Computational screening of dipeptidyl peptidase IV inhibitors from micoroalgal metabolites by pharmacophore modeling and molecular docking

Dipeptidyl peptidase IV (DPP‐IV) catalyzes conversion of GLP‐1 (glucagon like peptide 1) to inert structure, which results in insufficient secretion of insulin and increase in postprandial blood glucose level. The present study attempts to identify novel inhibitors from bioactive metabolites present in microalgae against DPP‐IV through virtual screening, molecular docking, and pharmacophore modeling for the active target. Possible binding modes of all 60 ligands against DPP‐IV receptor were constructed using MTiOpenScreen virtual screening server. Pharmacophore model was built based on identified 38 DPP‐IV test ligands by using the web‐based PharmaGist program which encompasses hydrogen‐bond acceptors, hydrophobic groups, spatial features, and aromatic rings. The pharmacophore model having highest scores was selected to screen active DPP‐IV ligands. Highest scoring model was used as a query in ZincPharmer screening. All identified ligands were filtered, based on the Lipinski's rule‐of‐five and were subjected to docking studies. In the process of docking analyses, we considered different bonding modes of one ligand with multiple active cavities of DPP‐IV with the help of AutoDock 4.0. The docking analyses indicate that the bioactive constituents, namely, β‐stigmasterol, barbamide, docosahexaenoic acid, arachidonic acid, and harman showed the best binding energies on DPP‐IV receptor and hydrogen bonding with ASP545, GLY741, TYR754, TYR666, ARG125, TYR547, SER630, and LYS554 residues. This study concludes that docosahexaenoic acid, arachidonic acid, β‐stigmasterol, barbamide, harman, ZINC58564986, ZINC56907325, ZINC69432950, ZINC69431828, ZINC73533041, ZINC84287073, ZINC69849395, and ZINC10508406 act as possible DPP‐IV inhibitors.     

Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay,Hypotonia, Scoliosis,and Cerebellar Atrophy

The paradigm of a single gene associated with one specific phenotype and mode of inheritance has been repeatedly challenged. Genotype-phenotype correlations can often be traced to different mutation types, localization of the variants in distinct protein domains, or the trigger of or escape from nonsense-mediated decay. Using whole-exome sequencing, we identified homozygous variants in EMC1 that segregated with a phenotype of developmental delay, hypotonia, scoliosis, and cerebellar atrophy in three families. In addition, a de novo heterozygous EMC1 variant was seen in an individual with a similar clinical and MRI imaging phenotype. EMC1 encodes a member of the endoplasmic reticulum (ER)-membrane protein complex (EMC), an evolutionarily conserved complex that has been proposed to have multiple roles in ER-associated degradation, ER-mitochondria tethering, and proper assembly of multi-pass transmembrane proteins. Perturbations of protein folding and organelle crosstalk have been implicated in neurodegenerative processes including cerebellar atrophy. We propose EMC1 as a gene in which either biallelic or monoallelic variants might lead to a syndrome including intellectual disability and preferential degeneration of the cerebellum.     

Does education ‘trump’ nationality? Boundary-drawing practices among highly educated migrants from Turkey

Inspired by a super-diversity approach, this paper seeks to explore the influence of the ‘ethnic hierarchy’ of ‘old’ minority groups over the way ‘new’ migrants from Turkey negotiate their interaction in the daily life in three settings: Amsterdam, London and Barcelona. By focusing on highly educated migrants from Turkey who by virtue of their country of origin or religion are positioned at the bottom of ‘ethnic hierarchies’, it strives to understand the significance of these different sources of diversity in daily interaction. Applying boundary-drawing strategies developed for ethnic boundaries, this paper argues that education does not necessarily ‘trump’ nationality, but allows for substantial claims of difference. New migrants from Turkey carve out a space for themselves by on the one hand homogenizing Turkish or other Muslim communities through attributing ‘unwanted’ behaviours and on the other re-defining the boundaries of their individual identity with emphasis on different sources of diversity.     

