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.

scholarly journals Gamma-hexalactone flavoring causes DNA lesion and modulates cytokines secretion at non-cytotoxic concentrations

2019 ◽  
Vol 20 (S1) ◽  
Author(s):  
Luísa Zuravski ◽  
Taiane A. Escobar ◽  
Elizandra G. Schmitt ◽  
Queila D. F. Amaral ◽  
Fávero R. Paula ◽  
...  
Keyword(s):  
Comet Assay ◽  
In Silico ◽  
In Silico Analysis ◽  
Computational Prediction ◽  
Negative Control ◽  
Alcoholic Beverages ◽  
In Vitro Assays ◽  
In Vitro Tests ◽  
Dna Comet Assay

Abstract Background The γ-hexalactone is a flavoring agent for alcoholic beverages, teas, breads, dairy products, coffees, buttery products among others. It presents low molecular weight and exhibits sweet fruity aroma with nuances of nuts. As far as we know, both literature and government regulations have gaps regarding the safe use of the γ-hexalactone. In this context, the main objective of this work was to evaluate the effects of γ-hexalactone through in silico and in vitro approaches. Methods The in silico analysis was performed through four free online platforms (admetSAR, Osiris Property Explorer®, pkCSM platform and PreADMET) and consisted of comparative structural analysis with substances present in databases. The computational prediction was performed in the sense of complement and guide the in vitro tests. Regarding in vitro investigations, screening of cytotoxicity (assessed by cell proliferation and viability parameters) in lymphocytes exposed to γ-hexalactone for 72 h were carried out previously to determine non-cytotoxic concentrations. Following this screening, concentrations of 5.15, 0.515, and 0.0515 μM were selected for the study of the respective potentials: genotoxic (assessed by DNA comet assay), chromosomal mutation (analysis of micronucleus frequency) and immunomodulatory (cytokine quantification using ELISA immunoassay). The results of in vitro assays were compared by one-way analysis of variance (ANOVA), followed by Bonferroni’s post hoc test, conducted by statistic software. Results The platform PreADMET pointed out that γ-hexalactone is potentially mutagenic and carcinogenic. The comet assay data corroborate with these results demonstrating that γ-hexalactone at 5.15 μM caused lymphocytes DNA damage. In relation to cytokine secretion, the results indicate that lymphocytes were activated by γ-hexalactone at non-cytotoxic concentrations, involving an increase in the IL-1 levels in all tested concentrations, ranging from approximately 56 to 93%. The γ-hexalactone only at 5.15 μM induced increase in the levels of IL-6 (~ 60%), TNF-α (~ 68%) and IFN-γ (~ 29%), but decreased IL-10 (~ 46%) in comparison with the negative control (p < 0.05). No change was observed in total lymphocytes or in cell viability at the concentrations tested. Conclusions In summary, the γ-hexalactone demonstrated immunomodulatory and genotoxic effects at non-cytotoxic concentrations in healthy lymphocytes.

scholarly journals Evaluation of Computationally Designed Peptides against TWEAK, a Cytokine of the Tumour Necrosis Factor Ligand Family

2021 ◽  
Vol 22 (3) ◽  
pp. 1066
Author(s):  
Miriam Badia-Villanueva ◽  
Sira Defaus ◽  
Ruben Foj ◽  
David Andreu ◽  
Baldo Oliva ◽  
...  
Keyword(s):  
Tumour Necrosis Factor ◽  
Protein Interactions ◽  
In Silico ◽  
Tumour Necrosis ◽  
In Vitro Assays ◽  
Physical Interaction ◽  
Vitro Assay ◽  
Starting Point ◽  
Necrosis Factor

The tumour necrosis factor-like weak inducer of apoptosis (TWEAK) is a member of the tumour necrosis factor ligand family and has been shown to be overexpressed in tumoral cells together with the fibroblast growth factor–inducible 14 (Fn14) receptor. TWEAK-Fn14 interaction triggers a set of intracellular pathways responsible for tumour cell invasion and migration, as well as proliferation and angiogenesis. Hence, modulation of the TWEAK-Fn14 interaction is an important therapeutic goal. The targeting of protein-protein interactions by external agents, e.g., drugs, remains a substantial challenge. Given their intrinsic features, as well as recent advances that improve their pharmacological profiles, peptides have arisen as promising agents in this regard. Here, we report, by in silico structural design validated by cell-based and in vitro assays, the discovery of four peptides able to target TWEAK. Our results show that, when added to TWEAK-dependent cellular cultures, peptides cause a down-regulation of genes that are part of TWEAK-Fn14 signalling pathway. The direct, physical interaction between the peptides and TWEAK was further elucidated in an in vitro assay which confirmed that the bioactivity shown in cell-based assays was due to the targeting of TWEAK. The results presented here are framed within early pre-clinical drug development and therefore these peptide hits represent a starting point for the development of novel therapeutic agents. Our approach exemplifies the powerful combination of in silico and experimental efforts to quickly identify peptides with desirable traits.

