Molecular Binding Study of the Main Constituents of Thymus Migricus with Trimmer Spike Protein of Corona Virus by Molecular Docking

Thymus, which includes around 215 species, is an important genus of the Lamiaceae family. It comprises several species that are native to Iran and can serve as valuable medicinal plants because of their biological and pharmacological properties. Indeed, it is commonly used by the local inhabitants as an expectorant, antiseptic, antispasmodic, carminative, antirheumatic, and diuretic. Furthermore, this plants antibacterial, antifungal, and antiviral characteristics have made it a global source of potential antimicrobial agents. Analysis of the compounds of this plant by gas chromatography reveals the main compounds as the following: thymol (55.6 %), γ-terpinene (16.7 %), geraniol (4.6 %), p-cymene (4.0 %), limonene (2.6 %) E-Caryophyllene (1.9 %) and α-Pinene (1.8 %). The aim of this study was to investigate the molecular binding of the main components of Thyme migricus with the trimmer of spike protein of Corona virus by the molecular docking method. According to the method, first, the PDB file of ten main constituents of Thymus migricus was extracted from the Chemspider database. Then, the PDB file of trimmer of spike protein was obtained from the rcsb site. In the next step, molecular binding analysis was performed for each compound using HDOCK online software. This study showed that although all of the analyzed compounds were able to bind to the coronavirus spike trimmer to some extent, Carvacrol exhibited the lowest docking energy and RMSD. To validate the genuine effectiveness of Thymus migricus compounds, more in vitro and in vivo researches are needed

Fuzzy logic-based vehicle safety estimation using V2V communications and on-board embedded ROS-based architecture for safe traffic management system in hail city

Estimating the state of surrounding vehicles is crucial to either prevent or avoid collisions with other road users. However, due to insufficient historical data and the unpredictability of future driving tactics, estimating the safety status is a difficult undertaking. To address this problem, an intelligent and autonomous traffic management system based on V2V technology is proposed. The main contribution of this work is to design a new system that uses a real-time control system and a fuzzy logic algorithm to estimate safety. The robot operating system (ROS) is the foundation of the control architechture, which connects all the various system nodes and generates the decision in the form of a speech and graphical message. The safe path is determined by a safety evaluation system that combines sensor data with a fuzzy classifier. Moreover, the suitable information processed by each vehicle unit is shared in the group to avoid unexpected problems related to speed, sudden braking, unplanned deviation, street holes, road bumps, and any kind of street issues. The connection is provided through a network based on the ZigBee protocol. The results of vehicle tests show that the proposed method provides a more reliable estimate of safety as compared to other methods

Dama Gazelle (Nanger dama) conservation strategy 2019-2028

Produced following the workshop hosted by Al Ain Zoo in Al Ain, United Arab Emirates, 11-13 December 2018. Compiled and edited by: David Mallon, Lisa Banfield, Helen Senn & Hessa Al Qahtani.Peer reviewe

The Use of Nanobiotechnology in Immunology and Vaccination

Nanotechnology uses the unique properties of nanostructures with a size of 1 to 200 nanometers. Different nanoparticles have shown great promise for the production of new vaccines and drugs. Nanostructures can be used to deliver immunological compounds more effectively than microstructures to target sites. Different nanostructures can be applied to form a new generation of vaccines, adjuvants, and immune system drugs. The goal of nanotechnology is to better respond to a wide range of infectious and non-infectious diseases

The Capability of Anti-RpoD Oligonucleotides in Staphylococcus Aurous to Human Genes Targeting: A Bioinformatics Study

Introduction: Using antisense oligonucleotides for targeting essential genes is one of the new methods to control microbial infections. The aim of this study was to investigate four antisense oligonucleotides against rpoD gene of staphylococcus aurous, and to find the probable match in human genes. Method: First, rpoD gene of staphylococcus aurous was extracted from NCBI (National Center for Biotechnology Information) database. Then, its mRNA sequence was generated and four antisense were selected according to secondary structure of mRNA and thermodynamic parameters. Finally, matching of each selected antisense and all human genome with Nblast algorithm, was evaluated. Results: This study showed that according to secondary structure and thermodynamic parameters, antisense 1, GAAGAAGTTGGTA, was the best antisense, and had the least Overall ∆G. Matching antisense sequences showed that antisense 1, 2, and 4 had different targets at human mRNA level. But, antisense 3, GAAGCAATTAATT, was ideal and could target only rpoD gene. Conclusion: Given to secondary structure and thermodynamic parameters, the adequate antisense could be selected for target gene, but most of these antisense targeting other genes in human cells

