Multi-stage structure-based virtual screening approach towards identification of potential SARS-CoV-2 NSP13 helicase inhibitors

On account of its crucial role in the virus life cycle, SARS-COV-2 NSP13 helicase enzyme was exploited as a promising target to identify a novel potential inhibitor using multi-stage structure-based drug discovery approaches. Firstly, a 3D pharmacophore was generated based on the collected data from a protein-ligand interaction fingerprint (PLIF) study using key interactions between co-crystallised fragments and the NSP13 helicase active site. The ZINC database was screened through the generated 3D-pharmacophore retrieving 13 potential hits. All the retrieved hits exceeded the benchmark score of the co-crystallised fragments at the molecular docking step and the best five-hit compounds were selected for further analysis. Finally, a combination between molecular dynamics simulations and MM-PBSA based binding free energy calculations was conducted on the best hit (compound FWM-1) bound to NSP13 helicase enzyme, which identified FWM-1 as a potential potent NSP13 helicase inhibitor with binding free energy equals −328.6 ± 9.2 kcal/mol.     

Essential metals,vitamins and antioxidant enzyme activities in COVID-19 patients and their potential associations with the disease severity

BioMetals - The role of micronutrient deficiency in the pathogenesis of COVID-19 has been reviewed in the literature; however, the data are limited and conflicting. This study investigated the...     

Volatile Oils from the Aerial Parts of Eremophila maculata and Their Antimicrobial Activity

The essential oils isolated from the fresh flowers, fresh leaves, and both fresh and air‐dried stems of Eremophila maculata (Scrophulariaceae) were characterized by GC‐FID and GC/MS analyses. Sabinene was the major component in most of the oils, followed by limonene, α‐pinene, benzaldehyde, (Z)‐β‐ocimene, and spathulenol. The leaf and flower essential oils showed antibacterial and antifungal activity against five Gram‐positive and four Gram‐negative bacterial strains, multi‐resistant clinical isolates from patients, i.e., methicillin‐resistant Staphylococcus aureus (MRSA), as well as two yeasts. Minimum inhibitory concentrations (MICs) and minimum microbicidal concentrations (MMCs) were between 0.25 and 4 mg/ml.     

Development of silica-coated rare-earth doped strontium aluminate toward superhydrophobic,anti-corrosive and long-persistent photoluminescent epoxy coating

Long-persistent phosphorescent smart paints have the ability to continue glowing in the dark for a prolonged time period to function as energy-saving products. Herein, new epoxy/silica nanocomposite paints were prepared with different concentrations of lanthanide-doped aluminate nanoparticles (LAN; SrAl₂O₄:Eu²⁺,Dy³⁺). The LAN pigment was firstly coated with silicon dioxide (SiO₂) utilizing the heterogeneous precipitation technique to provide LAN-encapsulated between SiO₂ nanoparticles (LAN@SiO₂). The epoxy/silica/lanthanide-doped aluminate nanoparticles (ESLAN) nanocomposite paints were coated on steel. The prepared ESLAN paints were studied by transmission electron microscopy (TEM), Fourier-transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), X-ray fluorescence (XRF) analysis, and energy-dispersive X-ray spectroscopy (EDS). The transparency and coloration properties of the nanocomposite coated films were explored by CIE Lab parameters and photoluminescence spectra. The ultraviolet-induced luminescence properties of the transparent coated films demonstrated greenish phosphorescence at 518 nm upon excitation at 368 nm. Both hardness and hydrophobic activities were investigated. The anticorrosion activity of the nanocomposite films coated onto mild steel substrates immersed in aqueous sodium chloride (NaCl_(aq)) (3.5%) was studied by electrochemical impedance spectroscopy (EIS). The silica-containing coatings were monitored to exhibit anticorrosion properties. Additionally, the nanocomposite films with LAN@SiO₂ (25%) exhibited the optimized long-lasting luminescence properties in the dark for 90 min. The nanocomposite films showed highly reversible and durable long-lived phosphorescence.     

A system dynamics model of clinical decision thresholds for the detection of developmental-behavioral disorders

Background

Clinical decision-making has been conceptualized as a sequence of two separate processes: assessment of patients’ functioning and application of a decision threshold to determine whether the evidence is sufficient to justify a given decision. A range of factors, including use of evidence-based screening instruments, has the potential to influence either or both processes. However, implementation studies seldom specify or assess the mechanism by which screening is hypothesized to influence clinical decision-making, thus limiting their ability to address unexpected findings regarding clinicians’ behavior. Building on prior theory and empirical evidence, we created a system dynamics (SD) model of how physicians’ clinical decisions are influenced by their assessments of patients and by factors that may influence decision thresholds, such as knowledge of past patient outcomes. Using developmental-behavioral disorders as a case example, we then explore how referral decisions may be influenced by changes in context. Specifically, we compare predictions from the SD model to published implementation trials of evidence-based screening to understand physicians’ management of positive screening results and changes in referral rates. We also conduct virtual experiments regarding the influence of a variety of interventions that may influence physicians’ thresholds, including improved access to co-located mental health care and improved feedback systems regarding patient outcomes.

Results

Results of the SD model were consistent with recent implementation trials. For example, the SD model suggests that if screening improves physicians’ accuracy of assessment without also influencing decision thresholds, then a significant proportion of children with positive screens will not be referred and the effect of screening implementation on referral rates will be modest—results that are consistent with a large proportion of published screening trials. Consistent with prior theory, virtual experiments suggest that physicians’ decision thresholds can be influenced and detection of disabilities improved by increasing access to referral sources and enhancing feedback regarding false negative cases.

Conclusions

The SD model of clinical decision-making offers a theoretically based framework to improve understanding of physicians’ behavior and the results of screening implementation trials. The SD model is also useful for initial testing of hypothesized strategies to increase detection of under-identified medical conditions.

     

The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts

The Registry of Standard Biological Parts only accepts genetic parts compatible with the RFC 10 BioBrick format. This combined assembly and submission standard requires that four unique restriction enzyme sites must not occur in the DNA sequence encoding a part. We present evidence that this requirement places a nontrivial burden on iGEM teams developing large and novel parts. We further argue that the emergence of inexpensive DNA synthesis and versatile assembly methods reduces the utility of coupling submission and assembly standards and propose a submission standard that is compatible with current quality control strategies while nearly eliminating sequence constraints on submitted parts.