scholarly journals Molecular docking of ligands promising for IgG sorption from biological fluids

2020 ◽  
Vol 56 (1) ◽  
pp. 88-95 ◽  
Author(s):  
E. S. Pustsyulga ◽  
O. V. Gribovskaya ◽  
E. M. Ermola ◽  
V. P. Golubovich
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Amino Acid ◽  
Autoimmune Diseases ◽  
High Activity ◽  
Immunoglobulin G ◽  
Biological Fluids ◽  
Aromatic Amino Acids ◽  
Pathogenic Factor ◽  
High Level

Hyperproduction of immunoglobulin G (IgG) is a major pathogenic factor in autoimmune diseases. Specific sorbents are used to eliminate the high level of IgG. Molecular docking can be used as a tool for theoretical search for sorbent ligands for the IgG removal from biological fluids. Using docking, modeling of amino acid interactions with IgG ligands was performed. Based on the docking results, active amino acids were identified and possible combinations of them were proposed for the creation of diand tripeptide sequences. As a result, aromatic amino acids (Tyr, Trp, Phe), di-and tripeptides based on them (Trp-DTyr, Phe-DTyr, Trp-Phe-DTyr, Phe-Trp-DTyr) were found to have high activity for IgG proteins, and three peptides (Trp-Phe-DTyr, Phe-Trp-DTyr) not only show high activity to total IgG, but can also be divided in their activity relative to subclasses of class G immunoglobulins.

Single Amino Acid Based Self-Assemblies of Cysteine and Methionine

2018 ◽  
Author(s):  
Nidhi Gour ◽  
Bharti Koshti ◽  
Chandra Kanth P. ◽  
Dhruvi Shah ◽  
Vivek Shinh Kshatriya ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Aromatic Amino Acids ◽  
Neutral Condition ◽  
Single Amino Acid ◽  
Binding Assays ◽  
Human Neuroblastoma ◽  
Cytotoxicity Assays ◽  
First Time

We report for the very first time self-assembly of Cysteine and Methionine to discrenible strucutres under neutral condition. To get insights into the structure formation, thioflavin T and Congo red binding assays were done which revealed that aggregates may not have amyloid like characteristics. The nature of interactions which lead to such self-assemblies was purported by coincubating assemblies in urea and mercaptoethanol. Further interaction of aggregates with short amyloidogenic dipeptide diphenylalanine (FF) was assessed. While cysteine aggregates completely disrupted FF fibres, methionine albeit triggered fibrillation. The cytotoxicity assays of cysteine and methionine structures were performed on Human Neuroblastoma IMR-32 cells which suggested that aggregates are not cytotoxic in nature and thus, may not have amyloid like etiology. The results presented in the manuscript are striking, since to the best of our knowledge,this is the first report which demonstrates that even non-aromatic amino acids (cysteine and methionine) can undergo spontaneous self-assembly to form ordered aggregates.

Molecular Docking Analysis of Flavonoid Compounds with Matrix Metalloproteinase-8 for the Identification of Potential Effective Inhibitors

2020 ◽  
Vol 17 ◽  
Author(s):  
Amir Taherkhani ◽  
Athena Orangi ◽  
Shirin Moradkhani ◽  
Zahra Khamverdi
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Amino Acid ◽  
Matrix Metalloproteinase ◽  
Ligand Binding ◽  
Chronic Inflammation ◽  
Cancer Progression ◽  
Dimensional Structure ◽  
Control Test ◽  
Therapeutic Procedures