Triangular gold nanoparticles conjugated with peptide ligands: A new class of inhibitor for Candida albicans secreted aspartyl proteinase

et al.The aim of this study was to find the peptide ligands to inhibit Candida albicans secreted aspartyl proteinase 2 (Sap2). First, a ligand library, containing 300 different peptides, was constructed, and their interaction with Sap2 was separately calculated by molecular dynamic software. Second, 10 peptide ligands with the lowest intermolecular energy were selected. Then, triangular gold nanoparticles were synthesized, and separately conjugated with the peptide ligands. After synthesis, antifungal property and Sap inactivation of conjugated triangular gold nanoparticles, peptide ligands, and naked triangular gold nanoparticle were separately assessed, against thirty clinical isolates of C. albicans. In this study, we measured the uptake of conjugated and naked nanoparticles by atomic adsorption spectroscopy. This study showed that naked triangular gold nanoparticle and all conjugated triangular gold nanoparticles had high antifungal activity, but no peptide ligands had such activity. Of 300 peptide ligands, the peptide containing N-Cys-Lys-Lys-Arg-Met-Met-Lys-Ser-Met- Cys-C and its conjugate had the highest capability to inhibit Sap. Moreover, the uptake assay demonstrated that triangular gold nanoparticles conjugated with the peptide ligand had the highest uptake. © 2014 Elsevier Inc.This article financially supported by Farzaneh Haji Esmaeil Hajjar (Grant number 2-2013) and Department of Medical Nanotechnology, Pajoohesh Lab, Yazd, Iran (Grant number 1-2013). The authors thank the laboratory staff of the Yazd Pajoohesh medical lab. Jesus M. de la Fuente thanks MAT2011-26851-C02-01, Fondo Social Europeo, ERC-Starting Grant 239931-NANOPUZZLE, CDTI-INMUNOSWING, Shanghai 100 People Plan and ARAID for financial support.Peer Reviewe

Presentation of a nano-based tag for immunoassay, based on amine-modified bovine serum albumin nanoparticles

The aim of this study was to evaluate four immunoassays, based on amine-modified bovine serum albumin nanoparticles (AMBSANPs). First, the capability of nitrate absorption by AMBSANPs under different conditions was evaluated. Then, serial concentrations of pure ßHCG were added to wells coated with ßHCG antibody for immunoassays 1 and 2, and wells coated with ßHCG aptamer for immunoassays 3 and 4. Next, AMBSANPs conjugated with ßHCG antibody was added for immunoassays 1 and 3, and AMBSANPs conjugated with ßHCG aptamer were added for immunoassays 2 and 4. Finally, the optical density (OD) of each well was read at 340 nm, and compared with controls. Moreover, the concentration of ßHCG in the clinical samples was quantified by immunoassays 1, 2, 3, 4 and ELISA, and then compared. The effect of some serum interferences on these immunoassay methods was evaluated. The authors observed that the amount of nitrate absorption by AMBSANPs increased with an increase in H+ ion concentration and temperature, and decreased with an increase in ion strength. The correlation (R2) between ELISA and immunoassays 1, 2, 3 and 4 were 0.97, 0.97, 0.98, 0.99, respectively. It was found that the increase in the serum interferences led to a decrease in the measured ßHCG concentration.Peer Reviewe

The inhibition of Candida albicans secreted aspartyl proteinase by triangular gold nanoparticles

