1
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Menna M, Fiorentino F, Marrocco B, Lucidi A, Tomassi S, Cilli D, Romanenghi M, Cassandri M, Pomella S, Pezzella M, Del Bufalo D, Zeya Ansari MS, Tomašević N, Mladenović M, Viviano M, Sbardella G, Rota R, Trisciuoglio D, Minucci S, Mattevi A, Rotili D, Mai A. Novel non-covalent LSD1 inhibitors endowed with anticancer effects in leukemia and solid tumor cellular models. Eur J Med Chem 2022; 237:114410. [DOI: 10.1016/j.ejmech.2022.114410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/22/2022]
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2
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Mellini P, Marrocco B, Borovika D, Polletta L, Carnevale I, Saladini S, Stazi G, Zwergel C, Trapencieris P, Ferretti E, Tafani M, Valente S, Mai A. Pyrazole-based inhibitors of enhancer of zeste homologue 2 induce apoptosis and autophagy in cancer cells. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0150. [PMID: 29685965 DOI: 10.1098/rstb.2017.0150] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2017] [Indexed: 12/14/2022] Open
Abstract
Novel pyrazole-based EZH2 inhibitors have been prepared through a molecular pruning approach from known inhibitors bearing a bicyclic moiety as a central scaffold. The hit compound 1o (N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-methyl-1-phenyl-1H-pyrazole-4-carboxamide) showed low micromolar EZH2/PRC2 inhibition and high selectivity towards a panel of other methyltransferases. Moreover, 1o displayed cell growth arrest in breast MDA-MB231, leukaemia K562, and neuroblastoma SK-N-BE cancer cells joined to reduction of H3K27me3 levels and induction of apoptosis and autophagy.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Paolo Mellini
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Diana Borovika
- Department of Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles iela 21, Riga LV-1006, Latvia
| | - Lucia Polletta
- Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Viale Regina Elena 324, 00161 Roma, Italy
| | - Ilaria Carnevale
- Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Viale Regina Elena 324, 00161 Roma, Italy
| | - Serena Saladini
- Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Viale Regina Elena 324, 00161 Roma, Italy
| | - Giulia Stazi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Clemens Zwergel
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Peteris Trapencieris
- Department of Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles iela 21, Riga LV-1006, Latvia
| | - Elisabetta Ferretti
- Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Viale Regina Elena 324, 00161 Roma, Italy
| | - Marco Tafani
- Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Viale Regina Elena 324, 00161 Roma, Italy
| | - Sergio Valente
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy .,Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Roma, Italy
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3
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Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A. A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Cell Rep 2019; 27:387-399.e7. [PMID: 30970244 DOI: 10.1016/j.celrep.2019.03.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/28/2019] [Accepted: 03/15/2019] [Indexed: 12/25/2022] Open
Abstract
LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
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Affiliation(s)
- Chiara Marabelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Biagina Marrocco
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Simona Pilotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Sara Marchese
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Daniela Rhodes
- Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Sriram Subramaniam
- The University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
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4
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Mellini P, Marrocco B, Borovika D, Polletta L, Carnevale I, Saladini S, Stazi G, Zwergel C, Trapencieris P, Ferretti E, Tafani M, Valente S, Mai A. Correction to 'Pyrazole-based inhibitors of enhancer of zeste homologue 2 induce apoptosis and autophagy in cancer cells'. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0305. [PMID: 30061471 DOI: 10.1098/rstb.2018.0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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5
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Miele E, Valente S, Alfano V, Silvano M, Mellini P, Borovika D, Marrocco B, Po A, Besharat ZM, Catanzaro G, Battaglia G, Abballe L, Zwergel C, Stazi G, Milite C, Castellano S, Tafani M, Trapencieris P, Mai A, Ferretti E. The histone methyltransferase EZH2 as a druggable target in SHH medulloblastoma cancer stem cells. Oncotarget 2017; 8:68557-68570. [PMID: 28978137 PMCID: PMC5620277 DOI: 10.18632/oncotarget.19782] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/20/2017] [Indexed: 12/21/2022] Open
Abstract
The histone methyltransferase EZH2 plays a role in maintenance of the stem component of cancer, and its overexpression and/or mutation typically drives tumor aggressiveness, drug resistance and patients’ poor prognosis. In this study, we use mouse and human medulloblastoma stem-like cells belonging to the Sonic Hedgehog subgroup (SHH MB-SLCs) and demonstrate that genetic suppression of EZH2 reduces the level of its histone mark H3K27me3 and lowers proliferation and self-renewal. We designed an EZH2 inhibitor (EZH2i) as a simplified analog of EPZ005687 and GSK2816126, MC3629, and we tested its biological activity in SHH MB-SLCs. Pharmacological inhibition of EZH2 impairs SHH MB cells proliferation and self-renewal, and induces apoptosis in vitro. Finally, we generated xenograft MB-SLCs orthotopic tumors in nude mice to test MC3629 in vivo. In treated mice, we observed impairment of tumor growth, together with induction of apoptosis and reduction of proliferation and stemness. Overall, these findings describe EZH2 as a druggable target in MB and provide insight into the biological activity of MC3629 as an EZH2i.
