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.

New Nitric Oxide-Releasing Compounds as Promising Anti-Bladder Cancer Drugs.

Bladder cancer is a worldwide problem and improved therapies are urgently needed. In the search for newer strong antitumor compounds, herein, we present the study of three nitric oxide-releasing compounds and evaluate them as possible therapies for this malignancy. Bladder cancer cell lines T24 and 253J were used to evaluate the antiproliferative, antimigratory, and genotoxic effects of compounds. Moreover, we determined the NF-κB pathway inhibition, and finally, the survivin downregulation exerted by our molecules. The results revealed that compounds 1 and 3 exerted a high antiproliferative activity against bladder cancer cells through DNA damage and survivin downregulation. In addition, compound 3 reduced bladder cancer cell migration. We found that nitric oxide donors are promising molecules for the development of a new therapeutic targeting the underlying mechanisms of tumorigenesis and progression of bladder cancer.

Hypoxia and inflammation conditions differentially affect the expression of tissue transglutaminase spliced variants and functional properties of extravillous trophoblast cells.

PROBLEM: Persistent hypoxia and inflammation beyond early pregnancy are involved in a bad outcome because of defective trophoblast invasiveness. Tissue transglutaminase (TG2) coregulates several cell functions. An aberrant expression and/or transamidation activity could contribute to placental dysfunction. METHOD OF STUDY: The first-trimester trophoblast cell line (Swan-71) was used to study TG2 expression and cell functions in the absence or presence of inflammatory cytokines (TNF-α, IL-1ß) or chemical hypoxia (CoCl2 ). We analyzed The concentration of cytokines in the supernatant by ELISA; Cell migration by scratch assay; NF-κB activation by detection of nuclear p65 by immunofluorescence or flow cytometry using a Swan-71 NF-κB-hrGFP reporter cell line. Tissue transglutaminase expression was analyzed by immunoblot and confocal microscopy. Expression of spliced mRNA variants of tissue transglutaminase was analyzed by RT-PCR. Transamidation activity was assessed by flow cytometry using 5-(biotinamido)-pentylamine substrate. RESULTS: Chemical hypoxia and TGase inhibition, but not inflammatory stimuli, decreased Swan-71 migration. IL-6 production was also decreased by chemical hypoxia, but increased by inflammation. Intracellular TGase activity was increased by all stimuli, but NF-κB activation was observed only in the presence of proinflammatory cytokines. TG2 expression was decreased by CoCl2 and TNF-α. Translocation of TG2 and p65 to nuclei was observed only with TNF-α, without colocalization. Differential relative expression of spliced variants of mRNA was observed between CoCl2 and inflammatory stimuli. CONCLUSION: The observed decrease in total TG2 expression and relative increase in short variants under hypoxia conditions could contribute to impaired trophoblast invasion and impact on pregnancy outcome.

Generation and Characterization of Stable Redox-Reporter Mammalian Cell Lines of Biotechnological Relevance.

Cellular functions such as DNA replication and protein translation are influenced by changes in the intracellular redox milieu. Exogenous (i.e., nutrients, deterioration of media components, xenobiotics) and endogenous factors (i.e., metabolism, growth) may alter the redox homeostasis of cells. Thus, monitoring redox changes in real time and in situ is deemed essential for optimizing the production of recombinant proteins. Recently, different redox-sensitive variants of green fluorescent proteins (e.g., rxYFP, roGFP2, and rxmRuby2) have been engineered and proved suitable to detect, in a non-invasive manner, perturbations in the pool of reduced and oxidized glutathione, the major low molecular mass thiol in mammals. In this study, we validate the use of cytosolic rxYFP on two cell lines widely used in biomanufacturing processes, namely, CHO-K1 cells expressing the human granulocyte macrophage colony-stimulating factor (hGM-CSF) and HEK-293. Flow cytometry was selected as the read-out technique for rxYFP signal given its high-throughput and statistical robustness. Growth kinetics and cellular metabolism (glucose consumption, lactate and ammonia production) of the redox reporter cells were comparable to those of the parental cell lines. The hGM-CSF production was not affected by the expression of the biosensor. The redox reporter cell lines showed a sensitive and reversible response to different redox stimuli (reducing and oxidant reagents). Under batch culture conditions, a significant and progressive oxidation of the biosensor occurred when CHO-K1-hGM-CSF cells entered the late-log phase. Medium replenishment restored, albeit partially, the intracellular redox homeostasis. Our study highlights the utility of genetically encoded redox biosensors to guide metabolic engineering or intervention strategies aimed at optimizing cell viability, growth, and productivity.