Background: Matrix metalloproteinase-8 (MMP-8) participates in degradation of different types of collagens in the extracellular matrix and basement membrane. Up-regulation of the MMP-8 has been demonstrated in many of disorders including cancer development, tooth caries, periodontal/peri-implant soft and hard tissue degeneration, and acute/chronic inflammation. Therefore, MMP-8 has become an encouraging target for therapeutic procedures for scientists. We carried out molecular docking approach to study the binding affinity of 29 flavonoids, as drug candidates, with the MMP-8. Pharmacokinetic and toxicological properties of the compounds were also studied. Moreover, it was attempted to identify the most important amino acids participating in ligand binding based on degree of each of the amino acids in the ligand-amino acid interaction network for MMP-8. Methods: Three-dimensional structure of the protein was gained from the RCSB database (PDB ID: 4QKZ). AutoDock version 4.0 and Cytoscape 3.7.2 were used for molecular docking and network analysis, respectively. Notably, the inhibitor of the protein in the crystalline structure of the 4QKZ was considered as a control test. Pharmacokinetic and toxicological features of compounds were predicted using bioinformatic web tools. Post-docking analyses were performed using BIOVIA Discovery Studio Visualizer version 19.1.0.18287. Results and Discussions: According to results, 24 of the studied compounds considered to be top potential inhibitors for MMP-8 based on their salient estimated free energy of binding and inhibition constant as compared with the control test: Apigenin-7-glucoside, nicotiflorin, luteolin, glabridin, taxifolin, apigenin, licochalcone A, quercetin, isorhamnetin, myricetin, herbacetin, kaemferol, epicatechin, chrysin, amentoflavone, rutin, orientin, epiafzelechin, quercetin-3-rhamnoside, formononetin, isoliquiritigenin, vitexin, catechine, isoquercitrin. Moreover, His-197 was found to be the most important amino acid involved in the ligand binding for the enzyme. Conclusion: The results of the current study could be used in the prevention and therapeutic procedures of a number of disorders such as cancer progression and invasion, oral diseases, and acute/chronic inflammation. Although, in vitro and in vivo tests are inevitable in the future.

scholarly journals Determination of amino acids in human biological fluids by high-performance liquid chromatography: critical review

Amino Acids ◽  
2021 ◽  
Author(s):  
Grażyna Gałęzowska ◽  
Joanna Ratajczyk ◽  
Lidia Wolska
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Performance ◽  
Hplc Analysis ◽  
Limit Of Detection ◽  
Biological Fluids ◽  
Analytical Techniques ◽  
Epidemiological Studies ◽  
Preparation Conditions

AbstractThe quantitation and qualification of amino acids are most commonly used in clinical and epidemiological studies, and provide an excellent way of monitoring compounds in human fluids which have not been monitored previously, to prevent some diseases. Because of this, it is not surprising that scientific interest in evaluating these compounds has resurfaced in recent years and has precipitated the development of a multitude of new analytical techniques. This review considers recent developments in HPLC analytics on the basis of publications from the last few years. It helps to update and systematize knowledge in this area. Particular attention is paid to the progress of analytical methods, pointing out the advantages and drawbacks of the various techniques used for the preparation, separation and determination of amino acids. Depending on the type of sample, the preparation conditions for HPLC analysis change. For this reason, the review has focused on three types of samples, namely urine, blood and cerebrospinal fluid. Despite time-consuming sample preparation before HPLC analysis, an additional derivatization technique should be used, depending on the detection technique used. There are proposals for columns that are specially modified for amino acid separation without derivatization, but the limit of detection of the substance is less beneficial. In view of the fact that amino acid analyses have been performed for years and new solutions may generate increased costs, it may turn out that older proposals are much more advantageous.

Characterization of an isozyme of S-adenosylmethionine synthetase from rat liver

1984 ◽  
Vol 62 (5) ◽  
pp. 276-279 ◽  
Author(s):  
C. H. Lin ◽  
W. Chung ◽  
K. P. Strickland ◽  
A. J. Hudson
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Enzymatic Synthesis ◽  
Gel Filtration ◽  
Deae Cellulose ◽  
Aromatic Amino Acids ◽  
Adenosylmethionine Synthetase ◽  
Cellulose Column