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Affiliation(s)
- Evelina Miele
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome 00161, Italy.,Current address: Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù, 28 Children's Hospital, IRCCS, Rome 00165, Italy
| | - Sergio Valente
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Rome 00185, Italy
| | - Vincenzo Alfano
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Marianna Silvano
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Paolo Mellini
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Rome 00185, Italy
| | - Diana Borovika
- Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia
| | - Biagina Marrocco
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Rome 00185, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University of Rome, Rome 00161, Italy
| | | | - Giuseppina Catanzaro
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | | | - Luana Abballe
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Clemens Zwergel
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Rome 00185, Italy
| | - Giulia Stazi
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Rome 00185, Italy
| | - Ciro Milite
- Department of Pharmacy, University of Salerno, Fisciano 84084, Italy
| | - Sabrina Castellano
- Department of Pharmacy, University of Salerno, Fisciano 84084, Italy.,Department of Medicine and Surgery, University of Salerno, Baronissi 84084, Italy
| | - Marco Tafani
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | | | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Rome 00185, Italy.,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Rome 00185, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy.,Neuromed Institute, Località Camerelle, Pozzilli 86077, Italy
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6
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Marabelli C, Marrocco B, Mattevi A. The growing structural and functional complexity of the LSD1/KDM1A histone demethylase. Curr Opin Struct Biol 2016; 41:135-144. [DOI: 10.1016/j.sbi.2016.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
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7
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Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A. Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features. Sci Adv 2016; 2:e1601017. [PMID: 27626075 PMCID: PMC5017823 DOI: 10.1126/sciadv.1601017] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.
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Affiliation(s)
- Valentina Speranzini
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Biagina Marrocco
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Mariantonietta Forgione
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alessia Lucidi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Parinaz Mehdipour
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139 Milan, Italy
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire CB10 1SD, U.K
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Pasteur Institute–Cenci Bolognetti Foundation, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
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8
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Di Liddo R, Valente S, Taurone S, Zwergel C, Marrocco B, Turchetta R, Conconi MT, Scarpa C, Bertalot T, Schrenk S, Mai A, Artico M. Histone deacetylase inhibitors restore IL-10 expression in lipopolysaccharide-induced cell inflammation and reduce IL-1β and IL-6 production in breast silicone implant in C57BL/6J wild-type murine model. Autoimmunity 2016; 49:155-165. [PMID: 26789595 DOI: 10.3109/08916934.2015.1134510] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/16/2015] [Indexed: 12/29/2022]
Abstract
Among epigenetic enzymes, histone deacetylases (HDACs) are responsible for regulating the expression of an extensive array of genes by reversible deacetylation of nuclear histones as well as a large number of non-histone proteins. Initially proposed for cancer therapy, recently the interest for HDAC inhibitors (HDACi) as orally active, safe, and anti-inflammatory agents is rising due to their ability in reducing the severity of inflammatory and autoimmune diseases. In particular, selective HDAC3, HDAC6, and HDAC8 inhibitors have been described to downregulate the expression of pro-inflammatory cytokines (TNF-α, TGF-β, IL-1β, and IL-6). Herein, using KB31, C2C12, and 3T3-J2 cell lines, we demonstrated that, under lipopolysaccharide-induced in vitro inflammation, HDAC3/6/8 inhibitor MC2625 and HDAC6-selective inhibitor MC2780 were effective at a concentration of 30 ng/mL to downregulate mRNA expression of pro-inflammatory cytokines (IL-1β and IL-6) and to promote the transcription of IL-10 gene, without affecting the cell viability. Afterwards, we investigated by immunohistochemistry the activity of MC2625 and MC2780 at a concentration of 60 ng/kg animal weight to regulate silicone-triggered immune response in C57BL/6J female mice. Our findings evidenced the ability of such inhibitors to reduce host inflammation in silicone implants promoting a thickness reduction of peri-implant fibrous capsule, upregulating IL-10 expression, and reducing the production of both IL-1β and IL-6. These results underline the potential application of MC2625 and MC2780 in inflammation-related diseases.