scholarly journals In Silico and In Vitro Analysis of Multifunctionality of Animal Food-Derived Peptides

Foods ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 991 ◽  
Author(s):  
Lourdes Amigo ◽  
Daniel Martínez-Maqueda ◽  
Blanca Hernández-Ledesma
Keyword(s):  
Oxidative Stress ◽  
In Silico ◽  
Antioxidant Activities ◽  
In Vitro Study ◽  
In Silico Analysis ◽  
Integrated Approach ◽  
In Vitro Assays ◽  
Metabolic Disturbances ◽  
Ace Inhibitory

Currently, the associations between oxidative stress, inflammation, hypertension, and metabolic disturbances and non-communicable diseases are very well known. Since these risk factors show a preventable character, the searching of food peptides acting against them has become a promising strategy for the design and development of new multifunctional foods or nutraceuticals. In the present study, an integrated approach combining an in silico study and in vitro assays was used to confirm the multifunctionality of milk and meat protein-derived peptides that were similar to or shared amino acids with previously described opioid peptides. By the in silico analysis, 15 of the 27 assayed peptides were found to exert two or more activities, with Angiotensin-converting enzyme (ACE) inhibitory, antioxidant, and opioid being the most commonly found. The in vitro study confirmed ACE-inhibitory and antioxidant activities in 15 and 26 of the 27 synthetic peptides, respectively. Four fragments, RYLGYLE, YLGYLE, YFYPEL, and YPWT, also demonstrated the ability to protect Caco-2 and macrophages RAW264.7 cells from the oxidative damage caused by chemicals. The multifunctionality of these peptides makes them promising agents against oxidative stress-associated diseases.

scholarly journals In Vitro Anti-Tubulin Activity on MCF10A Cell Line and In Silico Rigid/Semiflexible-Residues Docking, of Two Lignans from Bursera Fagaroides var. Fagaroides

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6155
Author(s):  
Verónica Rodríguez-López ◽  
César Millán-Pacheco ◽  
Judith González-Christen ◽  
Maricruz Anaya-Ruíz ◽  
Omar Aristeo Peña-Morán
Keyword(s):  
Cell Line ◽  
In Silico ◽  
Topoisomerase Ii ◽  
In Silico Analysis ◽  
Stem Bark ◽  
Structural Basis ◽  
Mcf10a Cell ◽  
Binding Modes ◽  
In Silico Docking

Podophyllotoxins are natural lignans with known cytotoxic activity on several cell lines. The structural basis for their actions is mainly by the aryltetralin-lignan skeleton. Authors have proposed a cytotoxic mechanism of podophyllotoxins through the topoisomerase-II inhibition activity; however, several studies have also suggested that podophyllotoxins can inhibit the microtubules polymerization. In this work, the two possible mechanisms of action of two previously isolated compounds from the stem bark of Bursera fagaroides var. fagaroides: acetylpodophyllotoxin (1) and 5’-desmethoxydeoxypodophyllotoxin (2), was analyzed. An in vitro anti-tubulin epifluorescence on the MCF10A cell line and enzymatic topoisomerase II assays were performed. The binding affinities of compounds 1 and 2 in the colchicine binding site of tubulin by using rigid- and semiflexible-residues were calculated and compared using in silico docking methods. The two lignans were active by the in vitro anti-tubulin assay but could not inhibit TOP2 activity. In the in silico analysis, the binding modes of compounds into both rigid- and semiflexible-residues of tubulin were predicted, and only for the semiflexible docking method, a linear correlation between the dissociation constant and IC50 previously reported was found. Our results suggest that a simple semiflexible-residues modification in docking methods could provide an in vitro correlation when analyzing very structurally similar compounds.