An isozyme of S-adenosylmethionine synthetase has been purified to homogeneity by ammonium sulfate fractionation, DEAE-cellulose column chromatography, and gel filtration on a Sephadex G-200 column. The purified enzyme is very unstable and has a molecular weight of 120 000 consisting of two identical subunits. Amino acid analysis on the purified enzyme showed glycine, glutamate, and aspartate to be the most abundant and the aromatic amino acids to be the least abundant. It possesses tripolyphosphatase activity which can be stimulated five to six times by S-adenosylmethionine (20–40 μM). The findings support the conclusion that an enzyme-bound tripolyphosphate is an obligatory intermediate in the enzymatic synthesis of S-adenosylmethionine from ATP and methionine.

scholarly journals Involvement of calcium-sensing receptor activation in the alleviation of intestinal inflammation in a piglet model by dietary aromatic amino acid supplementation

2018 ◽  
Vol 120 (12) ◽  
pp. 1321-1331 ◽  
Author(s):  
Hongnan Liu ◽  
Bie Tan ◽  
Bo Huang ◽  
Jianjun Li ◽  
Jing Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Inflammatory Cytokines ◽  
Intestinal Inflammation ◽  
Aromatic Amino Acids ◽  
Dietary Supplementation ◽  
Basal Diet ◽  
Signalling Pathway ◽  
Protein Levels ◽  
Pro Inflammatory Cytokines

AbstractCa2+-sensing receptor (CaSR) represents a potential therapeutic target for inflammatory bowel diseases and strongly prefers aromatic amino acid ligands. We investigated the regulatory effects of dietary supplementation with aromatic amino acids – tryptophan, phenylalanine and tyrosine (TPT) – on the CaSR signalling pathway and intestinal inflammatory response. The in vivo study was conducted with weanling piglets using a 2 × 2 factorial arrangement in a randomised complete block design. Piglets were fed a basal diet or a basal diet supplemented with TPT and with or without inflammatory challenge. The in vitro study was performed in porcine intestinal epithelial cell line to investigate the effects of TPT on inflammatory response using NPS-2143 to inhibit CaSR. Dietary supplementation of TPT alleviated histopathological injury and decreased myeloperoxidase activity in intestine challenged with lipopolysaccharide. Dietary supplementation of TPT decreased serum concentration of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, IL-12, granulocyte-macrophage colony-stimulating factor, TNF-α), as well as the mRNA abundances of pro-inflammatory cytokines in intestine but enhanced anti-inflammatory cytokines IL-4 and transforming growth factor-β mRNA levels compared with pigs fed control diet and infected by lipopolysaccharide. Supplementation of TPT increased CaSR and phospholipase Cβ2 protein levels, but decreased inhibitor of NF-κB kinase α/β and inhibitor of NF-κB (IκB) protein levels in the lipopolysaccharide-challenged piglets. When the CaSR signalling pathway was blocked by NPS-2143, supplementation of TPT decreased the CaSR protein level, but enhanced phosphorylated NF-κB and IκB levels in IPEC-J2 cells. To conclude, supplementation of aromatic amino acids alleviated intestinal inflammation as mediated through the CaSR signalling pathway.

scholarly journals Rearing larvae and juveniles of rainbow trout with different amino acid nutrition

2020 ◽  
Author(s):  
V. Kondratiuk ◽  
Keyword(s):  
Amino Acids ◽  
Rainbow Trout ◽  
Amino Acid ◽  
Juvenile Fish ◽  
Control Group ◽  
Economic Optimization ◽  
Larvae And Juveniles ◽  
Experimental Fish ◽  
Juvenile Trout ◽  
High Level

