Manuela Villa

Cinnamic anilides as new mitochondrial permeability transition pore inhibitors endowed with ischemia-reperfusion injury protective effect in vivo.

In this account, we report the development of a series of substituted cinnamic anilides that represents a novel class of mitochondrial permeability transition pore (mPTP) inhibitors. Initial class expansion led to the establishment of the basic structural requirements for activity and to the identification of derivatives with inhibitory potency higher than that of the standard inhibitor cyclosporine-A (CsA). These compounds can inhibit mPTP opening in response to several stimuli including calcium overload, oxidative stress, and thiol cross-linkers. The activity of the cinnamic anilide mPTP inhibitors turned out to be additive with that of CsA, suggesting for these inhibitors a molecular target different from cyclophylin-D. In vitro and in vivo data are presented for (E)-3-(4-fluoro-3-hydroxy-phenyl)-N-naphthalen-1-yl-acrylamide 22, one of the most interesting compounds in this series, able to attenuate opening of the mPTP and limit reperfusion injury in a rabbit model of acute myocardial infarction.

Discovery of a Novel Inhibitor of Histone Lysine-Specific Demethylase 1A (KDM1A/LSD1) as Orally Active Antitumor Agent

We report the stereoselective synthesis and biological activity of a novel series of tranylcypromine (TCPA) derivatives (14a-k, 15, 16), potent inhibitors of KDM1A. The new compounds strongly inhibit the clonogenic potential of acute leukemia cell lines. In particular three molecules (14d, 14e, and 14g) showing selectivity versus MAO A and remarkably inhibiting colony formation in THP-1 human leukemia cells, were assessed in mouse for their preliminary pharmacokinetic. 14d and 14e were further tested in vivo in a murine acute promyelocytic leukemia model, resulting 14d the most effective. Its two enantiomers were synthesized: the (1S,2R) enantiomer 15 showed higher activity than its (1R,2S) analogue 16, in both biochemical and cellular assays. Compound 15 exhibited in vivo efficacy after oral administration, determining a 62% increased survival in mouse leukemia model with evidence of KDM1A inhibition. The biological profile of compound 15 supports its further investigation as a cancer therapeutic.

Cyclin-dependent kinase inhibitors: a survey of the recent patent literature

Since the mid-1990s cyclin-dependent kinase (CDK) inhibition has been the subject of an intense drug discovery effort in the pharmaceutical industry and in some academic institutions. Although only few compounds have at present progressed into human clinical trials, the prospect of finding safe agents useful in therapy, particularly in the cancer setting, is still positive. Some trends can be observed that witness the impact of recent findings in CDK basic biological research and technology advancements on the evolution of the patent literature on CDK inhibition. A patent literature review of small organic molecules as CDK inhibitors comprising the years 2001 – 2004 is presented here, as many of the major pharmaceutical companies have shown a continued effort in the field.

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.

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 IC50, 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, IC50 = 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 IC50 (0.162 μM), capable of inhibiting the target in cells.

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.

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 IC50 = 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 IC50 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.

Novel potent inhibitors of the histone demethylase KDM1A (LSD1), orally active in a murine promyelocitic leukemia model

BACKGROUND Histone lysine demethylases (KDMs) are well-recognized targets in oncology drug discovery. They function at the post-translation level controlling chromatin conformation and gene transcription. KDM1A is a flavin adenine dinucleotide-dependent amine oxidase, overexpressed in several tumor types, including acute myeloid leukemia, neuroblastoma and non-small-cell lung cancer. Among the many known monoamine oxidase inhibitors screened for KDM1A inhibition, tranylcypromine emerged as a moderately active hit, which irreversibly binds to the flavin adenine dinucleotide cofactor. MATERIAL & METHODS The KDM1A inhibitors 5a-w were synthesized and tested in vitro and in vivo. The biochemical potency was determined, modulation of target in cells was demonstrated on KDM1A-dependent genes and the anti-clonogenic activity was performed in murine acute promyelocytic Leukemia (APL) blasts. An in vivo efficacy experiment was conducted using an established murine promyelocytic leukemia model. RESULTS We report a new series of tranylcypromine derivatives substituted on the cyclopropyl moiety, endowed with high potency in both biochemical and cellular assays. CONCLUSION The most interesting derivative (5a) significantly improved survival rate after oral administration in a murine model of promyelocitic leukemia.

571 Novel potent inhibitors of the Histone Demethylase KDM1A: Synthesis, pharmacological evaluation and in vivo activity

KDM1A, a FAD dependent histone demethylase with high homology to amino-oxidases, is responsible of the demethylation of mono and dimethyl lysine 4 on histone H3. KDM1A is part of various transcriptional corepressor complexes and interacts with the co-repressor complex CoREST and histone deacetylases (HDAC) 1 and 2. KDM1A is an essential gene with important roles in different biological relevant processes, including hematopoietic maturation. Its activity has also been demonstrated on non histone substrates such as p53, DNMT1 and MYPT1. High expression and correlation with poor prognosis has been reported for KDM1A in several cancer types, such as neuroblastoma, prostate cancer and non small cell lung cancer. Moreover the high expression of KDM1A and its inverse correlation in hematological malignancies, mostly in acute myeloid leukemia, was observed. Furthermore the enzyme has been demonstrated to sustain the in vivo leukemiogenic potential of MLLAF9 expressing leukemia stem cells. In the light of these findings, KDM1A has been increasingly recognized as an attractive therapeutic target in oncology. We have developed a novel series of potent and irreversible KDM1A inhibitors based on tranylcypromine. The compounds were obtained by a versatile and scalable synthetic process which allows a stereoselective synthesis of the trans enantiomers of the cyclopropane ring. Biochemical and biological characterization of these inhibitors, including their transcriptional effect on KDM1A targets and efficacy in reducing colony forming ability in leukemia cells, will be reported, together with ADME and pharmacokinetic properties of selected compounds. Finally, the best inhibitors of the series induced after oral administration a significant survival increase and provided evidences of target modulation in an in vivo murine promyelocytic leukemia model.