Novel Hit Compounds as Putative Antifungals: The Case of Aspergillus fumigatus

The prevalence of invasive fungal infections has been dramatically increased as the size of the immunocompromised population worldwide has grown. Aspergillus fumigatus is characterized as one of the most widespread and ubiquitous fungal pathogens. Among antifungal drugs, azoles have been the most widely used category for the treatment of fungal infections. However, increasingly, azole-resistant strains constitute a major problem to be faced. Towards this direction, our study focused on the identification of compounds bearing novel structural motifs which may evolve as a new class of antifungals. To fulfil this scope, a combination of in silico techniques and in vitro assays were implemented. Specifically, a ligand-based pharmacophore model was created and served as a 3D search query to screen the ZINC chemical database. Additionally, molecular docking and molecular dynamics simulations were used to improve the reliability and accuracy of virtual screening results. In total, eight compounds, bearing completely different chemical scaffolds from the commercially available azoles, were proposed and their antifungal activity was evaluated using in vitro assays. Results indicated that all tested compounds exhibit antifungal activity, especially compounds 1, 2, and 4, which presented the most promising minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) values and, therefore, could be subjected to further hit to lead optimization

Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence.Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy –performed in a large and diverse chemolibrary– complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening.Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12–20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7–45 μM).Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known “garbage in, garbage out” machine learning principle

Nanosystems for the Encapsulation of Natural Products: The Case of Chitosan Biopolymer as a Matrix

Chitosan is a cationic natural polysaccharide, which has emerged as an increasingly interesting biomaterialover the past few years. It constitutes a novel perspective in drug delivery systems and nanocarriers’ formulations due to its beneficial properties, including biocompatibility, biodegradability and low toxicity. The potentiality of chemical or enzymatic modifications of the biopolymer, as well as its complementary use with other polymers, further attract the scientific community, offering improved and combined properties in the final materials. As a result, chitosan has been extensively used as a matrix for the encapsulation of several valuable compounds. In this review article, the advantageous character of chitosan as a matrix for nanosystemsis presented, focusing on the encapsulation of natural products. A five-year literature review is attempted covering the use of chitosan and modified chitosan as matrices and coatings for the encapsulation of natural extracts, essential oils or pure naturally occurring bioactive compounds are discussed

Deep Eutectic Solvents as Extraction Media for Valuable Flavonoids from Natural Sources

The present review article attempts to summarize the use of deep eutectic solvents in the extraction of flavonoids, one of the most important classes of plant secondary metabolites. All of the applications reviewed have reported success in isolation and extraction of the target compounds; competitive, if not superior, extraction rates compared with conventional solvents; and satisfactory behavior of the extract in the latter applications (such as direct analysis, synthesis, or catalysis), wherever attempted

Assessment of the Oxidative Desulfurization of Middle Distillate Surrogate Fuels with Spectroscopic Techniques

The oxidative desulfurization of five (5) model sulfur compounds and eleven (11) surrogate blends was investigated using the hydrogen peroxide (H2O2)-acetic acid (CH3COOH) system. Consequently, extractive desulfurization was carried out using conventional solvents. The model sulfur compounds, as well as the solvent, are present in petroleum middle distillates. The selection of the compounds was made so that they represent various kinds of sulfur compounds. The goal of this study was the implementation of a simple and economical oxidative and extractive system for the desulfurization of surrogate mixtures with an intermediate sulfur concentration 1% w/w, at the mild temperature of 70°C, and without the use of supplementary and assisting methods such as heterogeneous catalysis or ultrasound irradiation. The sulfur content was estimated using X-ray fluorescence. The progress of the oxidation reaction was monitored using liquid FT-IR. The solid sediments of the oxidation procedure were identified with solid-state FT-IR and 1H NMR spectroscopy

A novel thermophilic laccase-like multicopper oxidase from Thermothelomyces thermophila and its application in the oxidative cyclization of 2′,3,4-trihydroxychalcone

