Bambu and its applications in the discovery of active molecules against melanoma.

PURPOSE OR OBJECTIVE: Melanoma is one of the most dangerous forms of skin cancer and the discovery of novel drugs is an ongoing effort. Quantitative Structure Activity Relationship (QSAR) is a computational method that allows the estimation of the properties of a molecule, including its biological activity. QSAR models have been widely employed in the search for potential drug candidates, but also for agrochemicals and other molecules with applications in different branches of the industry. Here we present Bambu, a simple command line tool to generate QSAR models from high-throughput screening bioassays datasets. METHODS: The tool was developed using the Python programming language and relies mainly on RDKit for molecule data manipulation, FLAML for automated machine learning and the PubChem REST API for data retrieval. As a proof-of-concept we have employed the tool to generate QSAR models for melanoma cell growth inhibition based on HTS data and used them to screen libraries of FDA-approved drugs and natural compounds. Additionally, Bambu was compared to QSAR-Co, another automated tool for QSAR model generation. RESULTS: based on the developed tool we were able to produce QSAR models and identify a wide variety of molecules with potential melanoma cell growth inhibitors, many of which with anti-tumoral activity already described. The QSAR models are available through the URL http://caramel.ufpel.edu.br, and all data and code used to generate its models are available at Zenodo (https://doi.org/10.5281/zenodo.7495214). Bambu source code is available at GitHub (https://github.com/omixlab/bambu-v2). In the benchmark, Bambu was able to produce models with higher accuracy, recall, F1 and ROC AUC when compared to QSAR-Co for the selected datasets. CONCLUSIONS: Bambu is an free and open source tool which facilitates the creation of QSAR models and can be futurely applied in a wide variety of drug discovery projects.

Functional training improves peak oxygen consumption and quality of life of individuals with heart failure: a randomized clinical trial.

BACKGROUND: Functional training may be an effective non-pharmacological therapy for heart failure (HF). This study aimed to compare the effects of functional training with strength training on peak VO2 and quality of life in individuals with HF. METHODS: A randomized, parallel-design and examiner-blinded controlled clinical trial with concealed allocation, intention-to-treat and per-protocol analyses. Twenty-seven participants with chronic HF were randomly allocated to functional or strength training group, to perform a 12-week physical training, three times per week, totalizing 36 sessions. Primary outcomes were the difference on peak VO2 and quality of life assessed by cardiopulmonary exercise testing and Minnesota Living with Heart Failure Questionnaire, respectively. Secondary outcomes included functionality assessed by the Duke Activity Status Index and gait speed test, peripheral and inspiratory muscular strength, assessed by hand grip and manovacuometry testing, respectively, endothelial function by brachial artery flow-mediated dilation, and lean body mass by arm muscle circumference. RESULTS: Participants were aged 60 ± 7 years, with left ventricular ejection fraction 29 ± 8.5%. The functional and strength training groups showed the following results, respectively: peak VO2 increased by 1.4 ± 3.2 (16.9 ± 2.9 to 18.6 ± 4.8 mL.kg-1.min-1; p time = 0.011) and 1.5 ± 2.5 mL.kg-1.min-1 (16.8 ± 4.0 to 18.6 ± 5.5 mL.kg-1.min-1; p time = 0.011), and quality of life score decreased by 14 ± 15 (25.8 ± 14.8 to 10.3 ± 7.8 points; p time = 0.001) and 12 ± 28 points (33.8 ± 23.8 to 19.0 ± 15.1 points; p time = 0.001), but no difference was observed between groups (peak VO2: p interaction = 0.921 and quality of life: p interaction = 0.921). The functional and strength training increased the activity status index by 6.5 ± 12 and 5.2 ± 13 points (p time = 0.001), respectively, and gait speed by 0.2 ± 0.3 m/s (p time = 0.002) in both groups. CONCLUSIONS: Functional and strength training are equally effective in improving peak VO2, quality of life, and functionality in individuals with HF. These findings suggest that functional training may be a promising and innovative exercise-based strategy to treat HF. TRIAL REGISTRATION: NCT03321682. Registered date: 26/10/2017.

Chemoprotection mediated by açaí berry (Euterpe oleracea) in white shrimp Litopenaeus vannamei exposed to the cyanotoxin saxitoxin analyzed by in vivo assays and docking modeling.