An in vitro model mimicking the complement system to favor directed phagocytosis of unwanted cells

BACKGROUND: Opsonization, is the molecular mechanism by which target molecules promote interactions with phagocyte cell surface receptors to remove unwanted cells by induced phagocytosis. We designed an in vitro system to demonstrate that this procedure could be driven to eliminate adipocytes, using peptides mimicking regions of the complement protein C3b to promote opsonization and enhance phagocytosis. Two cell lines were used: (1) THP-1 monocytes differentiated to macrophages, expressing the C3b opsonin receptor CR1 in charge of the removal of unwanted coated complexes; (2) 3T3-L1 fibroblasts differentiated to adipocytes, expressing AQP7, to evaluate the potential of peptides to stimulate opsonization. (3) A co-culture of the two cell lines to demonstrate that phagocytosis could be driven to cell withdrawal with high efficiency and specificity. RESULTS: An array of peptides were designed and chemically synthesized p3691 and p3931 joined bound to the CR1 receptor activating phagocytosis (p < 0.033) while p3727 joined the AQP7 protein (p < 0.001) suggesting that opsonization of adipocytes could occur. In the co-culture system p3980 and p3981 increased lipid uptake to 91.2% and 89.0%, respectively, as an indicator of potential adipocyte phagocytosis. CONCLUSIONS: This in vitro model could help understand the receptor­ligand interaction in the withdrawal of unwanted macromolecules in vivo. The adipocyte-phagocytosis discussed may help to control obesity, since peptides of C3b stimulated the CR1 receptor, promoting opsonisation and phagocytosis of lipidcontaining structures, and recognition of AQP7 in the differentiated adipocytes, favored the phagocytic activity of macrophages, robustly supported by the co-culture strategy.

A Nitroalkene Benzoic Acid Derivative Targets Reactive Microglia and Prolongs Survival in an Inherited Model of ALS via NF-κB Inhibition.

Motor neuron degeneration and neuroinflammation are the most striking pathological features of amyotrophic lateral sclerosis (ALS). ALS currently has no cure and approved drugs have only a modest clinically therapeutic effect in patients. Drugs targeting different deleterious inflammatory pathways in ALS appear as promising therapeutic alternatives. Here, we have assessed the potential therapeutic effect of an electrophilic nitroalkene benzoic acid derivative, (E)-4-(2-nitrovinyl) benzoic acid (BANA), to slow down paralysis progression when administered after overt disease onset in SOD1G93A rats. BANA exerted a significant inhibition of NF-κB activation in NF-κB reporter transgenic mice and microglial cell cultures. Systemic daily oral administration of BANA to SOD1G93A rats after paralysis onset significantly decreased microgliosis and astrocytosis, and significantly reduced the number of NF-κB-p65-positive microglial nuclei surrounding spinal motor neurons. Numerous microglia bearing nuclear NF-κB-p65 were observed in the surrounding of motor neurons in autopsy spinal cords from ALS patients but not in controls, suggesting ALS-associated microglia could be targeted by BANA. In addition, BANA-treated SOD1G93A rats after paralysis onset showed significantly ameliorated spinal motor neuron pathology as well as conserved neuromuscular junction innervation in the skeletal muscle, as compared to controls. Notably, BANA prolonged post-paralysis survival by ~30%, compared to vehicle-treated littermates. These data provide a rationale to therapeutically slow paralysis progression in ALS using small electrophilic compounds such as BANA, through a mechanism involving microglial NF-κB inhibition.

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells.

