Leandro Oliveira Bortot Email & Phone Number

Campinas, São Paulo, Brasil

Responsible for the coordination, planning, execution and analysis of: (i) virtual screening assays to identify molecules that have high potential of interacting with molecular targets that have therapeutical potential; (ii) molecular dynamics simulations to solve problems related to the elucidation of ligand-receptor interaction modes or conformational changes.

Campinas, São Paulo, Brasil

• Implemented of an automated pipeline to execute, refine and analyze virtual screening assays that combines molecular dynamics simulations, docking and algorithms which were developed by our group (AutoDock Vina, AmberTools, GROMACS, Python, ArgParse, RdKit, OpenBabel, PyMOL). • Trained deep neural networks with data from molecular dynamics trajectories to build models that predict pharmacokinetic properties of drug candidate molecules (AmberTools, GROMACS, Python, SciKit-Learn, Keras, TensorFlow). • Trained more than 1 million neural network models to optimize its hyperparameters using parallel and distributed computing in clusters (Python, MultiProcessing, Jupyter NoteBooks, MatPloLlib, SeaBorn). • Obtained prediction error (RMSE and MSE) slightly smaller than the best model that was already published in the literature to predict pharmacokinetics properties of molecules that are drug or cosmetic candidates using deep neural networks with the fully connected and convolutional architectures (Python, NumPy, SKLearn, Keras/TensorFlow, RdKit, Mordred). • Mined an online database to build a dataset with more than 100,000 entries about toxicity of molecules (Python, BeautifulSoup4, Pandas).

Ribeirão Preto, São Paulo, Brazil

• Accelerated some structural analyzes that are performed by the research group by at least 16x using distributed computing (Python, MultiProcessing). • Accepted as Voluntary Teacher by Cursinho Popular Hypatia de Exatas (CPHE) from the Faculty of Philosophy, Sciences and Literature of Ribeirão Preto - University of São Paulo (FFCLRP -USP) after a teaching test and an interview. • Solved problems that the team was facing by performing structural bioinformatics analyzes of hundreds of 3D protein structures (Python, PyMOL). • Described the dynamic properties of new oligomeric forms of the human prion protein from a 3D structure that was determined by the research group under a novel crystallization condition (GROMACS).

Ribeirão Preto, São Paulo, Brazil

• Described the molecular mechanism for the recognition of glycosylated pathogens by a human receptor which is present in cells of the immune system. • Discovered an active molecule using computational drug repositioning. • Obtained R$ 247,000.00 (equivalent to U$ 61,750.00 – U$ 82,333.33 at the time) in grants. • Worked as Teaching Assistant for the “Physics I” undergraduate course which was part of the Pharmacy & Biochemistry undergraduate degree offered by the School of Pharmaceutical Sciences of Ribeirão Preto - University of São Paulo (FCFRP-USP). • Co-supervised one student of the Undergraduate Research Internship Institutional Program. • Collaborated as a member of a multinational team of 76 researchers dedicated to the protein structure prediction problem in 2016 (WeFold, CASP12). • Developed a method that uses structure-based criteria to select the most promising ligand-receptor complexes among 11.7 million possibilities generated by virtual screening.

Uppsala, Sweden

• Employed three methods to calculate the interaction free energy (Umbrella Sampling, Jarzynski’s Equality and MM/PBSA) of a carbohydrate-lectin complex. • Modeled a heterogeneous biomolecular system with 1,5 million atoms that represents the bacterial cytoplasm and simulated its dynamics for 3 μs. • Used more than 1000 processing cores simultaneously with Beskow, the 61º fastest supercomputer of the world at the time. • Participated, as opponent, in a Master’s degree defense. • Validated a force field for membrane simulations with GROMACS.

Ribeirão Preto, São Paulo, Brazil

• Described the influence of different metals on the structural dynamics of a metalloprotein which is involved in the immune response.

Doctor Of Science, Pharmaceutical Sciences

Field: Biological Chemistry and Physics Research Internship Abroad at the University of Uppsala (Sweden) during 2016-2017.

Pós-Graduação Lato Sensu - Especialização, Educação Financeira

Pós-Graduação Lato Sensu - Mba, Análise De Ações E Finanças

Bachelor'S Degree, Pharmacy And Biochemistry