MusteR - Sistema de Mineração de Contatos em Complexos Proteína-Ligantes
Abstract
The COVID-19 pandemic has shown how high the demand is for computational tools that aid in the process of discovering new drugs. In this context, analyzing how ligands interact with a biomolecular target has proven valuable in identifying compounds with greater pharmacological potential. To this end, we propose MusteR, a web tool for mining contact pattern motifs between protein-ligand complexes, based on atomic packing density. Its use will be demonstrated in characterizing the complex between the drug Boceprevir and the Mpro protease, an important therapeutic target in the search for antivirals against SARS-CoV-2.References
Araujo, B. M., & da Silveira, C. H. (2019a). GAPIN: uma Ferramenta para Visualização e Análise de Redes de Interações Atômicas Intermoleculares [UFMG]. [link].
Araújo, B. M., Coelho, A. L., Silveira, S. A., Romanelli, J. P. R., de Melo-Minardi, R. C., & da Silveira, C. H. (2019b). GAPIN: Grouped and Aligned Protein Interface Networks. In bioRxiv (p. 520833). https://doi.org/https://doi.org/10.1101/520833
Baker, B. M., & Murphy, K. P. (1997). Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase. Journal of Molecular Biology, 268(2), 557–569. https://doi.org/10.1006/jmbi.1997.0977
Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B (2023). shiny: Web Application Framework for R. R package version 1.7.4.9002, https://shiny.rstudio.com/
Rego, N., & Koes, D. (2015). 3Dmol.js: Molecular visualization with WebGL. Bioinformatics, 31(8), 1322–1324. https://doi.org/10.1093/bioinformatics/btu829
Rocha, R. E. O., Chaves, E. J. F., Fischer, P. H. C., Costa, L. S. C., Barden, G. I., Cruz, L. E. G., Guedes, F. C., Silveira, C. H. da, Scotti, M. T., Camargo, A. D., Machado, K. S., Werhli, A. V, Ferreira, R., Rocha, G., & De Lima, L. H. F. (2021). 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. Journal of Biomolecular Structure and Dynamics, 0(0), 1–22. https://doi.org/10.1080/07391102.2021.1924271
Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in Biology and Medicine, 137(July), 104851. https://doi.org/10.1016/j.compbiomed.2021.104851
Su W, Johnston B (2023). r3dmol: Create Interactive 3D Visualizations of Molecular Data. R package version 0.2.0, https://github.com/swsoyee/r3dmol
Araújo, B. M., Coelho, A. L., Silveira, S. A., Romanelli, J. P. R., de Melo-Minardi, R. C., & da Silveira, C. H. (2019b). GAPIN: Grouped and Aligned Protein Interface Networks. In bioRxiv (p. 520833). https://doi.org/https://doi.org/10.1101/520833
Baker, B. M., & Murphy, K. P. (1997). Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase. Journal of Molecular Biology, 268(2), 557–569. https://doi.org/10.1006/jmbi.1997.0977
Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B (2023). shiny: Web Application Framework for R. R package version 1.7.4.9002, https://shiny.rstudio.com/
Rego, N., & Koes, D. (2015). 3Dmol.js: Molecular visualization with WebGL. Bioinformatics, 31(8), 1322–1324. https://doi.org/10.1093/bioinformatics/btu829
Rocha, R. E. O., Chaves, E. J. F., Fischer, P. H. C., Costa, L. S. C., Barden, G. I., Cruz, L. E. G., Guedes, F. C., Silveira, C. H. da, Scotti, M. T., Camargo, A. D., Machado, K. S., Werhli, A. V, Ferreira, R., Rocha, G., & De Lima, L. H. F. (2021). 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. Journal of Biomolecular Structure and Dynamics, 0(0), 1–22. https://doi.org/10.1080/07391102.2021.1924271
Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in Biology and Medicine, 137(July), 104851. https://doi.org/10.1016/j.compbiomed.2021.104851
Su W, Johnston B (2023). r3dmol: Create Interactive 3D Visualizations of Molecular Data. R package version 0.2.0, https://github.com/swsoyee/r3dmol
Published
2023-06-27
How to Cite
SILVA, Welington Gonçalves; MATOS JÚNIOR, Cláudio Guimarães; VELOSO, Wandré Nunes de Pinho; ROMANELLI, João Paulo Roquim; SILVEIRA, Carlos Henrique da.
MusteR - Sistema de Mineração de Contatos em Complexos Proteína-Ligantes. In: TOOLS AND APPLICATIONS - BRAZILIAN SYMPOSIUM ON COMPUTING APPLIED TO HEALTHCARE (SBCAS), 23. , 2023, São Paulo/SP.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2023
.
p. 174-179.
ISSN 2763-8987.
DOI: https://doi.org/10.5753/sbcas_estendido.2023.231154.