BACKGROUND: During breast cancer progression, the epithelial to mesenchymal transition has been associated with metastasis and endocrine therapy resistance; however, the underlying mechanisms remain elusive. To gain insight into this process, we studied the transition undergone by MCF7-derived cells, which is driven by the constitutive nuclear expression of a MKL1 variant devoid of the actin-binding domain (MKL1 ΔN200). We characterized the adaptive changes that occur during the MKL1-induced cellular model and focused on regulation of translation machinery and metabolic adaptation. METHODS: We performed a genome-wide analysis at the transcriptional and translational level using ribosome profiling complemented with RNA-Seq and analyzed the expression of components of the translation machinery and enzymes involved in energy metabolism. NGS data were correlated with metabolomic measurements and quantification of specific mRNAs extracted from polysomes and western blots. RESULTS: Our results reveal the expression profiles of a luminal to basal-like state in accordance with an epithelial to mesenchymal transition. During the transition, the synthesis of ribosomal proteins and that of many translational factors was upregulated. This overexpression of the translational machinery appears to be regulated at the translational level. Our results indicate an increase of ribosome biogenesis and translation activity. We detected an extensive metabolic rewiring occurring in an already "Warburg-like" context, in which enzyme isoform switches and metabolic shunts indicate a crucial role of HIF-1α along with other master regulatory factors. Furthermore, we detected a decrease in the expression of enzymes involved in ribonucleotide synthesis from the pentose phosphate pathway. During this transition, cells increase in size, downregulate genes associated with proliferation, and strongly upregulate expression of cytoskeletal and extracellular matrix genes. CONCLUSIONS: Our study reveals multiple regulatory events associated with metabolic and translational machinery adaptation during an epithelial mesenchymal-like transition process. During this major cellular transition, cells achieve a new homeostatic state ensuring their survival. This work shows that ribosome profiling complemented with RNA-Seq is a powerful approach to unveil in-depth global adaptive cellular responses and the interconnection among regulatory circuits, which will be helpful for identification of new therapeutic targets.

The use of Prevotella bryantii 3C5 for modulation of the ruminal environment in an ovine model.

In the Southern Hemisphere, ruminants are mostly raised in grazing systems where animals consume forage and are supplemented with low amounts of concentrates. Concentrates are usually given separately and are rapidly ingested. This practice leads to changing rumen environment conditions during the day, may alter the rumen microbial metabolism and could affect host performance. The native ruminal Prevotella bryantii strain 3C5 was administered every 48h to wethers under experimental conditions simulating Southern-Hemisphere feeding to evaluate its potential as a rumen fermentation modulator. The inoculum potential was assessed on day 17. The ammonia nitrogen (NH3-N), volatile fatty acids and ruminal pH were monitored on a 24-h basis 19 days after the beginning of the experiment, and the microbial community structure was assessed by pyrosequencing. The administration of P. bryantii modified the fermentation products and daily pH values compared to the control. The NH3-N concentration in the rumen of treated animals was significantly higher than that of the untreated animals. Modification of the ruminal environment and fermentation pathways was achieved without altering the general structure of the microbial community or the potential methane production. P. bryantii 3C5 could be considered in potential probiotic formulations for ruminants in semi-intensive systems.

The use of Prevotella bryantii 3C5 for modulation of the ruminal environment in an ovine model

Abstract In the Southern Hemisphere, ruminants are mostly raised in grazing systems where animals consume forage and are supplemented with low amounts of concentrates. Concentrates are usually given separately and are rapidly ingested. This practice leads to changing rumen environment conditions during the day, may alter the rumen microbial metabolism and could affect host performance. The native ruminal Prevotella bryantii strain 3C5 was administered every 48 h to wethers under experimental conditions simulating Southern-Hemisphere feeding to evaluate its potential as a rumen fermentation modulator. The inoculum potential was assessed on day 17. The ammonia nitrogen (NH3-N), volatile fatty acids and ruminal pH were monitored on a 24-h basis 19 days after the beginning of the experiment, and the microbial community structure was assessed by pyrosequencing. The administration of P. bryantii modified the fermentation products and daily pH values compared to the control. The NH3-N concentration in the rumen of treated animals was significantly higher than that of the untreated animals. Modification of the ruminal environment and fermentation pathways was achieved without altering the general structure of the microbial community or the potential methane production. P. bryantii 3C5 could be considered in potential probiotic formulations for ruminants in semi-intensive systems.