Potent Inhibitory Effects of Some Phenolic Acids on Lactoperoxidase

Lactoperoxidase (LPO) plays a key role in immune response against pathogens. In this study, we examined the effects of some phenolic acids on LPO. For this purpose, bovine milk LPO was purified 380.85‐fold with a specific activity of 26.66 EU/mg and overall yield of 73.33% by using Amberlite CG‐50 H⁺ resin and CNBr‐activated Sepharose‐4B‐l ‐tyrosine‐sulfanilamide affinity chromatography. After purification, the in vitro effects of phenolic acids (tannic acid, 3,4‐dihydroxybenzoic acid, 3,5‐ dihydroxybenzoic acid, chlorogenic acid, sinapic acid, 4‐hydroxybenzoic acid, vanillic acid, salicylic acid, and 3‐hydroxybenzoic acid) were investigated on LPO. These phenolic acids showed potent inhibitory effect on LPO. K_i values for these phenolic acids were found as 0.0129 nM, 0.132 μM, 0.225 μM, 0.286 μM, 0.333 μM, 2.33 μM, 10.82 μM, 0.076 mM, and 0.405 mM, respectively. Sinapic acid and 4‐hydroxybenzoic acid exhibited noncompetitive inhibition; 3,4‐dihydroxybenzoic acid showed uncompetitive inhibition, and other phenolic acids showed competitive inhibition.     

Novel 4,4′-diether-2,2′-bipyridine cisplatin analogues are more effective than cisplatin at inducing apoptosis in cancer cell lines

The synthesis and characterization of dichloro(4,4′-bis[methoxy]-2,2′-bipyridine)platinum (1) and dichloro(4,4′-bis[3-methoxy-n-propyl]-2,2′-bipyridine)platinum (2) are described. As analogues to CDDP, these 4,4′-disubstituted 2,2′-bipyridine complexes exhibit decreased EC₅₀ values of 10–100 times in cancer cell lines of the lung, prostate, and melanoma with several combinations of complex and cell line less than 10 μM. Flow cytometry data indicate ‘blocks’ of MDA-MD-435 cycle by 1 (G2/M) and 2 (S). Observed cell survival trends in the presence of 1, 2 under ionizing radiation mimic those of CDDP. Preliminary structure activity relationships are discussed for the 4,4′-substitutions made on the bipyridine ring.     

Enhanced production of recombinant Staphylococcus simulans lysostaphin using medium engineering

Abstract

Staphylococcus aureus, among other staphylococcal species, developed multidrug resistance and causes serious health risks that require complex treatments. Therefore, the development of novel and effective strategies to combat these bacteria has been gaining importance. Since Staphylococcus simulans lysostaphin is a peptidoglycan hydrolase effective against staphylococcal species, the enzyme has a significant potential for biotechnological applications. Despite promising results of lysostaphin as a bacteriocin capable of killing staphylococcal pathogens, it is still not widely used in healthcare settings due to its high production cost. In this study, medium engineering techniques were applied to improve the expression yield of recombinant lysostaphin in E. coli. A new effective inducible araBAD promoter system and different mediums were used to enhance lysostaphin production. Our results showed that the composition of autoinduction media enhanced the amount of lysostaphin production 5-fold with the highest level of active lysostaphin at 30?°C. The production cost of 1000?U of lysostaphin was determined as 4-fold lower than the previously proposed technologies. Therefore, the currently developed bench scale study has a great potential as a large-scale fermentation procedure to produce lysostaphin efficiently.     

Changes in the expression levels of CB1 and GLP‐1R mRNAs and microRNAs 33a and 122 in the liver of type 2 diabetic rats treated with ghrelin

The aim of the study is to clarify the effect of ghrelin treatment on the messenger RNA (mRNA) expression of the cannabinoid receptor 1 (Cnr1/CB1) and glucagon‐like peptide 1 receptor (Glp1r/GLP‐1R) as well as microRNAs (miR)‐122 and miR‐33a in the liver of rats with type 2 diabetes mellitus (T2DM). Adult Sprague‐Dawley rats were divided into three groups: control (n = 7), T2DM (n = 7), and treatment (n = 7). Control animals received tap water. T2DM was induced by feeding 10% fructose in drinking water for 2 weeks followed by a single injection of streptozotocin (40 mg/kg, intraperitoneally [IP]). In the treatment group, diabetic rats were injected ghrelin (25 μg/kg, IP) for 14 days. Serum lipid profiles were evaluated, and mRNA expression levels of Cnr1 and Glp1r in the liver were detected using quantitative real‐time polymerase chain reaction (RT‐qPCR). In addition, miR‐122 and miR‐33a levels were measured using RT‐qPCR. Serum triglycerides, low‐density lipoprotein cholesterol, and very‐low‐density lipoprotein cholesterol significantly increased in the T2DM group compared with control rats but ghrelin treatment showed no effect on serum lipid levels. The mRNA expression levels of Cnr1 and Glp1r decreased in the T2DM group compared with the control group. These reductions were significantly increased in the T2DM group treated with ghrelin. Furthermore, the increase in miR‐33a expression level was reduced in the treatment group compared to rats with T2DM. Our findings suggested that ghrelin treatment may alter the mRNA expression levels of CB1 and GLP‐1R in the liver of rats with T2DM. The mRNA levels of Cnr1 and Glp1r may inversely correlate with the expression level of miR‐33a but not miR‐122.     

