SARS-CoV-2 PLpro Inhibition: Evaluating in Silico Repurposed Fidaxomicin's Antiviral Activity Through In Vitro Assessment.

The emergence of drug-resistant viruses and novel strains necessitates the rapid development of novel antiviral therapies. This need was particularly demanding during the COVID-19 pandemic. While de novo drug development is a time-consuming process, repurposing existing approved medications offers a more expedient approach. In our prior in silico screening of the DrugBank database, fidaxomicin emerged as a potential SARS-CoV-2 papain-like protease inhibitor. This study extends those findings by investigating fidaxomicin's antiviral properties in vitro. Our results support further exploration of fidaxomicin as a therapeutic candidate against SARS-CoV-2, given its promising in vitro antiviral activity and favorable safety profile.

Recent Computer-Aided Studies on Herbicides: A Short Review.

Current industrial herbicides have a negative impact on the environment and have widespread resistance, so computational studies on their properties, elimination, and overcoming resistance can be helpful. On the other hand, developing new herbicides, especially bioherbicides, is slow and costly. Therefore, computational studies that guide the design and search for new herbicides that exist in various plant sources, can alleviate the pain associated with the many obstacles. This review summarizes for the first time the most recent studies on both aspects of herbicides over 10 years.

In Silico Investigation of Selected Pesticides and Their Determination in Agricultural Products Using QuEChERS Methodology and HPLC-DAD.

In this study, we considered some pesticides as active substances within formulations for the protection of plant-based food in the Republic of Serbia in silico, because these pesticides have not often been investigated in this way previously, and in an analytical way, because there are not very many available fast, cheap, and easy methods for their determination in real agricultural samples. Seven pesticides were detected in selected agricultural products (tomatoes, cucumbers, peppers, and grapes) using the QuEChERS methodology and HPLC-DAD. Standard curves for the investigated pesticides (chlorantraniliprole, methomyl, metalaxyl, thiacloprid, acetamiprid, emamectin benzoate, and cymoxanil) show good linearity, with R2 values from 0.9785 to 0.9996. The HPLC-DAD method is fast, and these pesticides can be determined in real spiked samples in less than 15 min. We further characterized the pesticides we found in food based on physicochemical properties and molecular descriptors to predict the absorption, distribution, metabolism, elimination, and toxicity (ADMET) of the compounds. We summarized the data supporting their effects on humans using various computational tools to determine their potential adverse effects. The results of our prediction study show that all of the selected pesticides considered in this study have good oral bioavailability, and those with high toxicity, therefore, could be harmful to human health. Chlorantraniliprole was shown in a molecular docking study as a good starting point for a new Alzheimer's disease drug candidate.

Inhibition of SARS-CoV-2 Mpro with Vitamin C, L-Arginine and a Vitamin C/L-Arginine Combination.

BACKGROUND: Drug resistance is a critical problem in health care that affects therapy outcomes and requires new approaches to drug design. SARS-CoV-2 Mpro mutations are of concern as they can potentially reduce therapeutic efficacy. Viral infections are amongst the many disorders for which nutraceuticals have been employed as an adjunct therapy. The aim of this study was to examine the potential in vitro activity of L-arginine and vitamin C against SARS-CoV-2 Mpro. METHODS: The Mpro inhibition assay was developed by cloning, expression, purification, and characterization of Mpro. Selected compounds were then screened for protease inhibition. RESULTS: L-arginine was found to be active against SARS-CoV-2 Mpro, while a vitamin C/L-arginine combination had a synergistic antiviral action against Mpro. These findings confirm the results of our previous in silico repurposing study that showed L-arginine and vitamin C were potential Mpro inhibitors. Moreover, they suggest a possible molecular mechanism to explain the beneficial effect of arginine in COVID patients. CONCLUSIONS: The findings of the current study are important because they help to identify COVID-19 treatments that are efficient, inexpensive, and have a favorable safety profile. The results of this study also suggest a possible adjuvant nutritional strategy for COVID-19 that could be used in conjunction with pharmacological agents.

In Silico and In Vitro Inhibition of SARS-CoV-2 PLpro with Gramicidin D.

Finding an effective drug to prevent or treat COVID-19 is of utmost importance in tcurrent pandemic. Since developing a new treatment takes a significant amount of time, drug repurposing can be an effective option for achieving a rapid response. This study used a combined in silico virtual screening protocol for candidate SARS-CoV-2 PLpro inhibitors. The Drugbank database was searched first, using the Informational Spectrum Method for Small Molecules, followed by molecular docking. Gramicidin D was selected as a peptide drug, showing the best in silico interaction profile with PLpro. After the expression and purification of PLpro, gramicidin D was screened for protease inhibition in vitro and was found to be active against PLpro. The current study's findings are significant because it is critical to identify COVID-19 therapies that are efficient, affordable, and have a favorable safety profile.

