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Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules

Bcl-2 family anti-apoptotic proteins are overexpressed in several hematological and solid tumors, and contribute to tumor formation, progression, and resistance to therapy. They represent a promising therapeutic avenue to explore for cancer treatment. Venetoclax, a Bcl-2 inhibitor is currently used...

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Autores principales: Valentini, Elisabetta, D'Aguanno, Simona, Di Martile, Marta, Montesano, Camilla, Ferraresi, Virginia, Patsilinakos, Alexandros, Sabatino, Manuela, Antonini, Lorenzo, Chiacchiarini, Martina, Valente, Sergio, Mai, Antonello, Colotti, Gianni, Ragno, Rino, Trisciuoglio, Daniela, Del Bufalo, Donatella
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Ivyspring International Publisher 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8899577/
https://www.ncbi.nlm.nih.gov/pubmed/35265218
http://dx.doi.org/10.7150/thno.64233
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author Valentini, Elisabetta
D'Aguanno, Simona
Di Martile, Marta
Montesano, Camilla
Ferraresi, Virginia
Patsilinakos, Alexandros
Sabatino, Manuela
Antonini, Lorenzo
Chiacchiarini, Martina
Valente, Sergio
Mai, Antonello
Colotti, Gianni
Ragno, Rino
Trisciuoglio, Daniela
Del Bufalo, Donatella
author_facet Valentini, Elisabetta
D'Aguanno, Simona
Di Martile, Marta
Montesano, Camilla
Ferraresi, Virginia
Patsilinakos, Alexandros
Sabatino, Manuela
Antonini, Lorenzo
Chiacchiarini, Martina
Valente, Sergio
Mai, Antonello
Colotti, Gianni
Ragno, Rino
Trisciuoglio, Daniela
Del Bufalo, Donatella
author_sort Valentini, Elisabetta
collection PubMed
description Bcl-2 family anti-apoptotic proteins are overexpressed in several hematological and solid tumors, and contribute to tumor formation, progression, and resistance to therapy. They represent a promising therapeutic avenue to explore for cancer treatment. Venetoclax, a Bcl-2 inhibitor is currently used for hematological malignancies or is undergoing clinical trials for either hematological or solid tumors. Despite these progresses, ongoing efforts are focusing on the identification and development of new molecules targeting Bcl-2 protein and/or other family members. Methods: Machine learning guided virtual screening followed by surface plasmon resonance, molecular docking and pharmacokinetic analyses were performed to identify new inhibitors of anti-apoptotic members of Bcl-2 family and their pharmacokinetic profile. The sensitivity of cancer cells from different origin to the identified compounds was evaluated both in in vitro (cell survival, apoptosis, autophagy) and in vivo (tumor growth in nude mice) preclinical models. Results: IS20 and IS21 were identified as potential new lead compounds able to bind Bcl-2, Bcl-xL and Mcl-1 recombinant proteins. Molecular docking investigation indicated IS20 and IS21 could bind into the Beclin-1 BH3 binding site of wild type Bcl-2, Bcl-xL and Mcl-1 proteins. In particular, although the IS21 docked conformation did not show a unique binding mode, it clearly showed its ability in flexibly adapting to either BH3 binding sites. Moreover, both IS20 and IS21 reduced cell viability, clonogenic ability and tumor sphere formation, and induced apoptosis in leukemic, melanoma and lung cancer cells. Autophagosome formation and maturation assays demonstrated induction of autophagic flux after treatment with IS20 or IS21. Experiments with z-VAD-fmk, a pan-caspase inhibitor, and chloroquine, a late-stage autophagy inhibitor, demonstrated the ability of the two compounds to promote apoptosis by autophagy. IS21 also reduced in vivo tumor growth of both human leukemia and melanoma models. Conclusion: Virtual screening coupled with in vitro and in vivo experimental data led to the identification of two new promising inhibitors of anti-apoptotic proteins with good efficacy in the binding to recombinant Bcl-2, Bcl-xL and Mcl-1 proteins, and against different tumor histotypes.
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spelling pubmed-88995772022-03-08 Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules Valentini, Elisabetta D'Aguanno, Simona Di Martile, Marta Montesano, Camilla Ferraresi, Virginia Patsilinakos, Alexandros Sabatino, Manuela Antonini, Lorenzo Chiacchiarini, Martina Valente, Sergio Mai, Antonello Colotti, Gianni Ragno, Rino Trisciuoglio, Daniela Del Bufalo, Donatella Theranostics Research Paper Bcl-2 family anti-apoptotic proteins are overexpressed in several hematological and solid tumors, and contribute to tumor formation, progression, and resistance to therapy. They represent a promising therapeutic avenue to explore for cancer treatment. Venetoclax, a Bcl-2 inhibitor is currently used for hematological malignancies or is undergoing clinical trials for either hematological or solid tumors. Despite these progresses, ongoing efforts are focusing on the identification and development of new molecules targeting Bcl-2 protein and/or other family members. Methods: Machine learning guided virtual screening followed by surface plasmon resonance, molecular docking and pharmacokinetic analyses were performed to identify new inhibitors of anti-apoptotic members of Bcl-2 family and their pharmacokinetic profile. The sensitivity of cancer cells from different origin to the identified compounds was evaluated both in in vitro (cell survival, apoptosis, autophagy) and in vivo (tumor growth in nude mice) preclinical models. Results: IS20 and IS21 were identified as potential new lead compounds able to bind Bcl-2, Bcl-xL and Mcl-1 recombinant proteins. Molecular docking investigation indicated IS20 and IS21 could bind into the Beclin-1 BH3 binding site of wild type Bcl-2, Bcl-xL and Mcl-1 proteins. In particular, although the IS21 docked conformation did not show a unique binding mode, it clearly showed its ability in flexibly adapting to either BH3 binding sites. Moreover, both IS20 and IS21 reduced cell viability, clonogenic ability and tumor sphere formation, and induced apoptosis in leukemic, melanoma and lung cancer cells. Autophagosome formation and maturation assays demonstrated induction of autophagic flux after treatment with IS20 or IS21. Experiments with z-VAD-fmk, a pan-caspase inhibitor, and chloroquine, a late-stage autophagy inhibitor, demonstrated the ability of the two compounds to promote apoptosis by autophagy. IS21 also reduced in vivo tumor growth of both human leukemia and melanoma models. Conclusion: Virtual screening coupled with in vitro and in vivo experimental data led to the identification of two new promising inhibitors of anti-apoptotic proteins with good efficacy in the binding to recombinant Bcl-2, Bcl-xL and Mcl-1 proteins, and against different tumor histotypes. Ivyspring International Publisher 2022-02-28 /pmc/articles/PMC8899577/ /pubmed/35265218 http://dx.doi.org/10.7150/thno.64233 Text en © The author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions.
spellingShingle Research Paper
Valentini, Elisabetta
D'Aguanno, Simona
Di Martile, Marta
Montesano, Camilla
Ferraresi, Virginia
Patsilinakos, Alexandros
Sabatino, Manuela
Antonini, Lorenzo
Chiacchiarini, Martina
Valente, Sergio
Mai, Antonello
Colotti, Gianni
Ragno, Rino
Trisciuoglio, Daniela
Del Bufalo, Donatella
Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
title Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
title_full Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
title_fullStr Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
title_full_unstemmed Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
title_short Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
title_sort targeting the anti-apoptotic bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8899577/
https://www.ncbi.nlm.nih.gov/pubmed/35265218
http://dx.doi.org/10.7150/thno.64233
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