effector protein, SidJ, in complex with the eukaryotic Ca2+-binding regulator, calmodulin (CaM). The structure reveals that SidJ contains a protein kinase-like fold domain, which retains a majority of the characteristic kinase catalytic motifs. However, SidJ fails to demonstrate kinase activity. Instead, mass spectrometry and in vitro biochemical analyses demonstrate that SidJ modifies another Legionella effector SdeA, an unconventional phosphoribosyl ubiquitin ligase, by adding glutamate molecules to a specific residue of SdeA in a CaM-dependent manner. Furthermore, we show that SidJ-mediated polyglutamylation suppresses the ADP-ribosylation activity. Our work further implies that some pseudokinases may possess ATP-dependent activities other than conventional phosphorylation.

Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode

2019 ◽  
Vol 476 (12) ◽  
pp. 1843-1856 ◽  
Author(s):  
Cyril Hamiaux ◽  
Lesley Larsen ◽  
Hui Wen Lee ◽  
Zhiwei Luo ◽  
Prachi Sharma ◽  
...  
Keyword(s):  
In Silico ◽  
Binding Mode ◽  
Crystal Structure Analysis ◽  
Tolfenamic Acid ◽  
In Vitro Assays ◽  
Inhibition Mechanism ◽  
In Planta ◽  
Competitive Antagonist ◽  
In Silico Docking

Abstract Strigolactones (SLs) are multifunctional plant hormones regulating essential physiological processes affecting growth and development. In vascular plants, SLs are recognized by α/β hydrolase-fold proteins from the D14/DAD2 (Dwarf14/Decreased Apical Dominance 2) family in the initial step of the signaling pathway. We have previously discovered that N-phenylanthranilic acid derivatives (e.g. tolfenamic acid) are potent antagonists of SL receptors, prompting us to design quinazolinone and quinazolinedione derivatives (QADs and QADDs, respectively) as second-generation antagonists. Initial in silico docking studies suggested that these compounds would bind to DAD2, the petunia SL receptor, with higher affinity than the first-generation compounds. However, only one of the QADs/QADDs tested in in vitro assays acted as a competitive antagonist of SL receptors, with reduced affinity and potency compared with its N-phenylanthranilic acid ‘parent’. X-ray crystal structure analysis revealed that the binding mode of the active QADD inside DAD2's cavity was not that predicted in silico, highlighting a novel inhibition mechanism for SL receptors. Despite a ∼10-fold difference in potency in vitro, the QADD and tolfenamic acid had comparable activity in planta, suggesting that the QADD compensates for lower potency with increased bioavailability. Altogether, our results establish this QADD as a novel lead compound towards the development of potent and bioavailable antagonists of SL receptors.

In vitro degradability of feed proteins in the rumen: use of non-rumen proteases

2005 ◽  
Vol 56 (8) ◽  
pp. 797 ◽  
Author(s):  
M. Aslam Mirza ◽  
E. L. Miller
Keyword(s):  
Correlation Coefficient ◽  
Soybean Meal ◽  
Streptomyces Griseus ◽  
Correlation Coefficients ◽  
In Vitro Assays ◽  
Vitro Assay ◽  
Bacterial Protease ◽  
Ruminal Protein Degradability

Various feed proteins were incubated independently with bacterial protease from Streptomyces griseus (SGP), papain (Corica papaya), and ficin (Ficus glabrata) in a simple laboratory assay to predict ruminal protein degradability. The estimates obtained from in vitro assays were compared with those obtained from an in situ analysis using synthetic fibre bags. The rate and extent of degradation in vitro using proteases from non-rumen sources differed among substrates used. A high correlation coefficient (r2 = 0.99) was observed between N-degradability from the in vitro method using SGP and in situ estimates when soybean meal was the substrate. Soybean meal nitrogen (N) was almost completely hydrolysed (0.99) in vitro. The correlation coefficients were low and variable with assays using other enzymes. The correlation coefficient was also high (r2 = 0.77–0.84) with in vitro methods using either SGP, papain, or ficin when incubated with fish meal. The N disappearance from barley in vitro was slow to moderate. The ‘b’ estimate of barley obtained with the in vitro assay was significantly (P < 0.01) lower than that observed in situ. Slower proteolysis observed in barley may possibly be linked to poor accessibility of structural proteins rather than the degradability of N per se. None of the enzymes could rank barley in the same order as the in situ method.

