A5054067127- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Mosquito-borne diseases and control
- Enzyme Structure and Function
- Glycosylation and Glycoproteins Research
- Bacteriophages and microbial interactions
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Trypanosoma species research and implications
- Carbohydrate Chemistry and Synthesis
- 3D Printing in Biomedical Research
- Cannabis and Cannabinoid Research
- Pharmacogenetics and Drug Metabolism
- Trace Elements in Health
- Drug-Induced Hepatotoxicity and Protection
- Pharmacological Effects of Natural Compounds
- Spectroscopy and Quantum Chemical Studies
- Peptidase Inhibition and Analysis
- Alcohol Consumption and Health Effects
- Prion Diseases and Protein Misfolding
- Galectins and Cancer Biology
- Immune Response and Inflammation
- Virology and Viral Diseases
- Neurological diseases and metabolism
- Machine Learning in Bioinformatics
- Biochemical and Molecular Research
Universidade de São Paulo
2012-2022
Brazilian Center for Research in Energy and Materials
2020-2022
Brazilian Biosciences National Laboratory
2020-2022
Universidade de Ribeirão Preto
2017-2022
Uppsala University
2019
SUPERA Park of Innovation and Technology of Ribeirão Preto
2015
The Zika virus (ZIKV) is an arthropod-borne that belongs to the Flaviviridae family. ZIKV infection usually asymptomatic or associated with mild clinical manifestations; however, increased numbers of cases microcephaly and birth defects have been recently reported. To date, neither a vaccine nor antiviral treatment has become available control replication. Among natural compounds recognized for their medical properties, flavonoids, which can be found in fruits vegetables, possess biological...
The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over last decade for certain classes targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During collaboration, laboratories simultaneously competing with each other. Here, we present first attempt at "coopetition" in scientific research applied and refinement problems....
Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In data science era, structural biology has benefited from increasing availability biostructural due to advances determination and computational methods. this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated To fulfill need, we developed pyKVFinder, a Python package detect characterize structures for...
This work describes the synthesis of 1,2,3-triazole amino acid-derived-3-O-galactosides 1-6 and di-lactose-derived glycoconjugate 7 as potential galectin-3 inhibitors. The target compounds were synthesized by Cu(I)-catalyzed azide-alkyne cycloaddition reaction ('click chemistry') between azido-derived acids N3-ThrOBn, N3-PheOBn, N3-N-Boc-TrpOBn, N3-N-Boc-LysOBn, N3-O-tBu-AspOBn N3-l-TyrOH, corresponding alkyne-based sugar 3-O-propynyl-GalOMe, well click chemistry azido-lactose 2-propynyl...
Biomolecular crowding affects the biophysical and biochemical behavior of macromolecules compared with dilute environment in experiments on isolated proteins. Computational modeling simulation are useful tools to study how structural dynamics biological properties macromolecules. With increases computational power, large-scale all-atom explicit-solvent models prokaryote cytoplasm have now become possible. In this work, we built an atomistic model Escherichia coli composed 1.5 million atoms...
Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test strengths and weaknesses their computational methods. CASP has significantly advanced field but many hurdles still remain, which may require new ideas collaborations. In 2012 a web-based effort called WeFold, was initiated promote collaboration within community attract researchers from other fields contribute CASP. Members WeFold coopetition...
Biological processes are regulated mainly by the binding of small molecules into cavities distributed throughout biomolecular structure. Computational tools to detect these have an essential role in rational drug design. With exponential availability high-order 3D atomic structures and large sets models, must balance accuracy speed. In this sense, we developed parKVFinder, a parallelized software for geometry-based cavity detection. Here, described its functionalities presented easy-to-use...
Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved vesiculation processes induced a cluster of envelope (E) membrane (M) proteins dengue virus (DENV) using molecular dynamics simulations coarse-grained model. show that an arrangement three E-M heterotetramers (EM3) works as bending unit ordered five such units generates closed vesicle, reminiscent budding...