Recombination proteins and rescue of arrested replication forks

Recombination proteins play crucial roles in the rescue of inactivated replication forks in Escherichia coli. The enzymes that catalyze the repair of DNA double-strand breaks by a classical strand-exchange reaction (RecBCD, RecA) act in two well-characterized fork repair pathways. They repair the DNA double-strand end made when a replication fork runs into a single-strand interruption. They reset the DNA double-strand end generated by replication fork reversal when a component of the replication machinery is inactivated. In addition, recombination proteins also act at replication forks in ways other than the classical strand-exchange reaction. For example, the RuvAB enzyme that catalyzes Holliday junction branch-migration during homologous recombination is also able to catalyze replication fork reversal in certain replication mutants, i.e. to convert certain blocked replication forks into Holliday junctions. Finally, some of the actions of recombination proteins after replication impairment are still unclear, as for example in UV-irradiated cells, where RecFOR and RecA catalyze gap repair but also participate, in a yet undefined way, in "replisome reactivation".     

Finite element modeling of aponeurotomy: altered intramuscular myofascial force transmission yields complex sarcomere length distributions determining acute effects

Finite element modeling of aponeurotomized rat extensor digitorium longus muscle was performed to investigate the acute effects of proximal aponeurotomy. The specific goal was to assess the changes in lengths of sarcomeres within aponeurotomized muscle and to explain how the intervention leads to alterations in muscle length-force characteristics. Major changes in muscle length-active force characteristics were shown for the aponeurotomized muscle modeled with (1) only a discontinuity in the proximal aponeurosis and (2) with additional discontinuities of the muscles' extracellular matrix (i.e., when both myotendinous and myofascial force transmission mechanisms are interfered with). After muscle lengthening, two cut ends of the aponeurosis were separated by a gap. After intervention (1), only active slack length increased (by approximately 0.9 mm) and limited reductions in muscle active force were found (e.g., muscle optimum force decreased by only 1%) After intervention (2) active slack increased further (by 1.2 mm) and optimum length as well (by 2.0 mm) shifted and the range between these lengths increased. In addition, muscle active force was reduced substantially (e.g., muscle optimum force decreased by 21%). The modeled tearing of the intramuscular connective tissue divides the muscle into a proximal and a distal population of muscle fibers. The altered force transmission was shown to lead to major sarcomere length distributions [not encountered in the intact muscle and after intervention (1)], with contrasting effects for the two muscle fiber populations: (a) Within the distal population (i.e. fibers with no myotendinous connection to the muscles' origin), sarcomeres were much shorter than within the proximal population (fibers with intact myotendinous junction at both ends). (b) Within the distal population, from proximal ends of muscle fibers to distal ends, the serial distribution of sarcomere lengths ranged from the lowest length to high lengths. In contrast within the proximal population, the direction of the distribution was reversed. Such differences in distribution of sarcomere lengths between the proximal and distal fiber populations explain the shifts in muscle active slack and optimal lengths. Muscle force reduction after intervention (2) is explained primarily by the short sarcomeres within the distal population. However, fiber stress distributions showed contribution of the majority of the sarcomeres to muscle force: myofascial force transmission prevents the sarcomeres from shortening to nonphysiological lengths. It is concluded that interfering with the intramuscular myofascial force transmission due to rupturing of the intramuscular connective tissue leads to a complex distribution of sarcomere lengths within the aponeurotomized muscle and this determines the acute effects of the intervention on muscle length-force characteristics rather than the intervention with the myotendinous force transmission after which the intervention was named. These results suggest that during surgery, but also postoperatively, major attention should be focused on the length and activity of aponeurotomized muscle, as changes in connective tissue tear depth will affect the acute effects of the intervention.