Evaluation of the Probiotic Properties of Lacticaseibacillus casei 431® Isolated from Food for Special Medical Purposes§.

Research background: Increasing awareness of the importance of nutrition in health promotion and disease prevention has driven to the development of foods for special medical purposes (FSMPs). In this study, the probiotic strain Lacticaseibacillus paracasei ssp. paracasei (Lacticaseibacillus casei 431®) was incorporated into FSMPs to develop an innovative product. The aim was to investigate the influence of the FSMP matrix on the specific probiotic properties of L. casei 431® in vitro. Experimental approach: A series of in vitro experiments were performed as part of the probiotic approach. After evaluation of antibiotic susceptibility profiles, functional properties such as survival under simulated gastrointestinal tract (GIT) conditions, bile salt deconjugation activities, cholesterol assimilation, antagonistic activity against spoilage bacteria and adhesion to Caco-2 cell line monolayers and extracellular matrix proteins were investigated. Results and conclusions: The L. casei 431® strain, both the lyophilised strain and the strain isolated from the FSMP matrix, effectively survived the simulated adverse gastrointestinal conditions without significant effects of the food matrix. The effect of the FSMP matrix on the deconjugation activity of the bile salts of L. casei 431® was minimal; however, cholesterol assimilation was increased by 16.4 %. L. casei 431® had antibacterial activity against related lactic acid bacteria regardless of whether it was used in FSMPs or not. Conversely, the probiotic strain isolated from FSMP matrix had significantly higher inhibitory activity against six potential pathogens than the lyophilised culture. The autoaggregation ability of the L. casei 431® cells was not affected by the FSMP matrix. The adhesion of L. casei 431® bacterial cells to the extracellular matrix proteins was reduced after treatment with proteinase K, with the highest adhesion observed to laminin. The adhesion of L. casei 431® reduced the binding of E. coli 3014 by 1.81 log units and the binding of S. Typhimurium FP1 to Caco-2 cell lines by 1.85 log units, suggesting the potential for competitive exclusion of these pathogens. Novelty and scientific contribution: The results support the positive effect of the FSMP matrix on the specific probiotic properties of L. casei 431®, such as antibacterial activity, bile salt deconjugation and cholesterol assimilation, while the incorporation of this probiotic strain adds functional value to the FSMPs. The synergistic effect achieved by the joint application of L. casei 431® and innovative FSMP matrix contributed to the development of the novel formulation of an improved functional food product with added value.

Computational Studies on Selected Macrolides Active against Escherichia coli Combined with the NMR Study of Tylosin A in Deuterated Chloroform.

Although many antibiotics are active against Gram-positive bacteria, fewer also show activity against Gram-negative bacteria. Here, we present a combination of in silico (electron ion-interaction potential, molecular docking, ADMET), NMR, and microbiological investigations of selected macrolides (14-membered, 15-membered, and 16-membered), aiming to discover the pattern of design for macrolides active against Gram-negative bacteria. Although the conformational studies of 14-membered and 15-membered macrolides are abundant in the literature, 16-membered macrolides, and their most prominent representative tylosin A, have received relatively little research attention. We therefore report the complete 1H and 13C NMR assignment of tylosin A in deuterated chloroform, as well as its 3D solution structure determined through molecular modelling (conformational search) and 2D ROESY NMR. Additionally, due to the degradation of tylosin A in deuterated chloroform, other species were also detected in 1D and 2D NMR spectra. We additionally studied the anti-bacterial activity of tylosin A and B against selected Gram-positive and Gram-negative bacteria.

In Silico Screening of Natural Compounds for Candidates 5HT6 Receptor Antagonists against Alzheimer's Disease.

Alzheimer's disease (AD), a devastating neurodegenerative disease, is the focus of pharmacological research. One of the targets that attract the most attention for the potential therapy of AD is the serotonin 5HT6 receptor, which is the receptor situated exclusively in CNS on glutamatergic and GABAergic neurons. The neurochemical impact of this receptor supports the hypothesis about its role in cognitive, learning, and memory systems, which are of critical importance for AD. Natural products are a promising source of novel bioactive compounds with potential therapeutic potential as a 5HT6 receptor antagonist in the treatment of AD dementia. The ZINC-natural product database was in silico screened in order to find the candidate antagonists of 5-HT6 receptor against AD. A virtual screening protocol that includes both short-and long-range interactions between interacting molecules was employed. First, the EIIP/AQVN filter was applied for in silico screening of the ZINC database followed by 3D QSAR and molecular docking. Ten best candidate compounds were selected from the ZINC Natural Product database as potential 5HT6 Receptor antagonists and were proposed for further evaluation. The best candidate was evaluated by molecular dynamics simulations and free energy calculations.

