Characterization of cysteine protease inhibitors with antineoplastic activity by in silico and cell-based assays coupled with chemical analyses

• Grant number: 18/15904-6
• Support Opportunities: Regular Research Grants
• Start date: August 01, 2019
• End date: July 31, 2021
• Field of knowledge: Physical Sciences and Mathematics - Chemistry
• Principal Investigator: Andrei Leitão
• Grantee: Andrei Leitão
• Host Institution: Instituto de Química de São Carlos (IQSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• City of the host institution: São Carlos

Abstract

The drug discovery process is time-consuming and often leads to dead ends. This is especially true for the study of bioactive substance for cancer diseases, in which new therapeutic approaches are eagerly needed. Cathepsin inhibitors are described in the literature as potential novel antineoplastic compounds, inhibiting the migration and invasion of cancer cells. In this work, it is devised an integrated strategy combining in silico, synthesis and in vitro studies for dipeptidyl nitriles along with their peptoid derivatives against a set of cancer cell lines. The computational work will map a set of cathepsins (L, B, and S) and their inhibitors using molecular interaction fields coupled with chemometric analyses to define the physicochemical properties that are important for potency and selectivity. These in silico studies will guide the synthesis of a set of forty compounds, following by the characterization and bioassays. All tests are going to be based on pancreatic (MIA PaCa-2 and BxPC-3), liver (HepG2), prostate (DU145 and PC-3) and breast (MDA-MB-231) cancer cells, including non-tumorigenic cell lines to quantify the selectivity. The cytostatic activity in two and three-dimensional cell cultures is expected for these compounds according to our initial studies. Hence, a myriad of phenotypic studies involving the cell cycle arrest, inhibition of migration and colony formation should be evaluated along with combined therapy using known antineoplastic drugs. The mechanistic study comprises the analysis of the metabolism of the selective cysteine protease substrate Z-FR-MCA and profiling of distinct cysteine proteases using Western blot. Bioanalytical methods applying HPLC-MS techniques will provide the pharmacokinetics parameters related to compound permeability and stability to be coupled with the pharmacological response. These results altogether provide a glimpse for the complex chemical-biological interface in a drug discovery effort. (AU)

Scientific publications

(12)

(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)

BONATTO, VINICIUS; JATAI BATISTA, PEDRO HENRIQUE; CIANNI, LORENZO; DE VITA, DANIELA; SILVA, DANIEL G.; CEDRON, RODRIGO; TEZUKA, DAIANE Y.; DE ALBUQUERQUE, SERGIO; MORAES, CAROLINA BORSOI; FRANCO, CAIO HADDAD; et al. On the intrinsic reactivity of highly potent trypanocidal cruzain inhibitors. RSC MEDICINAL CHEMISTRY, v. 11, n. 11, p. 1275-1284, NOV 1 2020. (18/21749-3, 18/15904-6, 13/18009-4)

QUILLES, JR., JOSE C.; SHAMIM, ANWAR; TEZUKA, DAIANE Y.; BATISTA, PEDRO H. J.; LOPES, CARLA D.; DE ALBUQUERQUE, SERGIO; MONTANARI, CARLOS A.; LEITAO, ANDREI. Dipeptidyl nitrile derivatives suppress the Trypanosoma cruzi in vitro infection. Experimental Parasitology, v. 219, DEC 2020. (13/18009-4, 18/15904-6, 18/03985-1, 14/07292-0)

CARLOS, JORGE ANTONIO ELIAS GODOY; LIMA, KELI; COSTA-LOTUFO, LETICIA VERAS; LEITAO, ANDREI; MACHADO-NETO, JOAO AGOSTINHO. AD80, a multikinase inhibitor, exhibits antineoplastic effects in acute leukemia cellular models targeting the PI3K/STMN1 axis. INVESTIGATIONAL NEW DRUGS, v. 39, n. 4, p. 1139-1149, AUG 2021. (17/24993-0, 15/17177-6, 18/15904-6, 18/19372-9, 19/23864-7)

BONATTO, VINICIUS; SHAMIM, ANWAR; ROCHO, FERNANDA DOS R.; LEITAO, ANDREI; LUQUE, F. JAVIER; LAMEIRA, JERONIMO; MONTANARI, CARLOS A.. Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 61, n. 9, p. 4733-4744, SEP 27 2021. (20/04653-2, 20/06543-0, 18/15904-6)

