The potency of alpha-humulene as HER-2 inhibitor by molecular docking

HER-2 overexpression is present in approximately 20% of breast cancer. This research aims to study the interactions of α-humulene to HER-2 protein by using in silico molecular docking. The experiment was carried out by HER-2 protein preparation (PDB ID 3PP0), docking validation, α-humulene optimization, and α-humulene docking. The results showed that α-humulene had binding energy of -7.50 kcal/mol, Van der Waals binding energy of -7.48 kcal/mol, and electrostatic energy of -0.02 kcal/mol. α-Humulene is potential as anti-breast cancer towards HER-2 in silico.

Stabilization of the Interaction of the Compunds of Mallotus paniculatus Müll.Arg. on Gluthations S-Transferase (GSTs)

Gluthathione s-transferases (GSTs) play an important role against carcinogens, therapeutic drugs, and various types of cellular oxidative damage. Judging from its role in overcoming cellular oxidative damage, the activity of GSTs is one of the antioxidant enzymes. One of the plants that has been tested for its antioxidant ability is M. paniculatus. The content of M. paniculatus has been found so that it can be used to test the stability of the interaction between ligands and receptors. The aim of this research is to find compounds from M. paniculatus that have the potential to stabilize the interaction with the receptors. This docking method begins with ligand preparation and protein preparation followed by docking, visualization of interactions and analysis of the results. The research resulted in various docking scores with the various proteins involved. The stability of the interaction is obtained when the ligand binds to Glutathione S-transferase type A3 is hesperetin, sitosterol and sitosterol, to Glutathione S-transferase type theta-2 is β-daucostero, to Glutathione S-transferase type P is quercetin. Keywords: GSTs, M. paniculatus, docking

Structure based virtual docking and molecular dynamics guided identification of potential phytoconstituents from traditionally used female antifertility plant

Background: Oral contraceptives are very widely used agents to check unwanted pregnancies. They contain synthetic analogues of estrogen and progesterone hormones. Estrogen is an important hormone that plays a significant role in menstrual cycle, ovulation, fertilization and implantation. Estrogen receptor α (ERα) can modulate the ovulation, fertilization or receptivity of the uterus. Oral contraceptives pose mild to severe adverse effects such as menstrual cycle disorders, metabolic alterations and increased risk of cancers. It is essential to identify and screen alternative contraceptives that are safer to use. The present study was aimed at identifying the compounds from Cissampelos pareira that is traditionally used for antifertility activity. Methods: The compounds reported from the plant are collected and prepared using the protein preparation wizard. The protein, ERα was selected from protein data bank (1G5O) and prepared. The ligands were docked with the protein and the hits were selected for further screening of free energy calculation, induced fit docking and molecular dynamics simulations based on the respective scores and various interactions. Results: Among various compounds, Coclaurine and Norruffscine have been identified to interact with ERα and possess similar interactions as that of the endogenous ligand, estradiol. The compounds also showed drug-like properties in Qikprop analysis and promising result in the molecular dynamics simulation studies. Conclusion: Considering the dock scores, molecular interactions with the ERα receptor and energy calculations, the compounds Coclaurine and Norruffscine were found to have good binding properties. Further in vitro and in vivo evaluation are warranted for confirmation.

Study of a process of obtaining of protein preparation from sunflower seeds for application in food industry

The article deals with a study of processing methods of obtaining protein preparations from sunflower seeds. For obtaining of food-grade protein preparations from the defatted sunflower kernels phenolic compounds were additionally removed. Modern Russian and foreign literature sources devoted to the isolation of phenolic compounds from vegetable protein raw materials were analyzed. The objective of obtaining a light-colored food-grade protein preparation from sunflower seeds was solved through developing of a multi-stage extraction process with removal of various groups of non-protein compounds, including the stage of aqueous ethanol extraction and removal of phenolic compounds. Parameters of different stages of obtaining of protein substances from defatted sunflower seed kernels after removal of phenolic compounds were studied. These stages included alkaline extraction of protein and nitrogen-free extractives (NFE), separation of the insoluble residue, isoelectric precipitation of protein compounds from the clarified extract, neutralization of the protein suspension. Drying of the protein suspension was carried out on a laboratory spray installation Buchi Mini Spray Dryer with a temperature at the entrance of the dryer 180–190 ℃ and at the exit – up to 90 ℃. Protein preparations of light gray color were obtained with a crude protein content of 75,72% and 87,15% on dry matter basis, which corresponds to the crude protein content of commercial sunflower and soy protein concentrates. Solubility pattern of proteins and functional characteristics of finished protein preparations after spray drying have been analyzed. Based on the high fat-holding capacity and moderate fat-emulsifying properties of the obtained protein preparations it’s possible to recommend the obtained sunflower protein preparation for usage as a vegetable protein enricher and functional additive in food industry.