The use of Prevotella bryantii 3C5 for modulation of the ruminal environment in an ovine model

Abstract In the Southern Hemisphere, ruminants are mostly raised in grazing systems where animals consume forage and are supplemented with low amounts of concentrates. Concentrates are usually given separately and are rapidly ingested. This practice leads to changing rumen environment conditions during the day, may alter the rumen microbial metabolism and could affect host performance. The native ruminal Prevotella bryantii strain 3C5 was administered every 48 h to wethers under experimental conditions simulating Southern-Hemisphere feeding to evaluate its potential as a rumen fermentation modulator. The inoculum potential was assessed on day 17. The ammonia nitrogen (NH3-N), volatile fatty acids and ruminal pH were monitored on a 24-h basis 19 days after the beginning of the experiment, and the microbial community structure was assessed by pyrosequencing. The administration of P. bryantii modified the fermentation products and daily pH values compared to the control. The NH3-N concentration in the rumen of treated animals was significantly higher than that of the untreated animals. Modification of the ruminal environment and fermentation pathways was achieved without altering the general structure of the microbial community or the potential methane production. P. bryantii 3C5 could be considered in potential probiotic formulations for ruminants in semi-intensive systems.

In vitro activity and mode of action of distamycin analogues against African trypanosomes.

Distamycin, a natural polyamide containing three heterocycle rings with a polar end, has inspired several groups to prepare synthetic analogues, which proved to have anti-trypanosomal and anti-tumoral activity. We describe the synthesis of bi and tri thiazoles amides that harbor different substitutions at their ends and the evaluation of their anti-Trypanosoma brucei activity. The most active compound 10b showed better biological activity (EC50 310 nM and selectivity index 16) than the control drug nifurtimox (EC50 15 µM and selectivity index 10). Studies on the mode of action show that the parasiticidal activity of 10b originates from disruption of lysosomal homeostasis, which is followed by release of redox active iron, an increase in oxidizing species and collapse of cell membrane integrity. In this respect, our study suggests that non-charged lipophylic distamycins destabilize cell membranes.

HT-29 and Caco-2 reporter cell lines for functional studies of nuclear factor kappa B activation.

The NF-κB is a transcription factor which plays a key role in regulating biological processes. In response to signals, NF-κB activation occurs via phosphorylation of its inhibitor, which dissociates from the NF-κB dimer allowing the translocation to the nucleus, inducing gene expression. NF-κB activation has direct screening applications for drug discovery for several therapeutic indications. Thus, pathway-specific reporter cell systems appear as useful tools to screen and unravel the mode of action of probiotics and natural and synthetic compounds. Here, we describe the generation, characterization, and validation of human epithelial reporter cell lines for functional studies of NF-κB activation by different pro- and anti-inflammatory agents. Caco-2 and HT-29 cells were transfected with a pNF-κB-hrGFP plasmid which contains the GFP gene under the control of NF-κB binding elements. Three proinflammatory cytokines (TNF-α, IL-1ß, and LPS) were able to activate the reporter systems in a dose-response manner, which corresponds to the activation of the NF-κB signaling pathway. Finally, the reporter cell lines were validated using lactic acid bacteria and a natural compound. We have established robust Caco-2-NF-κB-hrGFP and HT-29-NF-κB-hrGFP reporter cell lines which represent a valuable tool for primary screening and identification of bacterial strains and compounds with a potential therapeutic interest.

Effect of native Lactobacillus murinus LbP2 administration on total fecal IgA in healthy dogs.

The objective of the present work was to determine the effect of Lactobacillus murinus strain LbP2 on canine fecal immunoglobulin A (IgA) levels. Seven dogs were orally treated with a 3-mL suspension of L. murinus LbP2 containing 5 × 10(9) colony-forming units on alternate days for 2 wk. Six dogs were treated with 3 mL of phosphate-buffered saline as placebo. Fecal samples were taken from the rectal ampulla on days 0 and 16, and the total canine fecal IgA concentration was determined with an immunoperoxidase assay kit. The IgA levels of individual dogs were compared with the nonparametric Wilcoxon test. Differences were considered significant when the P-value was less than 0.05. An increase in the total fecal IgA concentration was observed in the 7 dogs after treatment with L. murinus LbP2 (P = 0.01796). No differences were detected between the initial total fecal IgA values and those obtained at the end of placebo treatment. Thus, after oral administration L. murinus LbP2 showed potential immunomodulatory effects, an important property to assess in a microorganism being considered for use as a probiotic.