Saxitoxin (STX) is a neurotoxic cyanotoxin that also generate reactive oxygen species, leading to a situation of oxidative stress and altered metabolism. The Amazonian fruit açaí Euterpe oleracea possesses a high concentration of antioxidant molecules, a fact that prompted us to evaluate its chemoprotection activity against STX toxicity (obtained from samples of Trichodesmium sp. collected in the environment) in the shrimp Litopenaeus vannamei. For 30 days, shrimps were maintained in 16 aquaria containing 10 shrimps (15% salinity, pH 8.0, 24 °C, 12C/12D photoperiod) and fed twice daily with a diet supplemented with lyophilized açaí pulp (10%), in addition to the control diet. After, shrimps (7.21 ± 0.04 g) were exposed to the toxin added to the feed for 96 h. Four treatments were defined: CTR (control diet), T (lyophilized powder of Trichodesmium sp. 0.8 µg/g), A (10% of açaí) and the combination T + A. HPLC analysis showed predominance of gonyautoxin-1 concentrations (GTX-1) and gonyautoxin-4 concentrations (GTX-4). The results of molecular docking simulations indicated that all variants of STX, including GTX-1, can be a substrate of isoform mu of the glutathione-S-transferase (GST) enzyme since these molecules obtained similar values of estimated Free Energy of Binding (FEB), as well as similar final positions on the binding site. GSH levels were reduced in muscle tissues of shrimp in the T, A, and T + A treatments. Increased GST activity was observed in shrimp hepatopancreas of the T treatment and the gills of the A and T + A treatments. A decrease of protein sulfhydryl groups (P-SH) was observed in gills of shrimps from T + A treatment. A reduction in malondialdehyde (MDA) levels was registered in the hepatopancreas of the T + A treatment in respect to the Control, T, and A treatments. The use of açaí supplements in L. vannamei feed was able to partially mitigate the toxic effects caused by Trichodesmium sp. extracts, and points to mu GST isoform as a key enzyme for saxitoxin detoxification in L. vannamei, an issue that deserves further investigation.

E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces.

Background: The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods: Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results: The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion: Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1'/ß1', as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve.

A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers.

The main-protease (Mpro) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (MCoV2pro) with 12 mutations compared to SARS-CoV (MCoV1pro). Recent studies point out that these subtle differences lead to mobility variances at the active site loops with functional implications. We use metadynamics simulations and a sort of computational analysis to probe the dynamic, pharmacophoric and catalytic environment differences between the monomers of both enzymes. So, we verify how much intrinsic distinctions are preserved in the functional dimer of MCoV2pro, as well as its implications for ligand accessibility and optimized drug screening. We find a significantly higher accessibility to open binding conformers in the MCoV2pro monomer compared to MCoV1pro. A higher hydration propensity for the MCoV2pro S2 loop with the A46S substitution seems to exercise a key role. Quantum calculations suggest that the wider conformations for MCoV2pro are less catalytically active in the monomer. However, the statistics for contacts involving the N-finger suggest higher maintenance of this activity at the dimer. Docking analyses suggest that the ability to vary the active site width can be important to improve the access of the ligand to the active site in different ways. So, we carry out a multiconformational virtual screening with different ligand bases. The results point to the importance of taking into account the protein conformational multiplicity for new promissors anti MCoV2pro ligands. We hope these results will be useful in prospecting, repurposing and/or designing new anti SARS-CoV-2 drugs.Communicated by Ramaswamy H. Sarma.

Response to Awake Prone Position in Nonintubated Individuals With COVID-19.