Laccase-like multicopper oxidases (LMCOs) are a heterogeneous group of oxidases, acting mainly on phenolic compounds and which are widespread among many microorganisms, including Basidiomycetes and Ascomycetes. Here, we report the cloning, heterologous expression, purification and characterization of a novel LMCO from the thermophilic fungus Thermothelomyces thermophila. The 1953 bp lmco gene sequence comprises of 3 exons interrupted by 2 introns and according to the LccED database the translated sequence belongs to superfamily 6 of multicopper oxidases. After removal of the introns, the gene was transformed into Pichia pastoris, under the control of the alcohol oxidase (AOX1) promoter. The heterologous enzyme was purified with an apparent molecular weight of 80 kDa. TtLMCO1 displayed optimum activity at pH 4 and 50 °C and appeared thermostable up to 50 °C. A variety of phenolic compounds were oxidized by TtLMCO1, including standard laccase substrates such as ABTS and 2,6 dimethoxyphenol. The UV/Vis spectrum of purified TtLMCO1 indicates that it belongs to yellow laccase-like oxidases. The enzyme was used for the bioconversion of 2′,3,4-trihydroxychalcone to 3′,4′-dihydroxy-aurone, a bioactive aurone recently shown to possess inhibitory activity against several isoforms of the histone deacetylase complex (HDAC). Overall, the thermophilic yellow LMCO TtLMCO1 presents a number of superior properties with potential use in industrial biocatalysis

Current Trends in Green Solvents: Biocompatible Ionic Liquids

Biocompatible Ionic Liquids (Bio-ILs) are a new class of ILs that are task-specifically designed to derive from naturally occurring compounds and/or derivatives thereof, as well as molecules well known for their biocompatibility (e.g., active pharmaceutical ingredients or non-toxic bioactive compounds) in terms of sustainability and biocompatibility. Owing to their remarkable physicochemical properties that can be tailor made to comply with the requirements of each application, Bio-ILs have emerged as novel, efficient and green technology, appropriate for a vast variety of scientific fields. Herein, this review describes the state-of-the-art scientific research regarding the synthesis, characterization and applications of Bio-ILs reported in the literature for the period between 2020 and 2022

Encapsulation of the Natural Product Tyrosol in Carbohydrate Nanosystems and Study of Their Binding with ctDNA

Tyrosol, a natural product present in olive oil and white wine, possesses a wide range of bioactivity. The aim of this study was to optimize the preparation of nanosystems encapsulating tyrosol in carbohydrate matrices and the investigation of their ability to bind with DNA. The first encapsulation matrix of choice was chitosan using the ionic gelation method. The second matrix was β-cyclodextrin (βCD) using the kneading method. Coating of the tyrosol-βCD ICs with chitosan resulted in a third nanosystem with very interesting properties. Optimal preparation parameters of each nanosystem were obtained through two three-factor, three-level Box-Behnken experimental designs and statistical analysis of the results. Thereafter, the nanoparticles were evaluated for their physical and thermal characteristics using several techniques (DLS, NMR, FT-IR, DSC, TGA). The study was completed with the investigation of the impact of the encapsulation on the ability of tyrosol to bind to calf thymus DNA. The results revealed that tyrosol and all the studied systems bind to the minor groove of ctDNA. Tyrosol interacts with ctDNA via hydrogen bond formation, as predicted via molecular modeling studies and corroborated by the experiments. The tyrosol-chitosan nanosystem does not show any binding to ctDNA whereas the βCD inclusion complex shows analogous interaction with that of free tyrosol

L-Proline-Based Natural Deep Eutectic Solvents as Efficient Solvents and Catalysts for the Ultrasound-Assisted Synthesis of Aurones via Knoevenagel Condensation

Aurones are minor flavonoids that possess a wide variety of bioactivity, including antioxidant, anticancer, and enzyme inhibitory activity. L-proline-based natural deep eutectic solvents (NaDES) were synthesized and applied as solvents and catalysts for the Knoevenagel condensation reaction between benzofuranone and substituted benzaldehydes to produce aurones in high yields and purity. The reaction between benzofuranone and vanillin served as the model reaction. After screening three NaDESs, and testing microwave, as well as ultrasound as energy sources, we concluded that the optimum results are obtained using L-proline/glycerol 1:2 as catalyst and solvent and ultrasound irradiation. The scope of the reaction was evaluated using a variety of benzaldehydes, and the corresponding aurones were obtained in moderate to satisfactory yields (57–89%) and high purity. An important additional feature of the described methodology is the recyclability and reusability of the NaDES, which was recycled and effectively reused after 6 cycles