Publications by authors named "Federica Amigoni"

4 Publications

  • Page 1 of 1

Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure-Activity Relationship.

J Med Chem 2017 03 27;60(5):1693-1715. Epub 2017 Feb 27.

Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.

The balance of methylation levels at histone H3 lysine 4 (H3K4) is regulated by KDM1A (LSD1). KDM1A is overexpressed in several tumor types, thus representing an emerging target for the development of novel cancer therapeutics. We have previously described ( Part 1, DOI 10.1021.acs.jmedchem.6b01018 ) the identification of thieno[3,2-b]pyrrole-5-carboxamides as novel reversible inhibitors of KDM1A, whose preliminary exploration resulted in compound 2 with biochemical IC = 160 nM. We now report the structure-guided optimization of this chemical series based on multiple ligand/KDM1A-CoRest cocrystal structures, which led to several extremely potent inhibitors. In particular, compounds 46, 49, and 50 showed single-digit nanomolar IC values for in vitro inhibition of KDM1A, with high selectivity in secondary assays. In THP-1 cells, these compounds transcriptionally affected the expression of genes regulated by KDM1A such as CD14, CD11b, and CD86. Moreover, 49 and 50 showed a remarkable anticlonogenic cell growth effect on MLL-AF9 human leukemia cells.
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http://dx.doi.org/10.1021/acs.jmedchem.6b01019DOI Listing
March 2017

Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration.

J Med Chem 2017 03 27;60(5):1673-1692. Epub 2017 Feb 27.

Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.

Lysine specific demethylase 1 KDM1A (LSD1) regulates histone methylation and it is increasingly recognized as a potential therapeutic target in oncology. We report on a high-throughput screening campaign performed on KDM1A/CoREST, using a time-resolved fluorescence resonance energy transfer (TR-FRET) technology, to identify reversible inhibitors. The screening led to 115 hits for which we determined biochemical IC, thus identifying four chemical series. After data analysis, we have prioritized the chemical series of N-phenyl-4H-thieno[3, 2-b]pyrrole-5-carboxamide for which we obtained X-ray structures of the most potent hit (compound 19, IC = 2.9 μM) in complex with the enzyme. Initial expansion of this chemical class, both modifying core structure and decorating benzamide moiety, was directed toward the definition of the moieties responsible for the interaction with the enzyme. Preliminary optimization led to compound 90, which inhibited the enzyme with a submicromolar IC (0.162 μM), capable of inhibiting the target in cells.
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http://dx.doi.org/10.1021/acs.jmedchem.6b01018DOI Listing
March 2017

Kinase inhibitors for CNS diseases: an analysis of the recent patent literature.

Pharm Pat Anal 2012 May;1(2):177-92

Newron Pharmaceuticals, Via Ariosto 21, 20091 Bresso, Milan, Italy.

Protein kinases (PKs), as members of an important target class in current pharmaceutical research, have been mostly exploited so far in therapeutic areas such as oncology and inflammation. However, basic research on some PKs as key components of molecular mechanisms underlying neurodegeneration and neuroprotection may translate into new medicines for CNS diseases in the next few years. This review is an account of recent patents dealing with kinase inhibitors primarily designed for CNS indications. CNS-directed patents on kinase modulators published after 2008 were surveyed using SciFinder(®) and public patent search engines. Some PK targets, such as GSK-3β, CDK5, ROCK and p38α MAPK, continue to attract interest even though a clinical proof-of-concept is yet to be attained in a CNS setting. Less established PKs such as LRRK2, MLK, PAK and DAPK-1 hold promise as valuable targets of the future.
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http://dx.doi.org/10.4155/ppa.12.19DOI Listing
May 2012

Tricarbonyl-rhenium complexes of a thiol-functionalized amphoteric poly(amidoamine).

Biomacromolecules 2009 Dec;10(12):3273-82

Dipartimento di Chimica Inorganica, Metallorganica e Analitica L. Malatesta, Universita degli Studi di Milano, via Venezian 21, 20133 Milano, Italy.

An amphoteric thiol-functionalized poly(amidoamine) nicknamed ISA23SH(10%) was synthesized. Rhenium complexes 1 and 2, containing 0.5 and 0.8 equiv of rhenium, respectively, were easily obtained by reacting ISA23SH(10%) with [Re(CO)(3)(H(2)O)(3)](CF(3)SO(3)) in aqueous solution at pH 5.5. Both ISA23SH(10%), and its rhenium complexes were soluble in water under physiological conditions. The resultant solutions were stable, even in the presence of cysteine. Rhenium chelation occurred through the S and N atoms of the cysteamine moiety, as demonstrated by (1)H, (13)C, and (15)N NMR spectroscopy. The diffusion coefficients and the hydrodynamic radii of ISA23SH(10%) and complex 1 were determined by pulsed gradient spin echo (PGSE) NMR experiments. The radius of the rhenium complexes 1 and 2 was always slightly larger than that of the parent polymer. TEM analysis showed that both complexes form spherical nanoparticles with narrow size distributions. Consistent results were obtained by dynamic light scattering. The observed sizes were in good agreement with those evaluated by PGSE. Preliminary in vitro and in vivo biological studies have been performed on complexes 1 and 2 as well as on the parent ISA23SH(10%). Neither hemolytic activity of the two rhenium complexes and the parent polymer, up to a concentration of 5 mg/mL, nor cytotoxic effects were observed on Hela cell after 48 h at a concentration of 100 ng/mL. In vivo toxicological tests showed that ISA23SH(10%) is highly biocompatible, with a maximum tolerated dose (MTD) of 500 mg/kg. No toxic side effects were apparent after the intravenous injection in mice of the two rhenium complexes in doses up to 20 mg/kg.
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http://dx.doi.org/10.1021/bm9008638DOI Listing
December 2009