In Silico Prediction and Molecular Docking of SNPs in NRP1 Gene Associated with SARS-COV-2.

Neuropilin-1 (NRP1) which is a main transmembrane cell surface receptor acts as a host cell mediator resulting in increasing the SARS-Cov-2 infectivity and also plays a role in neuronal development, angiogenesis and axonal outgrowth. The goal of this study is to estimate the impact of single nucleotide polymorphisms (SNPs) in the NRP1 gene on the function, structure and stabilization of protein as well as on the miRNA-mRNA binding regions using bioinformatical tools. It is also aimed to investigate the changes caused by SNPs in NRP1 on interactions with drug molecule and spike protein. The missense type of SNPs was analyzed using SIFT, PolyPhen-2, SNAP2, PROVEAN, Mutation Assessor, SNPs&GO, PhD-SNP, I-Mutant 3.0, MUpro, STRING, Project HOPE, ConSurf, and PolymiRTS. Docking analyses were conducted by AutoDock Vina program. As a result, a total of 733 missense SNPs were determined within the NRP1 gene and nine SNPs were specified as damaging to the protein. The modelling results showed that wild and mutant type amino acids had some different properties such as size, charge, and hydrophobicity. Additionally, their three-dimensional structures of protein were utilized for confirmation of these differences. After evaluating the results, nine polymorphisms rs141633354, rs142121081, rs145954532, rs200028992, rs200660300, rs369312020, rs370117610, rs370551432, rs370641686 were determined to be damaging on the structure and function of NRP1 protein and located in conserved regions. The results of molecular docking showed that the binding affinity values are nearly the same for wild-type and mutant structures support that the mutations carried out are not in the focus of the binding site, therefore the ligand does not affect the binding energy. It is expected that the results will be useful for future studies.

Dataset on Catal's reagent: Sensitive detection of iron (II) sulfate using spectrophotometry.

Catal's reagent is characterized by spectroscopic methods such as fourier-transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), ultraviolet (UV)-visible spectrophotometry. Effects of different solvents such as methanol and ethanol on absorption spectrum of 1-(Dodecylthio)anthracene-9,10-dione (3) were present. Detection range of iron (II) sulfate using Catal's reagent was analyzed. Synthesis of 1-(Dodecylthio)anthracene-9,10-dione (3) was explained, and absorbances of various concentrations of iron (II) sulfate (0- 10 mg mL-1) were measured. The possible detection mechanism was also explained. The dataset is useful to improve the detection of iron (II) sulfate in various application fields such as environmental, agricultural, sensor, food, textile and cement industries. The study refers to: F. Ozkok, Y.M. Sahin, V. Enisoglu-Atalay, K. Asgarova, N. Onul, T. Catal, Sensitive Detection of Iron (II) Sulfate with a Novel Reagent using Spectrophotometry, Spectchim. Acta. A, 240 (2020), 118631. https://doi.org/10.1016/j.saa.2020.118631.

Sensitive detection of iron (II) sulfate with a novel reagent using spectrophotometry.

In this study, a novel reagent was developed for sensitive detection of iron (II) sulfate, spectrophotometrically. A novel thio-anthraquinone derivative, 1-(Dodecylthio)anthracene-9,10-dione (3), was synthesized from the chemical reaction of 1-Chloroanthraquinone (1) and 1-Dodecanethiol (2) by an original reaction method and was used in the preparation of the novel reagent called Catal's reagent. A synthesized thio-anthraquinone analogue (3) was purified by column chromatography, and its chemical structure was characterized by spectroscopic methods such as Fourier-transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and ultraviolet (UV)-visible spectrophotometry. The chemical and molecular structure of the developed thio-antraquinone derivative (3) was illuminated using computational methods with the GaussView5 and Gaussian09 programs. Various solvents including ethanol, methanol, and acetonitrile were examined in the preparation of the reagent. A concentration range from 0.2 mg mL-1 up to 10 mg mL-1 of iron (II) sulfate heptahydrate solution in distilled water was prepared. The absorption spectra of Catal's reagent (0.816 mM) showed three peaks between 185 nm-700 nm of wavelength. However, after the reaction with H2O2 and the 30 mM trisodium citrate dihydrate mixture in the presence of an iron sulfate (II) solution, a single peak was observed, producing a stable and reddish/brownish homogenous solution (λ max = 304 nm). The following concentrations of iron (II) sulfate heptahydrate was examined using developed protocol and the reagent, and the concentrations were measured spectrophotometrically at 304 nm, 0.2-1 mg mL-1. Absorbances of reaction mixtures of iron (II) sulfate remained stable up to 48 h. The results indicated that the novel Catal's reagent can be used for sensitive spectrophotometric detection of iron (II) sulfate in aqueous solutions.

Chemical and molecular characterization of metabolites from Flavobacterium sp.

In this study, a Flavobacterium sp. is isolated from natural spring, and identified using molecular techniques. Extracellular and intracellular secondary metabolites are identified using solid phase microextraction gas chromatography-mass spectrometry and ultra performance liquid chromatography. Cytotoxic activity of the extracellular compounds produced by the Flavobacterium sp. and quercetin as the standard are measured using ECV304 human endothelial cells in vitro. Our results show that Flavobacterim sp. isolate has the highest percentage of similarity with Flavobacterium cheonhonense strain ARSA-15 (99%). Quercetin is detected as the major extracellular compound produced by the Flavobacterium sp. Methanol extract of Flavobacterium sp. resulted in a higher cell viability results when compared to DMSO extracts. Computational chemistry approach was used and it has been found that polar solvent (methanol) contributed to higher antioxidant activity. In conclusion, Flavobacterium sp. can be used to produce quercetin for industrial purposes.

Monitoring of neomycin sulfate antibiotic in microbial fuel cells.

Indirect detection and quantification of the neomycin sulfate antibiotic was accomplished in microbial fuel cells. Performance of the microbial fuel cells was examined on the basis of the following parameters; voltage generation, power density, current density and coulombic efficiencies. Removal of neomycin sulfate was monitored using LC-MS/MS in parallel with chemical oxygen demand and total carbohydrate removal. While neomycin sulfate was partially degraded, microbial fuel cell performance appeared to be affected and eventually inhibited by neomycin sulfate on a concentration-based fashion. In order to further examine the neomycin sulfate bio-sensing activity of the microbial fuel cell, a computational chemistry approach was used to obtain the information about the highest occupied molecular orbital-lowest unoccupied molecular orbital energy values of outer electron orbitals, their distribution, and ionization potentials (IPs). The results showed that electroactive bio-film-based MFCs can be used for sensitive detection of neomycin sulfate found in wastewaters.