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Effects of N-terminus modified Hx-amides on DNA binding affinity, sequence specificity, cellular uptake, and gene expression. Bioorg Med Chem Lett 2021; 47:128158. [PMID: 34058343 DOI: 10.1016/j.bmcl.2021.128158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Five X-HxIP (Hx-amides) 6a-e, in which the N-terminus p-anisyl moiety is modified, were designed and synthesised with the purpose of optimising DNA binding, improving cellular uptake/nuclear penetration, and enhancing the modulation of the topoisomerase IIα (TOP2A) gene expression. The modifications include a fluorophenyl group and other heterocycles bearing different molecular shapes, size, and polarity. Like their parent compound HxIP 3, all five X-HxIP analogues bind preferentially to their cognate sequence 5'-TACGAT-3', which is found embedded on the 5' flank of the inverted CCAAT box-2 (ICB2) site in the TOP2A gene promoter, and inhibit protein complex binding. Interestingly, the 4-pyridyl analog 6a exhibits greater binding affinity for the target DNA sequence and abolishes the protein:ICB2 interaction in vitro, at a lower concentration, compared to the prototypical compound HxIP 3. Analogues 6b-e, display improved DNA sequence specificity, but reduced binding affinity for the cognate sequence, relative to the unmodified HxIP 3, with polyamides 6b and 6e being the most sequence selective. However, unlike 3 and 6b, 6a was unable to enter cells, access the nucleus and thereby affect TOP2A gene expression in confluent human lung cancer cells. These results show that while DNA binding affinity and sequence selectivity are important, consideration of cellular uptake and concentration in the nucleus are critical when exerting biological activity is the desired outcome. By characterising the DNA binding, cellular uptake and gene regulatory properties of these small molecules, we can elucidate the determinants of the elicited biological activity, which can be impacted by even small structural modifications in the polyamide molecular design.
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Nardone V, Chaves-Sanjuan A, Lapi M, Airoldi C, Saponaro A, Pasqualato S, Dolfini D, Camilloni C, Bernardini A, Gnesutta N, Mantovani R, Nardini M. Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin. Cells 2020; 9:E2370. [PMID: 33138093 PMCID: PMC7692634 DOI: 10.3390/cells9112370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 12/27/2022] Open
Abstract
NF-Y is a transcription factor (TF) comprising three subunits (NF-YA, NF-YB, NF-YC) that binds with high specificity to the CCAAT sequence, a widespread regulatory element in gene promoters of prosurvival, cell-cycle-promoting, and metabolic genes. Tumor cells undergo "metabolic rewiring" through overexpression of genes involved in such pathways, many of which are under NF-Y control. In addition, NF-YA appears to be overexpressed in many tumor types. Thus, limiting NF-Y activity may represent a desirable anti-cancer strategy, which is an ongoing field of research. With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. We focused on suramin given its high water-solubility that is an important factor for in vitro testing, since NF-Y is sensitive to DMSO. By electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), STD NMR, X-ray crystallography, and molecular dynamics (MD) simulations, we showed that suramin binds to the histone fold domains (HFDs) of NF-Y, preventing DNA-binding. Our analyses, provide atomic-level detail on the interaction between suramin and NF-Y and reveal a region of the protein, nearby the suramin-binding site and poorly conserved in other HFD-containing TFs, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications.
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Affiliation(s)
- Valentina Nardone
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Michela Lapi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
| | - Andrea Saponaro
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Sebastiano Pasqualato
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy;
| | - Diletta Dolfini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Carlo Camilloni
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Andrea Bernardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Nerina Gnesutta
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Roberto Mantovani
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
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3
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Li Petri G, Spanò V, Spatola R, Holl R, Raimondi MV, Barraja P, Montalbano A. Bioactive pyrrole-based compounds with target selectivity. Eur J Med Chem 2020; 208:112783. [PMID: 32916311 PMCID: PMC7455853 DOI: 10.1016/j.ejmech.2020.112783] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
The discovery of novel synthetic compounds with drug-like properties is an ongoing challenge in medicinal chemistry. Natural products have inspired the synthesis of compounds for pharmaceutical application, most of which are based on N-heterocyclic motifs. Among these, the pyrrole ring is one of the most explored heterocycles in drug discovery programs for several therapeutic areas, confirmed by the high number of pyrrole-based drugs reaching the market. In the present review, we focused on pyrrole and its hetero-fused derivatives with anticancer, antimicrobial, and antiviral activities, reported in the literature between 2015 and 2019, for which a specific target was identified, being responsible for their biological activity. It emerges that the powerful pharmaceutical and pharmacological features provided by the pyrrole nucleus as pharmacophore unit of many drugs are still recognized by medicinal chemists. Pyrrole nucleus is one of the most explored heterocycle in drug discovery. Pyrrole derivatives exhibit antitumor, antimicrobial and antiviral activities. Targets involved in their biological activities were identified. SAR to underline their most important features were discussed.