L'objectif de la présente étude était de déterminer l'effet de la souche Lactobacillus murinus LbP2 sur les niveaux d'immunoglobulines A (IgA) fécales chez le chien. Sept chiens ont reçu oralement 3 mL d'une suspension de L. murinus LbP2 contenant 5 × 109 unités formatrices de colonies à chaque 2 jours pendant 2 semaines. Six chiens ont reçu 3 mL de saline tamponnée comme placebo. Des échantillons de fèces ont été prélevés au niveau de l'ampoule rectale aux jours 0 et 16, et la concentration d'IgA canine totale déterminée au moyen d'une épreuve d'immunoperoxydase. Les niveaux d'IgA des chiens individuels ont été comparés avec le test non-paramétrique de Wilcoxon. Les différences étaient considérées significatives lorsque la valeur de P était inférieure à 0,05. Une augmentation dans la concentration d'IgA fécale totale a été observée dans les sept chiens après traitement avec L. murinus LbP2 (P = 0,01796). Aucune différence ne fut détectée entre les valeurs initiales des IgA fécales totales et celles à la fin du traitement avec le placebo. Ainsi, l'administration orale de L. murinus LbP2 montre des effets immunomodulateurs potentiels, une propriété intéressante à évaluer chez un microorganisme considéré pour usage comme probiotique.(Traduit par Docteur Serge Messier).

In vitro activity of potential probiotic Lactobacillus murinus isolated from the dog.

AIMS: The aim of this study was to isolate and identify Lactobacillus spp. isolates from faeces of a healthy dog, and to characterize their potential as probiotics in order to evaluate their possible use as probiotics for dogs. METHODS AND RESULTS: An in vitro approach was used to characterize the isolates as potential probiotics including the evaluation of pH and bile salts tolerance, production of antimicrobial substances, biofilm formation on glass and polystyrene surfaces, aggregation ability and adhesion to canine intestinal mucus. The isolates survived to different pH and bile salts conditions, inhibited the in vitro growth of Escherichia coli and Clostridium perfringens, and adhered to glass and intestinal mucus. CONCLUSIONS: The properties shown by these isolates may indicate that they could colonize and persist in the gastrointestinal tract and induce beneficial effects to the host. SIGNIFICANCE AND IMPACT OF STUDY: The evaluation of native canine isolates and future experimental feeding assays may be useful tools to develop probiotics to improve animal health and reduce the risk of gastrointestinal disorders.

Vaginal lactic acid bacteria in the mare: evaluation of the probiotic potential of native Lactobacillus spp. and Enterococcus spp. strains.

Lactic acid bacteria (LAB) are important members of the human vaginal microbiota and their presence is considered beneficial. However, little is known about native vaginal bacteria in other animal species such as the horse. The aim of this work was to quantify the vaginal lactic acid bacteria and lactobacilli of mares and to establish if selected equine vaginal lactic acid bacteria, particularly Lactobacillus and Enterococcus spp. strains, could exhibit potential as probiotics. The vaginal lactic acid bacteria and lactobacilli of 26 mares were quantified by plate counts. Five strains (three Lactobacillus spp. and two Enterococcus spp.) were characterised and adhesion to vaginal epithelial cells, antimicrobial activity and ability to form biofilms were evaluated. Lactic acid bacteria were recovered from the 26 samples and lactobacilli counts were detected in 18 out of 26 mares (69%). Probiotic properties tested in this study varied among the isolates and showed promising features for their use as equine probiotics.

Vaginal lactic acid bacteria in healthy and ill bitches and evaluation of in vitro probiotic activity of selected isolates.

The concentrations of lactic acid bacteria (LAB) in 42 vaginal samples from healthy and ill bitches were determined. Eight isolates belonging to the genera Lactobacillus and Enterococcus were selected and identified and their in vitro antimicrobial activity against canine pathogens and their ability to adhere to canine vaginal epithelial cells were determined. There was no correlation between the concentrations of vaginal LAB and clinical status, body temperature, vaginal pH, or age. Although the animals were either well or suffering from various illnesses, LAB were found in almost every sample, and the selected isolates showed promising probiotic-related features. These findings are significant for the design of strategies for the modulation of vaginal microbiota by vaginal LAB isolates.