Development and Validation Molecular Docking Analysis of Human serum albumin (HSA)

Background: HAS (Human Serum Albumin) is a highly water-soluble globular plasma protein, with a relative molecular weight (g/mol) of 67 KDa, consisting of 585 amino acid residues. In this study, we have investigated the interaction of the crystal structures complexed in human serum albumin at resolutions of 2.8 to 2.0: Camptothecin, 9-amino-camptothecin, Etoposide, Teniposide, Bicalutamide and Idarubicin, using a bioinformatic approach, estimated by Pyrx Virtual Screen Tool and AMDock ( AMDock, Assisted Molecular Docking). We have analyzed a validated protocol, studying several parameters, as Binding Affinity, RMSD value, Ligand Efficiency, and Inhibition constant (Ki value). Methods: Human Serum Albumin protein preparation was characterized with several programs, as Chimera, MGLTools 1.5.6, Swiss PDB Viewer Software to perform docking analysis by Autodock Vina estimated with Pyrx Software. Results: In this work, we found crystalized camptothecin, 9-amino-camptothecin and teniposide, gave excellent results for Binding Affinity, (kcal/mol), RMSD value (A ), inhibition constant Ki value (nM): -Binding Affinity of 9-amino-camptothecin (ca.-10 kcal/mol), camptothecin ( -9 kcal/mol) and teniposide ( -11 kcal/mol, -RMSD Value of 9 -amino-camptothecin (ca.1.8 A ), camptothecin (ca.2.2 A ) and teniposide (ca. 3.6 A), - Ki Value: 9 -amino-camptothecin (ca 59 nM), camptothecin ( ca 183 nM) and teniposide ( ca 9 nM), -Ligand efficiency: of 9 -amino-camptothecin(ca -0.35 kcal/mol) , camptothecin (ca -0.34 kcal/mol) and teniposide (ca -0.24 kcal/mol Conclusions: We explored the best three crystallized ligand in Human Serum Albumin. Moreover, we have observed a complete overlap, during the re-docking analysis phase, estimated by chimera Software. Therefore we have concluded that ID PDB Crystal 4L8U human serum albumin-Crystallised 9 -amino Camptothecin; ID PDB Crystal 4L9K human serum albumin- Crystallised Camptothecin and ID PDB Crystal 4L9Q human serum albumin-Crystallised teniposide be used as a possible as a reference template protein to be compared with the target protein, by Docking molecular analysis.

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.

The Mammalian Cytosolic Type 2 (R)-β-hydroxybutyrate Dehydrogenase (BDH2) is 4-oxo-L-proline Reductase (EC 1.1.1.104)

The early studies on chicken embryos revealed that exposition to 4-oxo-L-proline resulted in the explicit increase in 4-hydroxy-L-proline content in their tissues. In 1962, 4-oxo-L-proline reductase, an enzyme responsible for the reduction of 4-oxo-L-proline, was partially purified from rabbit kidneys and characterized biochemically, but only recently the molecular identity of the enzyme has been unveiled in our laboratory. The present investigation reports the purification, identification as well as biochemical characterization of 4-oxo-L-proline reductase. The enzyme was purified from rat kidneys about 280-fold. Following mass spectrometry analysis of the purified protein preparation, the mammalian cytosolic type 2 (R)-β-hydroxybutyrate dehydrogenase (BDH2) emerged as the only meaningful candidate for the reductase. Rat and human BDH2 were expressed in E. coli, purified, and shown to catalyze the reversible reduction of 4-oxo-L-proline to cis-4-hydroxy-L-proline, as confirmed by chromatographic and mass spectrometry analysis. Specificity studies carried out on both enzymes showed that 4-oxo-L-proline was the best substrate, particularly the human enzyme acted with 9400-fold higher catalytic efficiencies on 4-oxo-L-proline than on (R)-β-hydroxybutyrate. Finally, HEK293T cells efficiently metabolized 4-oxo-L-proline to cis-4-hydroxy-L-proline and simultaneously accumulated trans-4-hydroxy-L-proline in the culture medium, suggesting that 4-oxo-L-proline is most likely an inhibitor of trans-4-hydroxy-L-proline metabolism in human cells. We conclude that BDH2 is mammalian 4-oxo-L-proline reductase that converts 4-oxo-L-proline to cis-4-hydroxy-L-proline, and not to trans-4-hydroxy-L-proline as currently thought, and hypothesize that the enzyme may be considered as a potential source of cis-4-hydroxy-L-proline in mammalian tissues.