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Affiliation(s)
- Rosa Di Liddo
- Dipartimento Scienze del Farmaco, Università di Padova, Padova, Italy
| | - Sergio Valente
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Samanta Taurone
- Dipartimento Organi di Senso, Sapienza Università di Roma, Roma, Italy
| | - Clemens Zwergel
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Rosaria Turchetta
- Dipartimento Organi di Senso, Sapienza Università di Roma, Roma, Italy
| | | | - Carlotta Scarpa
- Dipartimento di Neuroscienze, Clinica di Chirurgia Plastica, Università di Padova, Padova, Italy, and
| | - Thomas Bertalot
- Dipartimento Scienze del Farmaco, Università di Padova, Padova, Italy
| | - Sandra Schrenk
- Dipartimento Scienze del Farmaco, Università di Padova, Padova, Italy
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Roma, Italy
| | - Marco Artico
- Dipartimento Organi di Senso, Sapienza Università di Roma, Roma, Italy
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9
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Reddy DN, Ballante F, Chuang T, Pirolli A, Marrocco B, Marshall GR. Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors. J Med Chem 2016; 59:1613-33. [PMID: 26681404 DOI: 10.1021/acs.jmedchem.5b01632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Selective inhibition of KDAC isoforms while maintaining potency remains a challenge. Using the largazole macrocyclic depsipeptide structure as a starting point for developing new KDACIs with increased selectivity, a combination of four different simplified largazole analogue (SLA) scaffolds with diverse zinc-binding groups (for a total of 60 compounds) were designed, synthesized, and evaluated against class I KDACs 1, 3, and 8, and class II KDAC6. Experimental evidence as well as molecular docking poses converged to establish the cyclic tetrapeptides (CTPs) as the primary determinant of both potency and selectivity by influencing the correct alignment of the zinc-binding group in the KDAC active site, providing a further basis for developing new KDACIs of higher isoform selectivity and potency.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Timothy Chuang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Adele Pirolli
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
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10
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Vianello P, Botrugno OA, Cappa A, Dal Zuffo R, Dessanti P, Mai A, Marrocco B, Mattevi A, Meroni G, Minucci S, Stazi G, Thaler F, Trifiró P, Valente S, Villa M, Varasi M, Mercurio C. Discovery of a Novel Inhibitor of Histone Lysine-Specific Demethylase 1A (KDM1A/LSD1) as Orally Active Antitumor Agent. J Med Chem 2016; 59:1501-17. [DOI: 10.1021/acs.jmedchem.5b01209] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Paola Vianello
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Oronza A. Botrugno
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Anna Cappa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Roberto Dal Zuffo
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paola Dessanti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Biagina Marrocco
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Giuseppe Meroni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Saverio Minucci
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- Department
of Biosciences, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Giulia Stazi
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
| | - Florian Thaler
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paolo Trifiró
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sergio Valente
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
| | - Manuela Villa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Mario Varasi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- Genextra Group, DAC s.r.l., Via
Adamello 16, 20139 Milan, Italy
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11
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Piano V, Benjamin DI, Valente S, Nenci S, Marrocco B, Mai A, Aliverti A, Nomura DK, Mattevi A. Discovery of Inhibitors for the Ether Lipid-Generating Enzyme AGPS as Anti-Cancer Agents. ACS Chem Biol 2015; 10:2589-97. [PMID: 26322624 DOI: 10.1021/acschembio.5b00466] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dysregulated ether lipid metabolism is an important hallmark of cancer cells. Previous studies have reported that lowering ether lipid levels by genetic ablation of the ether lipid-generating enzyme alkyl-glycerone phosphate synthase (AGPS) lowers key structural and oncogenic ether lipid levels and alters fatty acid, glycerophospholipid, and eicosanoid metabolism to impair cancer pathogenicity, indicating that AGPS may be a potential therapeutic target for cancer. In this study, we have performed a small-molecule screen to identify candidate AGPS inhibitors. We have identified several lead AGPS inhibitors and have structurally characterized their interactions with the enzyme and show that these inhibitors bind to distinct portions of the active site. We further show that the lead AGPS inhibitor 1a selectively lowers ether lipid levels in several types of human cancer cells and impairs their cellular survival and migration. We provide here the first report of in situ-active pharmacological tools for inhibiting AGPS, which may provide chemical scaffolds for future AGPS inhibitor development for cancer therapy.