Objective(s): The aim of this study was to synthesize triangular gold nanoparticles, and then to evaluate their capability for inhibition of Candida albicans secreted aspartyl proteinase 2(Sap2). Materials and Methods: To synthesize the nanoparticles, hydrogen tetrachloroaurate and hexadecyl trimethyl ammonium bromide were incubated in presence of Sn(IV) meso-tetra(N-methyl-4-pyridyl) porphine tetratosylate chloride, and then characterized. Next, thirty clinical isolates of Candida albicans were obtained from patients suffering from vaginal candidiasis. Each Candida albicans isolate was first cultured in YCB-BSA medium, incubated for 24 h at 35 ºC. Then, 100 µL of triangular gold nanoparticles at three concentrations (16, 32, and 64 µg/mL) were added to Candida suspension, and incubated for 24 and 48 h at 35 ºC. To evaluate Sap activity, 0.1 mL of medium and 0.4 mL of 0.1 M sodium citrate buffer (pH 3.2) containing BSA 1% w/v were added, and incubated 15 minutes at 37 ºC. Then, the optical density of each tube was read at 280 nm. Enzyme activity was expressed as the amount (µM) of tyrosine equivalents released per min per ml of culture supernatant. Results: This study showed that the size of the nanoparticles was 70±50 nm. Sap activity evaluation demonstrated triangular gold nanoparticles could inhibit the enzyme, and the higher incubation time and concentration led to more decrease of Sap activity. Conclusion:For the first time, we demonstrated triangular gold nanoparticles as a novel inhibitor of Sap enzyme which may be useful for treatment of candidiasis.

The validation of artificial anti‐monkeypox antibodies by in silico and experimental approaches

Abstract As a result of smallpox immunization programs that ended more than 40 years ago, a significant portion of the world's population is not immune. Moreover, due to the lack of anti‐monkeypox drugs and vaccines against monkeypox, the spread of this virus may be the beginning of another challenge. In this study, novel antibodies against monkeypox virus were modeled based on a heavy chain of human antibody and a small peptide fragment. Docking of modeled antibodies with C19L protein showed the range of docking energy, and root‐mean‐square deviation (RMSD) was from −124 to −154 kcal/mL and 4–6 angstrom, respectively. Also, docking of modeled antibodies‐C19L complex with gamma Fc receptor type I illustrated the range of docking energy, and RMSD was from −132 to −155 kcal/ml and 5–7 angstrom, respectively. Moreover, molecular dynamics simulation showed that antibody 62 had the highest stability with the lowest energy level and RMSD. Interestingly, no modeled antibodies had immunogenicity, allergenicity, and toxicity. Although all of them had good stability, only antibodies 25, 28, 54, and 62 had a half‐life of >10 h. Moreover, the interaction between C19L protein and anti‐C19L antibodies (wild‐type and synthetic) was evaluated by the SPR method. We found that KD in synthetic antibodies was lower than wild antibody. In terms of δH°, TδS°, and δG°, the results were consistent with binding parameters. Here, the lowest value of thermodynamic parameters was obtained for antibody 62. These data show that the synthetic antibodies, especially antibody 62, had a higher affinity than the wild‐type antibody

Immunoinformatics design and synthesis of a multi-epitope vaccine against Helicobacter pylori based on lipid nanoparticles

Abstract Helicobacter pylori (H. pylori) is responsible for various chronic or acute diseases, such as stomach ulcers, dyspepsia, peptic ulcers, gastroesophageal reflux, gastritis, lymphoma, and stomach cancers. Although specific drugs are available to treat the bacterium's harmful effects, there is an urgent need to develop a preventive or therapeutic vaccine. Therefore, the current study aims to create a multi-epitope vaccine against H. pylori using lipid nanoparticles. Five epitopes from five target proteins of H. pylori, namely, Urease, CagA, HopE, SabA, and BabA, were used. Immunogenicity, MHC (Major Histocompatibility Complex) bonding, allergenicity, toxicity, physicochemical analysis, and global population coverage of the entire epitopes and final construct were carefully examined. The study involved using various bioinformatic web tools to accomplish the following tasks: modeling the three-dimensional structure of a set of epitopes and the final construct and docking them with Toll-Like Receptor 4 (TLR4). In the experimental phase, the final multi-epitope construct was synthesized using the solid phase method, and it was then enclosed in lipid nanoparticles. After synthesizing the construct, its loading, average size distribution, and nanoliposome shape were checked using Nanodrop at 280 nm, dynamic light scattering (DLS), and atomic force microscope (AFM). The designed vaccine has been confirmed to be non-toxic and anti-allergic. It can bind with different MHC alleles at a rate of 99.05%. The construct loading was determined to be about 91%, with an average size of 54 nm. Spherical shapes were also observed in the AFM images. Further laboratory tests are necessary to confirm the safety and immunogenicity of the multi-epitope vaccine