scholarly journals Leucine-Rich Diet Modulates the Metabolomic and Proteomic Profile of Skeletal Muscle during Cancer Cachexia

Cancers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1880 ◽  
Author(s):  
Bread Cruz ◽  
André Oliveira ◽  
Lais Rosa Viana ◽  
Leisa Lopes-Aguiar ◽  
Rafael Canevarolo ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Cancer Cachexia ◽  
Energy Generation ◽  
In Vitro Assays ◽  
Proteomic Profile ◽  
Adult Rats ◽  
Vitro Assay ◽  
Tumour Bearing

Background: Cancer-cachexia induces a variety of metabolic disorders, including skeletal muscle imbalance. Alternative therapy, as nutritional supplementation with leucine, shows a modulatory effect over tumour damage in vivo and in vitro. Method: Adult rats distributed into Control (C), Walker tumour-bearing (W), control fed a leucine-rich diet (L), and tumour-bearing fed a leucine-rich diet (WL) groups had the gastrocnemius muscle metabolomic and proteomic assays performed in parallel to in vitro assays. Results: W group presented an affected muscle metabolomic and proteomic profile mainly related to energy generation and carbohydrates catabolic processes, but leucine-supplemented group (WL) recovered the energy production. In vitro assay showed that cell proliferation, mitochondria number and oxygen consumption were higher under leucine effect than the tumour influence. Muscle proteomics results showed that the main affected cell component was mitochondria, leading to an impacted energy generation, including impairment in proteins of the tricarboxylic cycle and carbohydrates catabolic processes, which were modulated and improved by leucine treatment. Conclusion: In summary, we showed a beneficial effect of leucine upon mitochondria, providing information about the muscle glycolytic pathways used by this amino acid, where it can be associated with the preservation of morphometric parameters and consequent protection against the effects of cachexia.

scholarly journals Enterotoxins production, biofilm formation and antimicrobial resistance of Staphylococcus aureus strains isolated from refrigerated raw cow milk

2019 ◽  
Vol 42 ◽  
pp. e45231
Author(s):  
Camila Lampugnani ◽  
Maike Taís Maziero Montanhini ◽  
Maria Emilene Martino Campos‐Galvão ◽  
Luis Augusto Nero ◽  
Luciano dos Santos Bersot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Biofilm Formation ◽  
Raw Milk ◽  
Cow Milk ◽  
In Vitro Assays ◽  
Vitro Assay ◽  
Milk Samples ◽  
Adherence Ability

This study aimed to isolate Staphylococcus aureus in refrigerated raw cow milk, and identify the presence of enterotoxin-expression genes, enterotoxin production and adherence ability, and antimicrobial resistance potential of the isolated strains. Fifty raw milk samples obtained in different dairy farms were analyzed for S. aureus and evaluated in the isolates the presence of genes associated with the production of major staphylococcal enterotoxins and biofilm formation. In vitro assays were also performed to evaluate the production of enterotoxins and adherence ability, and the antimicrobial resistance. One half (25/50) of raw milk samples presented coagulase-positive staphylococci and 95.2% of the isolates were confirmed to be S. aureus. Among them, 42.4% were carrying genes for enterotoxins production; however, only one isolate was able to produce enterotoxins. All S. aureus isolates were carrying at least two genes associated with biofilm formation and 95.2% isolates was able to adhere upon the in vitro assay. All isolates demonstrated antimicrobial resistance potential to one or more of the tested antibiotics.

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