AI-driven covalent drug design strategies targeting main protease (m) against SARS-CoV-2: structural insights and molecular mechanisms.

The emergence of new SARS-CoV-2 variants has raised concerns about the effectiveness of COVID-19 vaccines. To address this challenge, small-molecule antivirals have been proposed as a crucial therapeutic option. Among potential targets for anti-COVID-19 therapy, the main protease (M) of SARS-CoV-2 is important due to its essential role in the virus's life cycle and high conservation.

An overview of the vaccine platforms to combat COVID-19 with a focus on the subunit vaccines.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that has caused the recent coronavirus disease (COVID-19) global pandemic. The current approved COVID-19 vaccines have shown considerable efficiency against hospitalization and death. However, the continuation of the pandemic for more than two years and the likelihood of new strain emergence despite the global rollout of vaccination highlight the immediate need for the development and improvement of vaccines.

design of a multi-epitope vaccine against the spike and the nucleocapsid proteins of the Omicron variant of SARS-CoV-2.

Computational studies can comprise an effective approach to treating and preventing viral infections. Since 2019, the world has been dealing with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most important achievement in this short period of time in the effort to reduce morbidity and mortality was the production of vaccines and effective antiviral drugs.

Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant.

Since the new variant of SARS-CoV-2, Omicron (BA.1) has raised serious concerns, it is important to investigate the effects of mutations in the NTD and RBD domains of the spike protein for the development of COVID-19 vaccines. In this study, computational analysis of the Wuhan and Omicron NTDs and RBDs in their unbound and bound states to mAb 4A8 and ACE2 were performed.

Exploration of potential inhibitors for SARS-CoV-2 Mpro considering its mutants via structure-based drug design, molecular docking, MD simulations, MM/PBSA, and DFT calculations.

The main protease (Mpro) of SARS-COV-2 plays a vital role in the viral life cycle and pathogenicity. Due to its specific attributes, this 3-chymotrypsin like protease can be a reliable target for the drug design to combat COVID-19. Since the advent of COVID-19, Mpro has undergone many mutations.

Radioprotective Role of Vitamins C and E against the Gamma Ray-Induced Damage to the Chemical Structure of Bovine Serum Albumin.

Radioprotective effects of vitamin C and vitamin E as a water-soluble and a lipid-soluble agent, respectively, were investigated at the molecular level during the imposition of gamma radiation-induced structural changes to bovine serum albumin (BSA) at the therapeutic dose of 3 Gy. Secondary and tertiary structural changes of control and irradiated BSA samples were investigated using circular dichroism and fluorescence spectroscopy. The preirradiation tests showed nonspecific and reversible binding of vitamins C and E to BSA.

Doxorubicin-loaded, pH-sensitive Albumin Nanoparticles for Lung Cancer Cell Targeting.

In recent decades, scientific and medical communities have continuously sought new methods and chemistries to improve the treatment of cancer. Among many types of nanoparticles considered as carriers for drug delivery, the protein ones count among the safest. The present study aimed to investigate the physicochemical and biological effects of the supplementation of albumin nanoparticles with doxorubicin (DOX).

Development and characterization of a thermostable GH11/GH10 xylan degrading chimeric enzyme.

Xylanases are categorized into different family groups, two of which are glycoside hydrolases 10 (GH10) and 11 (GH11) families. These well-characterized xylanases demonstrate different modes of action in hydrolysis of xylans. Imitating certain types of microorganisms to produce bifunctional enzymes such as engineered xylanases has gained considerable attention among researchers.

Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design.

With the onset of the COVID-19 pandemic, the amount of data on genomic and proteomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stored in various databases has exponentially grown. A large volume of these data has led to the production of equally immense sets of immunological data, which require rigorous computational approaches to sort through and make sense of. Immunoinformatics has emerged in the recent decades as a field capable of offering this approach by bridging experimental and theoretical immunology with state-of-the-art computational tools.

Theranostic applications of stimulus-responsive systems based on carbon dots.

Over recent years, many different nanoparticle-based drug delivery systems (NDDSs) have been developed. Recently the development of stimulus-responsive NDDSs has come into sharper focus. Carbon dots (CDs) possess outstanding features such as useful optical properties, good biocompatibility, and the ability for easy surface modification.

Comparative molecular dynamics study of the receptor-binding domains in SARS-CoV-2 and SARS-CoV and the effects of mutations on the binding affinity.

Here, we report on a computational comparison of the receptor-binding domains (RBDs) on the spike proteins of severe respiratory syndrome coronavirus-2 (SARS-CoV-2) and SARS-CoV in free forms and as complexes with angiotensin-converting enzyme 2 (ACE2) as their receptor in humans. The impact of 42 mutations discovered so far on the structure and thermodynamics of SARS-CoV-2 RBD was also assessed. The binding affinity of SARS-CoV-2 RBD for ACE2 is higher than that of SARS-CoV RBD.

Enantioseparation of mandelic acid on vancomycin column: Experimental and docking study.

So far, no detailed view has been expressed regarding the interactions between vancomycin and racemic compounds including mandelic acid. In the current study, a chiral stationary phase was prepared by using 3-aminopropyltriethoxysilane and succinic anhydride to graft carboxylated silica microspheres and subsequently by activating the carboxylic acid group for vancomycin immobilization. Characterization by elemental analysis, Fourier transform infrared spectroscopy, solid-state nuclear magnetic resonance, and thermogravimetric analysis demonstrated effective functionalization of the silica surface.