Structure-Activity Relationship Study of an Alkynylphosphonate and a Vynilphosphonate Analogues of Calcitriol

2020 ◽  
Vol 16 ◽  
Author(s):  
Silvina Mariela Grioli ◽  
Eliana Noelia Alonso ◽  
Evangelina Mascaró ◽  
Santiago Armando Stabile ◽  
María Julia Ferronato ◽  
...  
Keyword(s):  
Cell Lines ◽  
In Silico ◽  
Rational Design ◽  
Parent Compound ◽  
In Vitro Assays ◽  
Antitumoral Activity ◽  
Lateral Side ◽  
Antitumor Effects ◽  
In Silico Studies

Background: 1α,25-dihydroxyvitamin D3 (calcitriol) shows potent growth-inhibitory properties on different can-cer cell lines but its hypercalcemic effects have severely hampered its therapeutic application. Therefore, it is important todevelop synthetic calcitriol analogues that retain or even increase its antitumoral effects and lack hypercalcemic activity. Based on previous evidence of the potent antitumor effects of the synthetic alkynylphosphonate EM1 analogue, we have now synthesized a derivative called SG. Objective: The aim of the present work is to evaluate the calcemic activity and the antitumor effect of SG, comparing these effects with those exerted by calcitriol and with those previously published for EM1. In addition, we propose to analyse by in silico studies the chemical structure-biological function relationship of these molecules. Methods: We performed the synthesis of vinylphosphonate SG analogue; in vitro assays on different cancer cell lines; in vivo assays on mice; and in silico assays applying computational molecular modelling. Results: The SG compound lacks hypercalcemic activity, similar to the parent compound EM1. However, the antitumor ac-tivity was blunted, as no antiproliferative or antimigratory effects were observed. By in silico assays, we demostrated that SG analogue has lower affinity for the VDR-ligand binding domain than EM1 compound, due to lack of interaction with the important residues His305 and His397. Conclusion: These results demonstrate that chemical modification in the lateral side chain of the SG analogue affects the antitumoral activity observed previously for EM1 but does not affect the calcemic activity. These results contribute to the rational design and synthesis of novel calcitriol analogues.

scholarly journals In vitro anti-inflammatory resorcinol derivatives and their in silico analysis

2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Rahen Mahmuda ◽  
Tran Quang De ◽  
Negar Sultana Shoshi ◽  
Khadija Akhter Poly ◽  
Pranoy Saha ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Hydroxyl Groups ◽  
Binding Modes ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Lead Generation ◽  
Anti Inflammatory ◽  
Dose Dependent

Resorcinol with its two hydroxyl groups was derivatized in laboratory to observe the anti-inflammatory potential in vitro. Subsequently in silico docking analysis was done for observing the binding modes in cyclooxygenase enzyme to have idea about the subsequent possible developments. At the doses of 200 mg/ml and 400 mg/ml. the compounds showed the anti-inflammatory property, where 02 offered dose dependent 51% and 70% of inhibition of heat induced hemolysis respectively. The scaffold thus poses as an interesting pharmacophore suitable for lead generation for the inflammatory disorders.

scholarly journals In silico Elucidation of Dihydroquinine Mechanism of Action against Toxoplasma gondii

2022 ◽  
Author(s):  
Joseph A. Ayariga ◽  
Aarin M. Huffman ◽  
Audrey Napier ◽  
BK Robertson ◽  
Daniel Abugri
Keyword(s):  
Mechanism Of Action ◽  
In Silico ◽  
In Silico Analysis ◽  
Trna Synthetase ◽  
In Vitro Assays ◽  
In Vivo Models ◽  
Translational Machinery ◽  
Calcium Dependent

Dihydroquinine (DHQ), is a quinine-based compound with anti-malarial properties. However, little is known about its mechanism of action against T. gondii inhibition, which shares similar biology with Plasmodium spp. In order to explore DHQ activity as an inhibitor of T. gondii using in vitro assays, we first used an in silico approach to decipher its mechanisms of action based on previous knowledge about its disruption of nucleic acid and protein synthesis. An in silico study was performed on T. gondii parasite replication, transcriptional and translational machinery to decipher the binding potentials of DHQ to some top selected enzymes. We report for the first time, using an in silico analysis that showed that DHQ binds strongly to DNA gyrase, Calcium Dependent Protein Kinase 1 (CDPK 1), and prolyl tRNA synthetase and thus could affect DNA replication, transcriptional and translational activities in T. gondii. Also, we found DHQ to effectively bind to mitochondria detoxifying enzymes (i.e., superoxide dismutase (SOD), peroxidoxin, and Catalase (CAT)). In conclusion, DHQ could be a lead compound for the treatment of toxoplasmosis when successfully evaluated using in vitro and in vivo models to confirm its effectiveness and safety.