To examine whether the hydroalcoholic extract from Baccharis dracunculifolia leaves (BdE) modulates human neutrophil oxidative metabolism, degranulation, phagocytosis and microbial killing capacity.In-vitro assays based on chemiluminescence, spectrophotometry, flow cytometry polarimetry were used, as well docking calculations.At concentrations that effectively suppressed metabolism elicited by soluble particulate stimuli (<10 μg/ml), without clear signs of cytotoxicity, BdE (1) inhibited...
Abstract This study presents the synthesis of novel protected O‐glycosylated amino acid derivatives 1 and 2 , containing βGalNAc‐SerOBn βGalNAc‐ThrOBn units, respectively, as mimetics natural Tn antigen (αGalNAc‐Ser/Thr), along with solid‐phase assembly glycopeptides NHAcSer‐Ala‐Pro‐Asp‐Thr[αGalNAc]‐Arg‐Pro‐Ala‐Pro‐Gly‐BSA ( 3 ‐BSA) NHAcSer‐Ala‐Pro‐Asp‐Thr[βGalNAc]‐Arg‐Pro‐Ala‐Pro‐Gly‐BSA 4 ‐BSA), bearing αGalNAc‐Thr or βGalNAc‐Thr MUC1 tumor mucin glycoproteins. According to ELISA tests,...
The Protein Structure Prediction (PSP) problem is concerned about the prediction of native structure a protein from its amino acid sequence. PSP challenging and computationally open problem. Therefore, several researches methodologies have been developed for it. This paper presents application protpred-GROMACS, an evolutionary framework PSP, in structural energetic contexts. performance mono-objective algorithm was compared with other methodologies, such as multi-objective algorithm, coarse...
The Protein Structure Prediction (PSP) problem is concerned about the prediction of native tertiary structure a protein in respect to its amino acids sequence. PSP challenging and computationally open problem. Therefore, several researches methodologies have been developed for it. In this way, developers are working integrate frameworks order improve their capabilities make use more straightforward. This paper presents application NSGA-II algorithm using structural energetic properties...
The recently introduced microphysiological systems (MPS) cultivating human organoids are expected to perform better than animals in the preclinical tests phase of drug developing process because they genetically and recapitulate interplay among tissues. In this study, intestinal barrier (emulated by a co-culture Caco-2 HT-29 cells) liver equivalent spheroids made differentiated HepaRG cells hepatic stellate were integrated into two-organ chip (2-OC) microfluidic device assess some...
The recently introduced microphysiological systems (MPS) cultivating human organoids are expected to perform better than animals in the preclinical tests phase of drug developing process because they genetically and recapitulate interplay among tissues. In this study, intestinal barrier (emulated by a co-culture Caco-2 HT-29 cells) liver equivalent spheroids made differentiated HepaRG cells hepatic stellate were integrated into two-organ chip (2-OC) microfluidic device assess some...
Abstract Prion disease is caused by the misfolding of cellular prion protein, PrP C , into a self-templating conformer, Sc . Nuclear magnetic resonance (NMR) and X-ray crystallography revealed 3D structure globular domain possibility its dimerization via an interchain disulfide bridge that forms due to swap or non-covalent association two monomers. On contrary, composed complex heterogeneous ensemble poorly defined conformations quaternary arrangements are related different patterns...
Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to dilute environment present in experiments made with isolated proteins. Computational modeling simulation are useful tools study how structural dynamics biological properties macromolecules. As computational power increased, simulating large scale all-atom explicit solvent models prokaryote cytoplasm become possible. In this work, we build an atomistic model Escherichia coli composed...
Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to dilute environment present in experiments made with isolated proteins. Computational modeling simulation are useful tools study how structural dynamics biological properties macromolecules. As computational power increased, simulating large scale all-atom explicit solvent models prokaryote cytoplasm become possible. In this work, we build an atomistic model Escherichia coli composed...