Graphite/gold nanoparticles electrode for direct protein attachment: characterization and gas sensing application.

In this work, graphite/gold nanoparticles (G/AuNPs) were synthesized through a facile chemical method, and its potential application for direct protein attachment for electrochemical detection of carbon monoxide (CO) was investigated. The preparation of G/AuNPs electrodes was optimized by synthesizing the nanoparticles in different concentration of HAuCl.3HO at various temperatures.

Hydroxyapatite as a biomaterial - a gift that keeps on giving.

The synthetic analogue to biogenic apatite, hydroxyapatite (HA) has a number of physicochemical properties that make it an attractive candidate for diagnosis, treatment of disease and augmentation of biological tissues. Here we describe some of the recent studies on HA, which may provide bases for a number of new medical applications. The content of this review is divided to different medical application modes utilizing HA, including tissue engineering, medical implants, controlled drug delivery, gene therapies, cancer therapies and bioimaging.

Colloidal graphene oxide enhances the activity of a lipase and protects it from oxidative damage: Insights from physicochemical and molecular dynamics investigations.

Physical adsorption of lipase from Thermomyces lanuginosus onto single-layer sheets of graphene oxide (GO) was studied using the response surface methodology to evaluate the physicochemical factors - temperature, pH, ionic strength, and concentration - affecting the enzymatic activity and the immobilization efficiency. The immobilization efficiency and the activity of the enzyme were inversely proportional to each other. Specifically, higher pH values increased the immobilization efficacy, but produced changes in the aggregation state and secondary structure of the enzyme, thus decreasing its activity.

Design, development and evaluation of PEGylated rhGH with preserving its bioactivity at highest level after modification.

Modification of recombinant proteins with polyethylene-glycol (PEG) can improve their pharmacokinetic properties, although their bioactivity may be reduced after PEGylation due to structural changes. In this study, simultaneous optimization of PEGylation efficiency and preserved bioactivity of recombinant human growth hormone (rhGH) was investigated. In this regard, experiments were designed by the response surface methodology (RSM)-central composite design (CCD) utilizing design expert software.

The effect of non-thermal atmospheric plasma on the production and activity of recombinant phytase enzyme.

Atmospheric pressure cold plasma (ACP) is introduced as a useful tool in a variety of biological applications. Proteins are the most abundant macromolecules in living systems with a central role in all biological processes. These organic molecules are modified by ACP exposure that is responsible for many of ACP's biological effects.

Effect of size and chemical composition of graphene oxide nanoparticles on optical absorption cross-section.

Photothermal therapy with various nanoparticles, as photothermal transducers, is a widely researched technique. A continuous wave (CW) laser is employed during this procedure. The therapeutic setup is slightly modified to measure the optical absorption cross-section of the graphene oxide (GO), by mitigating the effects of heat diffusion and light scattering.

An isolate of Potato Virus X capsid protein from N. benthamiana: Insights from homology modeling and molecular dynamics simulation.

Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood.

Recombinant Acetylcholinesterase purification and its interaction with silver nanoparticle.

Although the use of silver nanoparticles (AgNPs) has substantial benefits, their entrance into the environment, food chain, and human body and their toxicity have come under serious scrutiny. Multiple noncovalent attractive forces between AgNPs and bio-macromolecules are responsible for immediate corona formation upon exposure to biological tissue. Here, the influence of AgNPs with neuro-enzyme Acetylcholinesterase (AChE) was investigated.

Continuous fast Fourier transforms cyclic voltammetry as a new approach for investigation of skim milk k-casein proteolysis, a comparative study.

Cheese production is relied upon the action of Rennet on the casein micelles of milk. Chymosin assay methods are usually time consuming and offline. Herein, we report a new electrochemical technique for studying the proteolysis of K-casein.

Homology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase.

With consumers growing increasingly aware of environmental issues, industries find enzymes as a reasonable alternative over physical conditions and chemical catalysts. Amylases are important hydrolase enzymes, which have been widely used in variety of industrial process such as pharmaceutical, food, and fermentation industries. Among amylases α-Amylase is in maximum demand due to its wide range of applications.

Caseoperoxidase, mixed β-casein-SDS-hemin-imidazole complex: a nano artificial enzyme.

A novel peroxidase-like artificial enzyme, named "caseoperoxidase", was biomimetically designed using a nano artificial amino acid apo-protein hydrophobic pocket. This four-component nano artificial enzyme containing heme-imidazole-β-casein-SDS exhibited high activity growth and k(cat) performance toward the native horseradish peroxidase demonstrated by the steady state kinetics using UV-vis spectrophotometry. The hydrophobicity and secondary structure of the caseoperoxidase were studied by ANS fluorescence and circular dichroism spectroscopy.

Effects of 940 MHz EMF on bioluminescence and oxidative response of stable luciferase producing HEK cells.

The effects of mobile phone frequency electromagnetic field (RF-EMF, 940 MHz) on a stable cell line (HEK293T) harbouring the firefly luciferase gene were evaluated. A waveguide exposure system with 1 W input power provided the mean specific absorption rate of ≈0.09 W kg(-1) in 35 mm Petri dishes.