The article considers the efficiency of using complete compound feeds with different levels of lysine and methionine in rearing larvae and juveniles of rainbow trout. The purpose of the experiment was to establish the effect of different amino acid levels in nutrition of juvenile trout on its productivity. For this purpose, five experimental groups were formed by the method of analogues. The experiment lasted 35 days and was divided into two periods: equalizing (5 days) and main (30 days). During the equalizing period, the experimental fish consumed feed of the control group. In the main period, the levels of lysine and methionine in experimental feeds for different experimental groups of trout ranged from 2.9 to 3.3% and from 0.95 to 3.15%, respectively. It is proved that increasing the content of lysine and methionine in feed for larvae and juveniles of rainbow trout to the levels of 3.2 and 1.1%, respectively, promotes increase in their weight by 10.7% (p <0.01) and growth intensity - by 6.4-11.1%, while further increase in these amino acids content in the feed reduces the productivity of fish. Polynomial equations for determining the juvenile fish weight at any stage of rearing at a high level of determination for each of the experimental groups have been calculated. It was found that with an increase in the content of lysine and methionine in feed to the levels of 3.2 and 1.1%, respectively, reduces feed costs per 1 kg of weight gain in trout larvae and juveniles by 4.1%, and a further increase in levels of these amino acids to 3.3 and 1.15%, respectively, increase this index by 1.1%. The experimental fish survival ranged from 83.9 to 85.1%. In the production of trout according to the criteria of maximum productivity and to the economic optimization criteria, it is recommended to use complete feed with the level of lysine - 3.2% and methionine - 1.1% for feeding trout larvae and juveniles.

scholarly journals AMINO ACID COMPOSITION OF LEAVES OF THREE SPECIES OF ARTEMISIA L. GROWING IN THE ELTON REGION

2021 ◽  
pp. 219-225
Author(s):  
Галина Табаленкова
Keyword(s):  
Amino Acids ◽  
Czech Republic ◽  
Amino Acid ◽  
Dry Weight ◽  
Biologically Active ◽  
Raw Material ◽  
Buffer System ◽  
Amino Acid Analyzer ◽  
Growing Conditions ◽  
High Level

The results of studies of the qualitative composition and quantitative content of amino acids (AAs) in the leaves of three plant species of the genus Artemisia, widespread in the Elton region, were presented. Protein AAs were determined on an AAA T-339 amino acid analyzer (Czech Republic) after hydrolysis of a sample in 6N HCl at 105 °C for 24 h, free AAs – on an AAA-400 amino acid analyzer (Czech Republic) in a lithium buffer system. The protein AAs amount varied from 66 mg / g in A. lerchiana to 113 mg / g dry weight in A. santonica. 17 AAs were found in composition of these species, aspartic and glutamic acids were dominant. The content of free AAs varied from 4.4 mg / g in A. santonica to 8.3 mg / g dry weight in A. pauciflora. 14 AAs have been identified, among them proline was the predominant free AA. The share of proline was 75-81% of the total free AAs. Among the minor components, 3-4 compounds with a content above 2% dominated. The free AAs contain 3 non-proteinogenic ones (ornithine, citruline, and γ-aminobutyric acid). A. lerchiana and A. pauciflora species were similar in protein and free amino acids, probably due to the same growing conditions. A high level of free proline, together with a complex of biologically active substances in Artemisia species, which grow abundantly in the Elton region, allow to consider the possibility of their use as a medicinal raw material.

scholarly journals Комбинационное рассеяние света в хирально чистых и рацемической фазах поликристаллов триптофана и тирозина

2019 ◽  
Vol 127 (10) ◽  
pp. 541
Author(s):  
В.С. Горелик ◽  
М.Ф. Умаров ◽  
Ю.П. Войнов
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Raman Spectra ◽  
Spectral Range ◽  
Phase State ◽  
Source Parameters ◽  
Low Frequency ◽  
Aromatic Amino Acids ◽  
Chiral Phase ◽  
Left Handed

AbstractRaman spectra of tryptophan and tyrosine polycrystals have been analyzed in a wide spectral range by fiber-optic spectroscopy. The Raman spectra have been recorded with a BWS465-785H spectrometer in the spectral range of 0–2700 cm^–1 using a 785-nm cw laser as an excitation source. Parameters of the Raman spectra are compared for three crystalline phase modifications of aromatic amino acids: left-handed, right-handed, and racemic phase. The presence of strong Raman satellites, the characteristics of which change depending on the type of the chiral phase state of amino acid, is found in the low-frequency Raman spectra of tryptophan and tyrosine amino acid lattices. The results obtained can be used for monitoring the chiral purity of bioactive preparations containing amino acids.

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