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Affiliation(s)
- Valentina Piano
- Department
of Biology and Biotechnology, University of Pavia, via Ferrata
9, 27100 Pavia, Italy
| | - Daniel I. Benjamin
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Sergio Valente
- Department
of Drug Chemistry and Technologies, University “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Simone Nenci
- Department
of Biology and Biotechnology, University of Pavia, via Ferrata
9, 27100 Pavia, Italy
| | - Biagina Marrocco
- Department
of Drug Chemistry and Technologies, University “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, University “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
- Pasteur Institute, Cenci Bolognetti Foundation, P.le A. Moro 5, Roma 00185, Italy
| | - Alessandro Aliverti
- Department
of Biosciences, University of Milano, Via Festa del Perdono, 7, 20122 Milano, Italy
| | - Daniel K. Nomura
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, via Ferrata
9, 27100 Pavia, Italy
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12
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Valente S, Rodriguez V, Mercurio C, Vianello P, Saponara B, Cirilli R, Ciossani G, Labella D, Marrocco B, Monaldi D, Ruoppolo G, Tilset M, Botrugno OA, Dessanti P, Minucci S, Mattevi A, Varasi M, Mai A. Pure enantiomers of benzoylamino-tranylcypromine: LSD1 inhibition, gene modulation in human leukemia cells and effects on clonogenic potential of murine promyelocytic blasts. Eur J Med Chem 2015; 94:163-74. [DOI: 10.1016/j.ejmech.2015.02.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 12/12/2022]
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13
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Valente S, Rodriguez V, Mercurio C, Vianello P, Saponara B, Cirilli R, Ciossani G, Labella D, Marrocco B, Ruoppolo G, Botrugno OA, Dessanti P, Minucci S, Mattevi A, Varasi M, Mai A. Pure Diastereomers of a Tranylcypromine-Based LSD1 Inhibitor: Enzyme Selectivity and In-Cell Studies. ACS Med Chem Lett 2015; 6:173-7. [PMID: 25699146 DOI: 10.1021/ml500424z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 12/08/2014] [Indexed: 12/13/2022] Open
Abstract
The pure four diastereomers (11a-d) of trans-benzyl (1-((4-(2-aminocyclopropyl)phenyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamate hydrochloride 11, previously described by us as LSD1 inhibitor, were obtained by enantiospecific synthesis/chiral HPLC separation method. Tested in LSD1 and MAO assays, 11b (S,1S,2R) and 11d (R,1S,2R) were the most potent isomers against LSD1 and were less active against MAO-A and practically inactive against MAO-B. In cells, all the four diastereomers induced Gfi-1b and ITGAM gene expression in NB4 cells, accordingly with their LSD1 inhibition, and 11b and 11d inhibited the colony forming potential in murine promyelocytic blasts.
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Affiliation(s)
- Sergio Valente
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Veronica Rodriguez
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Ciro Mercurio
- Genextra
Group, DAC s.r.l., Via Adamello 16, 20139 Milano, Italy
| | - Paola Vianello
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Bruna Saponara
- Department
of Therapeutic Research and Medicines Evaluation, Italian National Institute of Health, Via Regina Elena 299, 00161 Roma, Italy
| | - Roberto Cirilli
- Department
of Therapeutic Research and Medicines Evaluation, Italian National Institute of Health, Via Regina Elena 299, 00161 Roma, Italy
| | - Giuseppe Ciossani
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Donatella Labella
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Giovanni Ruoppolo
- Department
of Sense Organs, Sapienza University of Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - Oronza A. Botrugno
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paola Dessanti
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Saverio Minucci
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Department
of Biosciences, University of Milan, 20100 Milan, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Mario Varasi
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
- Pasteur
Institute−Cenci Bolognetti Foundation, Sapienza University of Roma, P.le A. Moro 5, 00185 Roma, Italy
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14
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Rotili D, Tarantino D, Nawrozkij MB, Babushkin AS, Botta G, Marrocco B, Cirilli R, Menta S, Badia R, Crespan E, Ballante F, Ragno R, Esté JA, Maga G, Mai A. Exploring the Role of 2-Chloro-6-fluoro Substitution in 2-Alkylthio-6-benzyl-5-alkylpyrimidin-4(3H)-ones: Effects in HIV-1-Infected Cells and in HIV-1 Reverse Transcriptase Enzymes. J Med Chem 2014; 57:5212-25. [DOI: 10.1021/jm500284x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Dante Rotili
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Domenico Tarantino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Maxim B. Nawrozkij
- Volgograd State Technical University, pr. Lenina, 28, 400131 Volgograd, Russia
| | | | - Giorgia Botta
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Roberto Cirilli
- Dipartimento