Identification of SARS-CoV-2 Papain-like Protease (PLpro) Inhibitors Using Combined Computational Approach.

In the current pandemic, finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 PLpro promotes viral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and therefore is an attractive drug target. In this study, we used a combined in silico virtual screening for candidates for SARS-CoV-2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS-CoV-2 PLpro inhibitors that we propose for further experimental testing.

Recent Advances in Electrochemical Determination of Pesticides.

Widespread usage of pesticides in agricultural practice caused their residues to appear in water and food products intended for human consumption. The potential toxicity of these resources has raised awareness about pesticide tracking in the environment. Development of reliable electrochemical sensors for the on-site determination of pesticide concentrations is envisioned as an alternative to conventional chromatographic methods which are robust, expensive and require skilled work force. Modification of the working electrode surface can result in enhanced electrochemical response towards selected pesticide making such electrode convenient sensor for facile and efficient determination of pesticides in low concentrations. New generation of nanomaterials is applied in electrode modification in order to improve its sensitivity and selectivity. The present review summarizes significant advances in voltammetric detection of pesticides for the period of the past five years. The major focus of this review is set to the types of carbon and oxide based materials, metal nanoparticles, composites and other materials employed to upgrade standard electrode configurations such as glassy carbon and carbon paste electrodes, boron doped diamond electrodes, screen printed and film electrodes, metal and amalgam, and other kinds of electrodes.

Multiwalled carbon nanotubes modified with MoO2 nanoparticles for voltammetric determination of the pesticide oxyfluorfen.

A glassy carbon electrode was functionalized by MoO2 nanoparticle-decorated multiwalled carbon nanotubes (MWCNTs) and examined as a working electrode in oxyfluorfen (OXY) detection by differential pulse stripping voltammetry (DPSV). Measurement parameters were as follows: initial potential - 0.1 V, end potential + 0.5 V, accumulation potential - 0.15 V, accumulation time 80 s, and scan rate 50 mV s-1. A stripping potential of + 0.315 V vs. Ag/AgCl was employed. The pPesticide oxyfluorfen was determined in model samples by DPSV with good reproducibility (RSD <2.4%) in the concentration range 2.5 to 34.5 ng mL-1, with r = 0.99 and a limit of detection of 1.5 ng mL-1. These results are in the same range as those of HPLC/DAD, which is used as the comparative method. Recovery for OXY determination in a real river water sample was 102%. Analyses in Briton-Robinson buffer has shown to be pH dependent with the best response at pH 6.0. Structural characterization of MoO2-MWCNT by Raman spectroscopy, field emission scanning electron microscopy, high-resolution transmission electron microscopy, and X-ray crystallography revealed a preserved MWCNT structure decorated with firmly attached clusters of MoO2 nanoparticles. Graphical abstract Glassy carbon electrode functionalized by MoO2 nanoparticle-decorated multiwalled carbon nanotubes is used as a working electrode in the voltammetric determination of pesticide oxyfluorfen in water.

The Targeted Pesticides as Acetylcholinesterase Inhibitors: Comprehensive Cross-Organism Molecular Modelling Studies Performed to Anticipate the Pharmacology of Harmfulness to Humans In Vitro.

Commercially available pesticides were examined as Mus musculus and Homo sapiens acetylcholinesterase (mAChE and hAChE) inhibitors by means of ligand-based (LB) and structure-based (SB) in silico approaches. Initially, the crystal structures of simazine, monocrotophos, dimethoate, and acetamiprid were reproduced using various force fields. Subsequently, LB alignment rules were assessed and applied to determine the inter synaptic conformations of atrazine, propazine, carbofuran, carbaryl, tebufenozide, imidacloprid, diuron, monuron, and linuron. Afterwards, molecular docking and dynamics SB studies were performed on either mAChE or hAChE, to predict the listed pesticides' binding modes. Calculated energies of global minima (Eglob_min) and free energies of binding (∆Gbinding) were correlated with the pesticides' acute toxicities (i.e., the LD50 values) against mice, as well to generate the model that could predict the LD50s against humans. Although for most of the pesticides the low Eglob_min correlates with the high acute toxicity, it is the ∆Gbinding that conditions the LD50 values for all the evaluated pesticides. Derived pLD50 = f(∆Gbinding) mAChE model may predict the pLD50 against hAChE, too. The hAChE inhibition by atrazine, propazine, and simazine (the most toxic pesticides) was elucidated by SB quantum mechanics (QM) DFT mechanistic and concentration-dependent kinetic studies, enriching the knowledge for design of less toxic pesticides.