TEZUKA, DAIANE YUKIE; DE ALBUQUERQUE, SERGIO; MONTANARI, CARLOS ALBERTO; LEITAO, ANDREI. Discovery of 2-aminopyridine Derivatives with Antichagasic and Antileishmanial Activity Using Phenotypic Assays. LETTERS IN DRUG DESIGN & DISCOVERY, v. 17, n. 7, p. 867-872, 2020. (13/18009-4, 18/15904-6)

ZANIN, LUCAS LIMA; BRITO MATOS, THIAGO KELVIN; LEITAO, ANDREI; ELLENA, JAVIER; MELEIRO PORTO, ANDRE LUIZ. Biocatalytic Kinetic Resolution to Access Enantiomerically Enriched Dihydropyrimidinone/Thiones through Recognition of a Remote Stereocentre. EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, v. N/A, p. 9-pg., 2022-06-20. (19/07654-2, 18/15904-6, 16/20155-7, 17/15850-0)

BONATTO, VINICIUS; LAMEIRO, RAFAEL F.; ROCHO, FERNANDA R.; LAMEIRA, JERONIMO; LEITAO, ANDREI; MONTANARI, CARLOS A.. Nitriles: an attractive approach to the development of covalent inhibitors. RSC MEDICINAL CHEMISTRY, v. 14, n. 2, p. 18-pg., 2022-11-07. (21/01633-3, 20/04653-2, 18/15904-6)

FERREIRA, IRLON M.; JIMENEZ, DAVID E. Q.; LOPES, SAMUEL Q.; DE OLIVEIRA, ALEX DE NAZARE; MATOS, MATEUS J. S.; PORTO, ANDRE L. M.. Ene-reductases: Contribution from Brazilian fungi in organic synthesis. RESULTS IN CHEMISTRY, v. 5, p. 12-pg., 2023-05-26. (18/15904-6, 19/07654-2, 16/20155-7)

FÁBIO R. RIGOLIN; CARLA A. LEITE; WILLIAN G. BIROLLI; ANDRÉ L. M. PORTO; MIRNA H. R. SELEGHIM. Biodegradation of the Pyrethroid Pesticide Gamma-Cyhalothrin by Fungi from a Brazilian Cave. Journal of the Brazilian Chemical Society, v. 35, n. 8, 2024-03-11. (18/15904-6, 17/19721-0, 16/20155-7, 19/07654-2)

ALVES, LUANA; SANTOS, DEBORAH A.; CENDRON, RODRIGO; ROCHO, FERNANDA R.; MATOS, THIAGO K. B.; LEITAO, ANDREI; MONTANARI, CARLOS A.. Nitrile-based peptoids as cysteine protease inhibitors. Bioorganic & Medicinal Chemistry, v. 41, JUL 1 2021. (13/18009-4, 18/15904-6, 18/09961-7)

BRITO MATOS, THIAGO KELVIN; JATAI BATISTA, PEDRO HENRIQUE; ROCHO, FERNANDA DOS REIS; DE VITA, DANIELA; PEARCE, NICHOLAS; KELLAM, BARRIE; MONTANARI, CARLOS ALBERTO; LEITAO, ANDREI. Synthesis and matched molecular pair analysis of covalent reversible inhibitors of the cysteine protease CPB. Bioorganic & Medicinal Chemistry Letters, v. 30, n. 18, SEP 15 2020. (16/07946-5, 18/15904-6, 13/18009-4)

PADOVAN, RODRIGO NOGUEIRA; CARVALHO, LUCAS SPONTON DE; BERGO, PATRICIA LUISA DE SOUZA; XAVIER, CHUBRAIDER; LEITAO, ANDREI; NETO, ALVARO JOSE DOS SANTOS; LANCAS, FERNANDO MAURO; AZEVEDO, EDUARDO BESSA. Degradation of hormones in tap water by heterogeneous solar TiO2-photocatalysis: Optimization, degradation products identification, and estrogenic activity removal. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING, v. 9, n. 6, DEC 2021. (11/24137-0, 18/15904-6)