Understanding the biological function of Natural Products' scaffolds from Databases for the design of active compounds for the treatment of infectious diseases

• Grant number: 19/05967-3
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: May 01, 2019
• End date: April 30, 2023
• Field of knowledge: Physical Sciences and Mathematics - Chemistry
• Principal Investigator: Adriano Defini Andricopulo
• Grantee: Marilia Valli
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated research grant: 13/07600-3 - CIBFar - Center for Innovation in Biodiversity and Drug Discovery, AP.CEPID

Abstract

Biodiversity provides exclusive chemical scaffolds for the design of active compounds and is the main source of drugs approved worldwide (67% are either a natural product, semi-synthetic derivative, macromolecule isolated from an organism or have a pharmacophore group inspired by natural products). Natural products are efficient models for medicinal chemistry because they comprise scaffolds and structural properties that were evolutionary chosen with the ability to interact or bind to protein targets. Cataloged molecular diversity plays a key role in the discovery, design and development of drugs. If the chemical information from the biodiversity is properly accessible, organized and cataloged it may be much more useful for the design of new active molecules. Data repositories have enormously contributed to studies in several scientific fields such as medicine, chemistry, biology, taxonomy, ecology and environmental areas, and are one of the most important tools for drug discovery.The first natural product library from Brazilian biodiversity (NuBBE Database) was originally created by our research group and has proven to be an important resource for several areas of studies. Currently, this database contains more than 2,000 compounds, freely accessible online (http://nubbe.iq.unesp.br/portal/nubbedb.html) providing valuable and integrative data such as chemical, spectral, biological, taxonomic, geographic and pharmacological information. This database is an important research tool for drug design, medicinal chemistry, molecular modeling and for a wide variety of computational studies. The design of drugs is mainly based on the knowledge of the mechanisms by which bioactive molecules interact with pharmacological targets. The structure-based drug design (SBDD) by means of molecular modeling is one of the most efficient strategies used to evaluate the interaction of active compounds and its biological target and improve pharmacodynamics. This is a useful method to identify crucial intermolecular interactions in the process of molecular recognition and for the selection of hits that bind or fit to the target protein binding cavity.The focus of this project is to use a computational molecular modeling approach to identify scaffolds and hits in the natural products from the NuBBE database in order to generate information for the design of new prototypes for the treatment of neglected diseases. Additionally, the project aims at continuing the ongoing expansion of NuBBE Database in order to catalog secondary metabolites already described from Brazilian biodiversity, so that Brazil can provide the most complete natural products database of the equatorial and tropical environments.

Scientific publications

(11)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DE FREITAS, LARISSA; VALLI, MARILIA; DAMETTO, ALESSANDRA C.; PENNACCHI, PAULA C.; ANDRICOPULO, ADRIANO D.; MARIA-ENGLER, SILVYA S.; BOLZANI, VANDERLAN S.. Advanced Glycation End Product Inhibition by Alkaloids from Ocotea paranapiacabensis for the Prevention of Skin Aging. Journal of Natural Products, v. 83, n. 3, SI, p. 649-656, MAR 27 2020. (14/50926-0, 19/05967-3, 13/07600-3)

ASSE JUNIOR, LEONARDO RANDER; KRONENBERGER, THALES; MAGALHAES SERAFIM, MATEUS SA; SOUSA, YAMARA VIANA; FRANCO, ISABELLA DRUMOND; VALLI, MARILIA; BOLZANI, VANDERLAN DA SILVA; MONTEIRO, GUSTAVO CLARO; BRUNO PRATES, JOAO LUCAS; KROON, ERNA GEESSIEN; et al. Virtual screening of antibacterial compounds by similarity search of Enoyl-ACP reductase (FabI) inhibitors. Future Medicinal Chemistry, v. 12, n. 1, p. 51-68, JAN 2020. (19/05967-3, 14/50926-0, 13/07600-3)

VALLI, MARILIA; ATANAZIO, LETICIA CRISTINA VIEIRA; MONTEIRO, GUSTAVO CLARO; COELHO, ROBERTA RAMOS; DEMARQUE, DANIEL PECORARO; ANDRICOPULO, ADRIANO DEFINI; ESPINDOLA, LAILA SALMEN; BOLZANI, VANDERLAN DA SILVA. The Potential of Biologically Active Brazilian Plant Species as a Strategy to Search for Molecular Models for Mosquito Control. Planta Medica, v. 87, n. 01/02, p. 6-23, FEB 2021. (14/50926-0, 13/07600-3, 19/05967-3)