Biological and In silico Studies on Synthetic Analogues of Tyrosine Betaine as Inhibitors of Neprilysin - A Drug Target for the Treatment of Heart Failure

2018 ◽  
Vol 24 (17) ◽  
pp. 1899-1904
Author(s):  
Daniel Fabio Kawano ◽  
Marcelo Rodrigues de Carvalho ◽  
Mauricio Ferreira Marcondes Machado ◽  
Adriana Karaoglanovic Carmona ◽  
Gilberto Ubida Leite Braga ◽  
...  
Keyword(s):  
Heart Failure ◽  
Secondary Metabolites ◽  
Structural Similarity ◽  
Structural Features ◽  
Major Constituent ◽  
Binding Modes ◽  
Starting Point ◽  
In Silico Studies ◽  
Nep Inhibition

Background: Fungal secondary metabolites are important sources for the discovery of new pharmaceuticals, as exemplified by penicillin, lovastatin and cyclosporine. Searching for secondary metabolites of the fungi Metarhizium spp., we previously identified tyrosine betaine as a major constituent. Methods: Because of the structural similarity with other inhibitors of neprilysin (NEP), an enzyme explored for the treatment of heart failure, we devised the synthesis of tyrosine betaine and three analogues to be subjected to in vitro NEP inhibition assays and to molecular modeling studies. Results: In spite of the similar binding modes with other NEP inhibitors, these compounds only displayed moderate inhibitory activities (IC50 ranging from 170.0 to 52.9 µM). However, they enclose structural features required to hinder passive blood brain barrier permeation (BBB). Conclusions: Tyrosine betaine remains as a starting point for the development of NEP inhibitors because of the low probability of BBB permeation and, consequently, of NEP inhibition at the Central Nervous System, which is associated to an increment in the Aβ levels and, accordingly, with a higher risk for the onset of Alzheimer's disease.

In-silico Studies of Isolated Phytoalkaloid Against Lipoxygenase: Study Based on Possible Correlation

2018 ◽  
Vol 21 (3) ◽  
pp. 215-221
Author(s):  
Haroon Khan ◽  
Muhammad Zafar ◽  
Helena Den-Haan ◽  
Horacio Perez-Sanchez ◽  
Mohammad Amjad Kamal
Keyword(s):  
In Silico ◽  
Docking Studies ◽  
In Vivo Studies ◽  
In Vitro Assays ◽  
Chronic Obstructive ◽  
Lipoxygenase Inhibitors ◽  
Lipoxygenase Inhibition ◽  
In Silico Studies

Aim and Objective: Lipoxygenase (LOX) enzymes play an important role in the pathophysiology of several inflammatory and allergic diseases including bronchial asthma, allergic rhinitis, atopic dermatitis, allergic conjunctivitis, rheumatoid arthritis and chronic obstructive pulmonary disease. Inhibitors of the LOX are believed to be an ideal approach in the treatment of diseases caused by its over-expression. In this regard, several synthetic and natural agents are under investigation worldwide. Alkaloids are the most thoroughly investigated class of natural compounds with outstanding past in clinically useful drugs. In this article, we have discussed various alkaloids of plant origin that have already shown lipoxygenase inhibition in-vitro with possible correlation in in silico studies. Materials and Methods: Molecular docking studies were performed using MOE (Molecular Operating Environment) software. Among the ten reported LOX alkaloids inhibitors, derived from plant, compounds 4, 2, 3 and 1 showed excellent docking scores and receptor sensitivity. Result and Conclusion: These compounds already exhibited in vitro lipoxygenase inhibition and the MOE results strongly correlated with the experimental results. On the basis of these in vitro assays and computer aided results, we suggest that these compounds need further detail in vivo studies and clinical trial for the discovery of new more effective and safe lipoxygenase inhibitors. In conclusion, these results might be useful in the design of new and potential lipoxygenase (LOX) inhibitors.

Sign in / Sign up

Export Citation Format

Share Document