Development of a Database of Peptides with Potential for Pharmacological Intervention in Human Pathogen Molecular Targets.
DOI:
https://doi.org/10.53805/lads.v3i1.63Keywords:
Database, Peptides, Pathogens, In silico, Virtual ScreeningAbstract
Peptides are polymeric chains used as research objects in the search for new drugs with greater efficacy and fewer side effects. Therefore, we created three databases of antimicrobial peptides (GONZALEZ et al., 2023) using PubChem and ChEMBL. First we acquired the Simplified Molecular-Input Line-Entry System (SMILES) of several peptides belonging to different types of pathogens, namely bacteria, viruses, parasites, and fungi. Using the OpenBabel software, these SMILES had their file formats and structures converted to create: one database in one dimension SMI format, and two with three-dimensional MOL2 and PDB file formats. In total the three databases consists of 718 peptides that have been shown to possess inhibtory activity on molecular targets of clinically important pathogens.
References
ANVISA — NATIONAL HEALTH SURVEILLANCE AGENCY. BRAZILIAN PHARMACOPEIA. 6th ed. Brasília, DF: National Health Surveillance Agency, 2019.
ANVISA - NATIONAL HEALTH SURVEILLANCE AGENCY. Institutional. Available in: <https://www.gov.br/anvisa/pt-br/english/introduction >.
BRAZIL. Resolution No. 55, of December 16, 2010. Approves the regulation on the registration of new biological products and biological products and other measures.
ANVISA - National Health Surveillance Agency. Available at: <http://portal.anvisa.gov.br/legislacao/?inheritRedirect=true#/visualizar/28623>.
BERMAN, H. M., WESTBROOK, J., FENG, Z. et al. The Protein Data Bank, Nucleic Acids Research, Volume 28, Issue 1, 1 January 2000, Pages 235–242. DOI: https://doi.org/10.1093/nar/28.1.235.
CASTEL, G. et al. Phage display of combinatorial peptide libraries: application to antiviral research, Molecules, 2011, vol. 16 (p. 3499-3518).
CLARK, M.; CRAMER III, RICHARD, D.; VAN OPDENBOSCH, N. Validation of the general purpose tripos 5.2 force field. Journal of computational chemistry, v. 10, n. 8, p. 982-1012, 1989.
DALBY, A. et al. Description of Several Chemical Structure File Format Used by Computer Programs Developed at Molecular Design Limited. Journal of Chemical Information and Computer Sciences, v. 32, no. 3, p. 244-255, 1992.
CHEOHEN, C. F. A. R.; ANDRIOLO, B. V.; SILVA, M. L. Database of Active Pharmaceutical Ingredients (APIs) present in the Brazilian Pharmacopeia. Latin American Data in Science, [S. l.], v. 2, no. 1, p. 7–12, 2022. DOI: 10.53805/lads. v2i1.35. Available in: <https://ojs.datainscience.com.br/index.php/lads/article/view/35>.
GUEDES, I. A.; MAGALHÃES, C. S.; DARDENNE, L. E. Three-Dimensional Models. In: VERLI, H. (Ed.). Bioinformatics: from Biology to Molecular Flexibility. 1st Edition ed. São Paulo: SBBq, 2014. p. 148-171.
GONZALEZ, M. S. P.; CHEOHEN, C.; ANDRIOLO, B. V.; DA SILVA, M. L. “Database of Peptides with Potential for Pharmacological Intervention in Human Pathogen Molecular Targets”, Mendeley Data, V1, 2023. DOI: 10.17632/2zhgy9ggdv.1.
LOPEZ M. J.; Mohiuddin, S. S. Biochemistry, Essential Amino Acids. StatPearls, Treasure Island (FL): StatPearls published in January of 2022 -. Available in: <https://www.ncbi.nlm.nih.gov/books/NBK557845>.
MORRIS, G.; RUTH, H.; LINDSTROM. W. Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receiver flexibility. Journal of Computational Chemistry, (2009), 30(16).
NELSON, D. L; COX, M. M. Lehninger's Principles of Biochemistry. 6th ed. Porto Alegre: Artmed, 2014. 85-90 p.
O'BOYLE, N. M. et al. Open Babel: An open chemical toolbox. Journal of Cheminformatics, v. 3, no. 33, p. 1-14, 2011.
ROSE, A. J. Amino Acid Nutrition and Metabolism in Health and Disease. Nutrients. 2019;11(11):2623. Published 2019 Nov 1. DOI: 10.3390/nu11112623.
WEININGER, D. SMILES, a chemical language and information system. 1. Introduction and rules of encoding. J.Chem. Inf. Computer science 1988, 28, 31.
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