TELES, HENRIQUE R.; FERREIRA, LEONARDO L. G.; VALLI, MARILIA; COELHO, FERNANDO; ANDRICOPULO, ADRIANO D.. Hierarchical Clustering and Target-Independent QSAR for Antileishmanial Oxazole and Oxadiazole Derivatives. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 23, n. 16, p. 16-pg., 2022-08-01. (19/05967-3, 13/07600-3)

ZERAIK, MARIA LUIZA; PAULI, IVANI; DUTRA, LUIZ A.; CRUZ, RAQUEL S.; VALLI, MARILIA; PARACATU, LUANA C.; DE FARIA, CAROLINA M. Q. G.; XIMENES, VALDECIR F.; REGASINI, LUIS O.; ANDRICOPULO, ADRIANO D.; et al. Identification of a Prenyl Chalcone as a Competitive Lipoxygenase Inhibitor: Screening, Biochemical Evaluation and Molecular Modeling Studies. Molecules, v. 26, n. 8, APR 2021. (10/01506-7, 13/07600-3, 11/03017-6, 19/05967-3, 19/18445-5, 09/15457-0, 14/50926-0)

ALVES, NATALIA FELIX; RIBEIRO, DAYANE CASTRO; MANNOCHIO-RUSSO, HELENA; QUEIROZ, SUZANA APARECIDA SILVA; ZOCOLO, GUILHERME JULIAO; BOLZANI, VANDERLAN DA SILVA; VALLI, MARILIA. Advanced Glycation End Products Inhibitors from Talisia esculenta. REVISTA VIRTUAL DE QUIMICA, v. N/A, p. 7-pg., 2023-04-24. (20/11967-3, 13/07600-3, 14/50926-0, 19/05967-3)

DE OLIVEIRA, ALDO S.; VALLI, MARILIA; FERREIRA, LEONARDO L. G.; SOUZA, JULIA M.; KROGH, RENATA; MEIER, LIDIANE; ABREU, HEITOR R.; VOLTOLINI, BRUNA G.; LLANES, LUANA C.; NUNES, RICARDO J.; et al. Novel trypanocidal thiophen-chalcone cruzain inhibitors: structure- and ligand-based studies. Future Medicinal Chemistry, v. 14, n. 11, p. 14-pg., 2022-05-11. (13/07600-3, 15/06392-3, 19/05967-3)

TELES, HENRIQUE R.; VALLI, MARILIA; FERREIRA, LEONARDO L. G.; ANDRICOPULO, ADRIANO D.. Molecular Modeling, Virtual Screening, and Molecular Dynamics for Leishmania infantum Methionyl-tRNA Synthetase. Journal of Physical Chemistry B, v. N/A, p. 10-pg., 2022-12-19. (13/07600-3, 14/50926-0, 19/05967-3)

CHIPOLINE, INGRID C.; BRASIL, BEATRICE F. A. B.; NETO, JOSE S. S.; VALLI, MARILIA; KROGH, RENATA; CENCI, ARTHUR R.; TEIXEIRA, KEROLAIN F.; ZAPP, EDUARDO; BRONDANI, DANIELA; FERREIRA, LEONARDO L. G.; et al. Synthesis and investigation of the trypanocidal potential of novel 1,2,3-triazole-selenide hybrids. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, v. 243, p. 9-pg., 2022-08-31. (13/07600-3, 14/50926-0, 19/05967-3)

VALLI, MARILIA; SOUZA, JULIA MEDEIROS; CHELUCCI, RAFAEL CONSOLIN; BIASETTO, CAROLINA RABAL; ARAUJO, ANGELA REGINA; BOLZANI, VANDERLAN DA SILVA; ANDRICOPULO, ADRIANO DEFINI. Identification of natural cytochalasins as leads for neglected tropical diseases drug discovery. PLoS One, v. 17, n. 10, p. 13-pg., 2022-10-03. (19/06034-0, 13/07600-3, 14/50926-0, 19/05967-3)

DE FREITAS, LARISSA; VALLI, MARILIA; DAMETTO, ALESSANDRA C.; PENNACCHI, PAULA C.; ANDRICOPULO, ADRIANO D.; MARIA-ENGLER, SILVYA S.; BOLZANI, VANDERLAN S.. Advanced Glycation End Product Inhibition by Alkaloids from Ocotea paranapiacabensis for the Prevention of Skin Aging. Journal of Natural Products, v. 83, n. 3, p. 8-pg., 2020-03-27. (13/07600-3, 14/50926-0, 19/05967-3)