del Farmaco, Istituto Superiore di Sanità,, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sergio Menta
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Roger Badia
- IrsiCaixa,
Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Emmanuele Crespan
- Istituto
di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Flavio Ballante
- Rome Center
for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
- Department
of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, 700 South Euclid Avenue, St. Louis, Missouri 00185, United States
| | - Rino Ragno
- Rome Center
for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - José A. Esté
- IrsiCaixa,
Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Giovanni Maga
- Istituto
di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Antonello Mai
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
- Istituto
Pasteur—Fondazione Cenci Bolognetti, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
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15
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Rotili D, Tarantino D, Marrocco B, Gros C, Masson V, Poughon V, Ausseil F, Chang Y, Labella D, Cosconati S, Di Maro S, Novellino E, Schnekenburger M, Grandjenette C, Bouvy C, Diederich M, Cheng X, Arimondo PB, Mai A. Properly substituted analogues of BIX-01294 lose inhibition of G9a histone methyltransferase and gain selective anti-DNA methyltransferase 3A activity. PLoS One 2014; 9:e96941. [PMID: 24810902 PMCID: PMC4014597 DOI: 10.1371/journal.pone.0096941] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/14/2014] [Indexed: 11/21/2022] Open
Abstract
Chemical manipulations performed on the histone H3 lysine 9 methyltransferases (G9a/GLP) inhibitor BIX-01294 afforded novel desmethoxyquinazolines able to inhibit the DNA methyltransferase DNMT3A at low micromolar levels without any significant inhibition of DNMT1 and G9a. In KG-1 cells such compounds, when tested at sub-toxic doses, induced the luciferase re-expression in a stable construct controlled by a cytomegalovirus (CMV) promoter silenced by methylation (CMV-luc assay). Finally, in human lymphoma U-937 and RAJI cells, the N-(1-benzylpiperidin-4-yl)-2-(4-phenylpiperazin-1-yl)quinazolin-4-amine induced the highest proliferation arrest and cell death induction starting from 10 µM, in agreement with its DNMT3A inhibitory potency.
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Affiliation(s)
- Dante Rotili
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, IT
| | - Domenico Tarantino
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, IT
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, IT
| | | | | | | | | | - Yanqi Chang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Donatella Labella
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, IT
| | | | - Salvatore Di Maro
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Napoli, IT
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Napoli, IT
| | - Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Luxembourg, Luxembourg
| | - Cindy Grandjenette
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Luxembourg, Luxembourg
| | - Celine Bouvy
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Luxembourg, Luxembourg
| | - Marc Diederich
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Luxembourg, Luxembourg
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | | | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, IT
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Roma, IT
- * E-mail:
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16
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Rotili D, Tomassi S, Conte M, Benedetti R, Tortorici M, Ciossani G, Valente S, Marrocco B, Labella D, Novellino E, Mattevi A, Altucci L, Tumber A, Yapp C, King ONF, Hopkinson RJ, Kawamura A, Schofield CJ, Mai A. Pan-histone demethylase inhibitors simultaneously targeting Jumonji C and lysine-specific demethylases display high anticancer activities. J Med Chem 2013; 57:42-55. [PMID: 24325601 DOI: 10.1021/jm4012802] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In prostate cancer, two different types of histone lysine demethylases (KDM), LSD1/KDM1 and JMJD2/KDM4, are coexpressed and colocalize with the androgen receptor. We designed and synthesized hybrid LSD1/JmjC or "pan-KDM" inhibitors 1-6 by coupling the skeleton of tranylcypromine 7, a known LSD1 inhibitor, with 4-carboxy-4'-carbomethoxy-2,2'-bipyridine 8 or 5-carboxy-8-hydroxyquinoline 9, two 2-oxoglutarate competitive templates developed for JmjC inhibition. Hybrid compounds 1-6 are able to simultaneously target both KDM families and have been validated as potential antitumor agents in cells. Among them, 2 and 3 increase H3K4 and H3K9 methylation levels in cells and cause growth arrest and substantial apoptosis in LNCaP prostate and HCT116 colon cancer cells. When tested in noncancer mesenchymal progenitor (MePR) cells, 2 and 3 induced little and no apoptosis, respectively, thus showing cancer-selective inhibiting action.
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Affiliation(s)
- Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome , P. le A. Moro 5, 00185 Rome, Italy
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