BACKGROUND: Prone positioning is used for patients with ARDS undergoing invasive mechanical ventilation; its effectiveness in nonventilated awake patients is unclear. We aimed to evaluate the effectiveness of the prone maneuver in decreasing the risk of intubation and increasing the odds of favorable events. METHODS: We prospectively evaluated 66 subjects with COVID-19-related moderate ARDS who were admitted to the ICU; treated with high-flow nasal cannula, noninvasive ventilation, a reservoir mask, or a nasal cannula; and subjected to awake prone maneuvers from March 1, 2020-August 30, 2020. The following factors were recorded at ICU admission: age, sex, prior illness, simplified acute physiology score 3, body mass index, and changes in gas exchange after and before prone positioning. Subjects were divided into a group of responders and nonresponders according to a 20% increase in the [Formula: see text]/[Formula: see text] ratio before and after the maneuver. The need for intubation within 48 h of the start of the maneuver was also evaluated. We also analyzed the differences in mortality, ICU length of stay, hospital length of stay, and duration of mechanical ventilation. A generalized estimating equation model was applied to preprone and postprone means. To control for confounding factors, multivariate Poisson regression was applied. RESULTS: Forty-one subjects age 54.1 y ± 12.9 were enrolled. Responders showed increased [Formula: see text] (P < .001), [Formula: see text] (P < .001), and [Formula: see text]/[Formula: see text] ratios (P < .001) with the maneuver and reduced breathing frequency. Responders had shorter lengths of stay in the ICU (P < .001) and hospital (P < .003), lower intubation rates at 48 h (P < .012), fewer days of ventilation (P < .02), and lower mortality (P < .001). Subjects who responded to the maneuver had a 54% reduction in the risk of ventilation and prolonged stay in the ICU. CONCLUSIONS: Among the responders to prone positioning, there were fewer deaths, shorter duration of mechanical ventilation, shorter ICU length of stay, and shorter hospital length of stay.

Phylogenetic analysis, computer modeling and catalytic prediction of an Amazonian soil ß-glucosidase against a soybean saponin.

Saponins are amphipathic glycosides with detergent properties present in vegetables. These compounds, when ingested, can cause difficulties in absorbing nutrients from food and even induce inflammatory processes in the intestine. There is already some evidence that saponins can be degraded by ß-glucosidases of the GH3 family. In the present study, we evaluated, through computational tools, the possibility of a ß-glucosidase (AMBGL17) obtained from a metagenomic analysis of the Amazonian soil, to catalytically interact with a saponin present in soybean. For this, the amino acid sequence of AMBGL17 was used in a phylogenetic analysis to estimate its origin and to determine its three-dimensional structure. The 3D structure of the enzyme was used in a molecular docking analysis to evaluate its interaction with soy saponin as a ligand. The results of the phylogenetic analysis showed that AMBGL17 comes from a microorganism of the phylum Chloroflexi, probably related to species of the order Aggregatinales. Molecular docking showed that soybean saponin can interact with the catalytic site of AMBGL17, with the amino acid GLY345 being important in this catalytic interaction, especially with a ß-1,2 glycosidic bond present in the carbohydrate portion of saponin. In conclusion, AMBGL17 is an enzyme with interesting biotechnological potential in terms of mitigating the anti-nutritional and pro-inflammatory effects of saponins present in vegetables used for human and animal food.

Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates.

Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure, abandonment or disease recurrence. It is therefore important to understand the evolutionary process of drug resistance in Mycobacterium tuberculosis. We here in describe the microevolution of drug resistance in serial isolates from six previously treated patients. Drug resistance was initially investigated through phenotypic methods, followed by genotypic approaches. The use of whole-genome sequencing allowed the identification of mutations in the katG, rpsL and rpoB genes associated with drug resistance, including the detection of rare mutations in katG and mixed populations of strains. Molecular docking simulation studies of the impact of observed mutations on isoniazid binding were also performed. Whole-genome sequencing detected 266 single nucleotide polymorphisms between two isolates obtained from one patient, suggesting a case of exogenous reinfection. In conclusion, sequencing technologies can detect rare mutations related to drug resistance, identify subpopulations of resistant strains, and identify diverse populations of strains due to exogenous reinfection, thus improving tuberculosis control by guiding early implementation of appropriate clinical and therapeutic interventions.

Relation between ABCB1 overexpression and COX2 and ALOX5 genes in human erythroleukemia cell lines.

This study aimed to characterize the relationship between the COX2 and ALOX5 genes, as well as their link with the multidrug resistance (MDR) phenotype in sensitive (K562) and MDR (K562-Lucena and FEPS) erythroleukemia cells. For this, the inhibitors of 5-LOX (zileuton) and COX-2 (acetylsalicylic acid-ASA) and cells with the silenced ABCB1 gene were used. The treatment with ASA caused an increase in the gene expression of COX2 and ABCB1 in both MDR cell lines, and a decrease in the expression of ALOX5 in the FEPS cells. Silencing the ABCB1 gene induced a decrease in COX2 expression and an increase in the ALOX5 gene. Treatment with zileuton did not alter the expression of COX2 and ABCB1. Cytometry data showed that there was an increase in ABCB1 protein expression after exposure to ASA. In addition, the increased activity of ABCB1 in the K562-Lucena cell line indicates that ASA may be a substrate for this efflux pump, corroborating the molecular docking that showed that ASA can bind to ABCB1. Regardless of the genetic alteration in COX2 and ABCB1, the direct relationship between these genes and the inverse relationship with ALOX5 remained in the MDR cell lines. We assume that ABCB1 can play a regulatory role in COX2 and ALOX5 during the transformation of the parental cell line K562, explaining the increased gene expression of COX2 and decreased ALOX5 in the MDR cell lines.

