Browsing by Author "Alves, Alexessander Couto"
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- Identifying 124 new anti-HIV drug candidates in a 37 billion-compound database: an integrated approach of machine learning (QSAR), molecular docking, and molecular dynamics simulationPublication . Cobre, Alexandre de Fátima; Ara, Anderson; Alves, Alexessander Couto; Neto, Moisés Maia; Fachi, Mariana Millan; Beca, Laize Botas; Tonin, Fernanda; Pontarolo, RobertoRecent data from the World Health Organization reveals that in 2023, 38.8 million people were living with HIV. Within this population, there were 1.5 million new cases and 650 thousand deaths attributed to the disease. This study employs an integrated approach involving QSAR-based machine learning models, molecular docking, and molecular dynamics simulations to identify potential compounds for inhibiting the bioactivity of the CC chemokine receptor type 5 (CCR5) protein, a key entry point for HIV. Using non-redundant experimental data from the CHEMBL database, 40 different machine learning algorithms were trained and the top four models (XGBoost, Histogram gradient Boosting, Light Gradient Boosted Machine, and Extra Trees Regression) were utilized to predict anti-HIV bioactivity for 37 billion compounds in the ZINC-22 database. The screening resulted in the identification of 124 new anti-HIV drug candidates, confirmed through molecular docking and dynamics simulations. The study underscores the therapeutic potential of these compounds, paving the way for further in vitro and in vivo investigations. The convergence of machine learning and experimental findings presents a promising avenue for significant advancements in pharmaceutical research, particularly in the treatment of viral diseases such as HIV. To guarantee the reproducibility of our study, we have made the Python code (Google Collab) and the associated database available on GitHub. You can access them through the following link: GitHub Link: https://github.com/AlexandreCOBRE/code
- Novel COVID-19 biomarkers identified through multi-omics data analysis: N-acetyl-4-O-acetylneuraminic acid, N-acetyl-L-alanine, N-acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristatePublication . Cobre, Alexandre de Fátima; Alves, Alexessander Couto; Gotine, Ana Raquel; Domingues, Karime Zeraik; Lazo, Raul Edison; Ferreira, Luana Mota; Tonin, Fernanda; Pontarolo, RobertoThis study aims to apply machine learning models to identify new biomarkers associated with the early diagnosis and prognosis of SARS-CoV-2 infection. Plasma and serum samples from COVID-19 patients (mild, moderate, and severe), patients with other pneumonia (but with negative COVID-19 RT-PCR), and healthy volunteers (control) from hospitals in four different countries (China, Spain, France, and Italy) were analyzed by GC-MS, LC-MS, and NMR. Machine learning models (PCA and PLS-DA) were developed to predict the diagnosis and prognosis of COVID-19 and identify biomarkers associated with these outcomes. A total of 1410 patient samples were analyzed. The PLS-DA model presented a diagnostic and prognostic accuracy of around 95% of all analyzed data. A total of 23 biomarkers (e.g., spermidine, taurine, L-aspartic, L-glutamic, L-phenylalanine and xanthine, ornithine, and ribothimidine) have been identified as being associated with the diagnosis and prognosis of COVID-19. Additionally, we also identified for the first time five new biomarkers (N-Acetyl-4-O-acetylneuraminic acid, N-Acetyl-L-Alanine, N-Acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate) that are also associated with the severity and diagnosis of COVID-19. These five new biomarkers were elevated in severe COVID-19 patients compared to patients with mild disease or healthy volunteers. The PLS-DA model was able to predict the diagnosis and prognosis of COVID-19 around 95%. Additionally, our investigation pinpointed five novel potential biomarkers linked to the diagnosis and prognosis of COVID-19: N-Acetyl-4-O-acetylneuraminic acid, N-Acetyl-L-Alanine, N-Acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate. These biomarkers exhibited heightened levels in severe COVID-19 patients compared to those with mild COVID-19 or healthy volunteers.