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Affiliation(s)
- Giovanna Li Petri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Virginia Spanò
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Roberto Spatola
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Ralph Holl
- Department of Chemistry, Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Maria Valeria Raimondi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy.
| | - Paola Barraja
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Alessandra Montalbano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
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4
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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Liu B, Pett L, Kiakos K, Patil PC, Satam V, Hartley JA, Lee M, Wilson WD. DNA-Binding Properties of New Fluorescent AzaHx Amides: Methoxypyridylazabenzimidazolepyrroleimidazole/pyrrole. Chembiochem 2018; 19:1979-1987. [PMID: 29974647 DOI: 10.1002/cbic.201800273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Indexed: 11/11/2022]
Abstract
DNA minor groove binding polyamides have been extensively developed to control abnormal gene expression. The establishment of novel, inherently fluorescent 2-(p-anisyl)benzimidazole (Hx) amides has provided an alternative path for studying DNA binding in cells by direct observation of cell localization. Because of the 2:1 antiparallel stacking homodimer binding mode of these molecules to DNA, modification of Hx amides to 2-(p-anisyl)-4-azabenzimidazole (AzaHx) amides has successfully extended the DNA-recognition repertoire from central CG [recognized by Hx-I (I=N-methylimidazole)] to central GC [recognized by AzaHx-P (P=N-methylpyrrole)] recognition. For potential targeting of two consecutive GG bases, modification of the AzaHx moiety to 2- and 3-pyridyl-aza-benzimidazole (Pyr-AzaHx) moieties was explored. The newly designed molecules are also small-sized, fluorescent amides with the Pyr-AzaHx moiety connected to two conventional five-membered heterocycles. Complementary biophysical methods were performed to investigate the DNA-binding properties of these molecules. The results showed that neither 3-Pyr-AzaHx nor 2-Pyr-AzaHx was able to mimic I-I=N-methylimidazole-N-methylimidazole to target GG dinucleotides specifically. Rather, 3-Pyr-AzaHx was found to function like AzaHx, f-I (f=formamide), or P-I as an antiparallel stacked dimer. 3-Pyr-AzaHx-PI (2) binds 5'-ACGCGT'-3' with improved binding affinity and high sequence specificity in comparison to its parent molecule AzaHx-PI (1). However, 2-Pyr-AzaHx is detrimental to DNA binding because of an unfavorable steric clash upon stacking in the minor groove.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA
| | - Luke Pett
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Pravin C Patil
- Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA
| | - Vijay Satam
- Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA
| | - John A Hartley
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Moses Lee
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA.,Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA.,Current address: M. J. Murdock Charitable Trust, 703 Broadway Street, Suite, 710, Vancouver, WA, 98660, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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7
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Kiakos K, Englinger B, Yanow SK, Wernitznig D, Jakupec MA, Berger W, Keppler BK, Hartley JA, Lee M, Patil PC. Design, synthesis, nuclear localization, and biological activity of a fluorescent duocarmycin analog, HxTfA. Bioorg Med Chem Lett 2018; 28:1342-1347. [PMID: 29548574 DOI: 10.1016/j.bmcl.2018.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/23/2018] [Accepted: 03/05/2018] [Indexed: 01/20/2023]
Abstract
HxTfA 4 is a fluorescent analog of a potent cytotoxic and antimalarial agent, TfA 3, which is currently being investigated for the development of an antimalarial vaccine, PlasProtect®. HxTfA contains a p-anisylbenzimidazole or Hx moiety, which is endowed with a blue emission upon excitation at 318 nm; thus enabling it to be used as a surrogate for probing the cellular fate of TfA using confocal microscopy, and addressing the question of nuclear localization. HxTfA exhibits similar selectivity to TfA for A-tract sequences of DNA, alkylating adenine-N3, albeit at 10-fold higher concentrations. It also possesses in vitro cytotoxicity against A549 human lung carcinoma cells and Plasmodium falciparum. Confocal microscopy studies showed for the first time that HxTfA, and by inference TfA, entered A549 cells and localized in the nucleus to exert its biological activity. At biologically relevant concentrations, HxTfA elicits DNA damage response as evidenced by a marked increase in the levels of γH2AX observed by confocal microscopy and immunoblotting studies, and ultimately induces apoptosis.
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Affiliation(s)
- Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, United Kingdom; Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria.
| | - Bernhard Englinger
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | | | - Debora Wernitznig
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Michael A Jakupec
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Walter Berger
- Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin C Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
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8
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Mantovani R. Nuclear factor Y in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:523-524. [PMID: 28279783 DOI: 10.1016/j.bbagrm.2017.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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