Mefloquine synergism with anti-tuberculosis drugs and correlation to membrane effects: Biologic, spectroscopic and molecular dynamics simulations studies.

Studies displaying the combination of mefloquine (MFL) with anti-tuberculosis (TB) substances are limited in the literature. In this work, the effect of MFL-association with two first-line anti-TB drugs and six fluoroquinolones was evaluated against Mycobacterium tuberculosis drug resistant strains. MFL showed synergistic interaction with isoniazid, pyrazinamide, and several fluoroquinolones, reaching fractional inhibitory concentration indexes (FICIs) ranging from 0.03 to 0.5. In order to better understand the observed results, two approaches have been explored: (i) spectroscopic responses attributed to the effect of MFL on physicochemical properties related to a liposomal membrane model composed by soybean asolectin; (ii) molecular dynamics (MD) simulation data regarding MFL interaction with a membrane model based on PIM2, a lipid constituent of the mycobacterial cell wall. FTIR and NMR data showed that MFL affects expressively the region between the phosphate and the first methylene groups of soybean asolectin membranes, disordering these regions. MD simulations results detected high MFL density in the glycolipid interface and showed that the drug increases the membrane lateral diffusion, enhancing its permeability. The obtained results suggest that synergistic activities related to MFL are attributed to its effect of lipid disorder and membrane permeability enhancement.

ABC proteins activity and cytotoxicity in zebrafish hepatocytes exposed to triclosan.

Chemicals such as triclosan are a concern because of their presence on daily products (soap, deodorant, hand sanitizers …), consequently this compound has an ubiquitous presence in the environment. Little is known about the effect of this bactericide on aquatic life. The aim of this study is to analyze triclosan exposure (24 h) to an in vitro model, zebrafish hepatocytes cell line (ZF-L), if it can be cytotoxic (mitochondrial activity, membrane stability and apoptosis) and if can activate ATP-binding cassette (ABC) proteins (activity, expression and protein/compound affinity). Triclosan was cytotoxic to hepatocytes when exposed to concentrations (1-4 mg/L). The results showed impaired mitochondria function, as well, plasma membrane rupture and an increase of apoptotic cells. We observed an ABC proteins activity inhibition in cells exposed to 0.5 and 1 mg/L. When ABCBs and ABCC2 proteins expression were analyzed, there was an increase of protein expression in both ABC proteins families on cells exposed to 1 mg/L of triclosan. On molecular docking results, triclosan and the fluorescent used as substrate (rhodamine) presented high affinity with all ABC proteins family tested, showing a greater affinity with ABCC2. In conclusion, this study showed that triclosan can be cytotoxic to ZF-L. Molecular docking indicated high affinity between triclosan and the tested pumps.

KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions.

MOTIVATION: Despite the progress made in studying protein-ligand interactions and the widespread application of docking and affinity prediction tools, improving their precision and efficiency still remains a challenge. Computational approaches based on the scoring of docking conformations with statistical potentials constitute a popular alternative to more accurate but costly physics-based thermodynamic sampling methods. In this context, a minimalist and fast sidechain-free knowledge-based potential with a high docking and screening power can be very useful when screening a big number of putative docking conformations. RESULTS: Here, we present a novel coarse-grained potential defined by a 3D joint probability distribution function that only depends on the pairwise orientation and position between protein backbone and ligand atoms. Despite its extreme simplicity, our approach yields very competitive results with the state-of-the-art scoring functions, especially in docking and screening tasks. For example, we observed a twofold improvement in the median 5% enrichment factor on the DUD-E benchmark compared to Autodock Vina results. Moreover, our results prove that a coarse sidechain-free potential is sufficient for a very successful docking pose prediction. AVAILABILITYAND IMPLEMENTATION: The standalone version of KORP-PL with the corresponding tests and benchmarks are available at https://team.inria.fr/nano-d/korp-pl/ and https://chaconlab.org/modeling/korp-pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.