We previously demonstrated that natural product‐inspired 3,4‐dihydropyrrolo1,2‐apyrazin‐1(2H)‐ones derivatives delivered potent and selective PIM kinases inhibitors however with non‐optimal ADME/PK ...properties and modest oral bioavailability. Herein, we describe a structure‐based scaffold decoration and a stereoselective approach to this chemical class. The synthesis, structure–activity relationship studies, chiral analysis, and pharmacokinetic data of compounds from this inhibitor class are presented herein. Compound 20c demonstrated excellent potency on PIM1 and PIM2 with exquisite kinases selectivity and PK properties that efficiently and dose‐dependently promoted c‐Myc degradation and appear to be promising lead compounds for further development.
We previously demonstrated that natural product‐inspired 3,4‐dihydropyrrolo1,2‐apyrazin‐1(2H)‐ones derivatives delivered potent and selective PIM kinases inhibitors however with non‐optimal ADME/PK ...properties and modest oral bioavailability. Herein, we describe a structure‐based scaffold decoration and a stereoselective approach to this chemical class. The synthesis, structure–activity relationship studies, chiral analysis, and pharmacokinetic data of compounds from this inhibitor class are presented herein. Compound 20c demonstrated excellent potency on PIM1 and PIM2 with exquisite kinases selectivity and PK properties that efficiently and dose‐dependently promoted c‐Myc degradation and appear to be promising lead compounds for further development.
PIM1 is over-expressed in multiple tumors, including prostate cancer (PCa). PIM1 upregulation is mediated by direct binding of the ERG transcription factor to its promoter. About 50% of PCa cases are ...characterized by the presence of the TMPRSS2/ERG fusion, leading to ERG over-expression and thus to PIM1 transcriptional activation. PIM kinases are considered as weak oncogenes, but when combined with additional genetic alterations can induce strong transforming effects. Here we show anti-proliferative activity of the newly described PIM1 inhibitor NMS-P645 in combination with the PI3K inhibitor GDC-0941 in TMPRSS2/ERG positive and negative PCa cells. Treatment with NMS-P645 alone can reverse PIM1-mediated pro-survival signals in prostate cells, such as activation of STAT3 through Tyr705 phosphorylation and resistance to taxane-based treatments, but does not exert a strong anti-tumoral effect. However, the simultaneous treatment with NMS-P645 and GDC-0941 induces a significant anti-proliferative response in PCa cells. These results support the use of combination strategies with PIM and PI3K inhibitors as effective treatment for PCa cases.
Abstract
The B-cell receptor (BCR) is a key survival molecule for normal B cells and for most B-cell malignancies, such as Chronic Lymphocytic Leukaemia (CLL) and Non-Hodgkin’s Lymphomas (NHL) ...including Diffuse Large B-cell Lymphomas (DLBCL). Small molecule inhibitors of key signaling kinases involved in the BCR pathway, such as the Btk inhibitor ibrutinib and the PI3Kdelta inhibitor idelalisib, have already demonstrated significant clinical activity. Spleen tyrosine kinase (Syk) is a non-receptor cytoplasmic tyrosine kinase that plays a fundamental role in BCR signaling initiation thus representing an additional potential therapeutic target for the inhibition of the BCR pathway. Here, we report the discovery and characterization of NMS-0963, a novel potent, selective and orally available Syk inhibitor, identified through an integrated medicinal chemistry and rational design approach. NMS-0963 showed potent inhibitory effect on Syk in an in vitro biochemical assay and displayed a good selectivity profile on a broad panel of kinases. On-target potency was confirmed in a cell-based assay using BaF3 cells engineered to express constitutively activated Syk, showing potent inhibition of Syk activity resulting in antiproliferative effect with IC50s in the low nanomolar range. Effective inhibition of BCR-mediated signaling pathway was observed in DLBCL-derived cell lines. NMS-0963 showed favourable ADME profile and good in vivo pharmacokinetic profiles after oral administration in mouse, rat and dog. Furthermore, NMS-963 demonstrated striking in vivo efficacy in tumor models of CD79/Myd88 mutated DLBCL, superior to competitors. Together with a permissive preclinical safety profile, these results support a rational for clinical development of NMS-0963 in DLBCL.
Citation Format: Grazia Saturno, Michele Modugno, Paolo Orsini, Giovanni Cervi, Laura Buffa, Ilaria Motto, Nilla Avanzi, Marisa Montemartini, Fabio Gasparri, Gemma Texido, Arturo Galvani, Antonella Isacchi. NMS-0963 is a novel potent, selective and orally available Syk inhibitor with promising preclinical activity in diffuse large B-cell lymphoma. abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4036.
Abstract
Introduction: Choline kinase alpha (ChoKα), the first enzyme in the Kennedy pathway that catalyzes the phosphorylation of free choline to phosphocholine (PCho), is responsible for the de ...novo biosynthesis of phosphatidylcholine (PC), the major phospholipid of cellular membranes. Aberrant choline metabolic profiles and concomitant ChoKα upregulation have been described in most human malignancies (i.e. breast, lung, ovary, liver) and have been found to correlate with advanced histological tumour grade. ChoKα, depletion by siRNA or shRNA inhibits growth and migration of different tumor cell lines both in vitro and in vivo, which is not observed for the ChoKβ isoform. Choline mimetic inhibitors of ChoKα (i.e. MN58b) have been shown to have antitumor activity in preclinical models, although their efficacy is hampered by a significant toxicity, possibly due to cross-reactivity with other choline-dependent proteins (transporters, enzymes). At NMS a high throughput screening (HTS) was performed with the objective to identify ATP-mimetic ChoKα inhibitors potentially less toxic than choline-mimetic compounds.
Methods: Hits from different classes were characterized for biochemical activity on ChoKα and ChoKβ and biochemical mechanism of inhibition. The binding site of selected ATP competitive inhibitors was confirmed by co-crystallization with ChoKα. On-target mechanism of action in cells was confirmed by analysing inhibition of PCho formation.
Result: Structure-based chemical expansion of Hits from one of the prioritized classes resulted in compounds with biochemical potencies in the single digit nanomolar range displaying selectivity vs ChoKβ as well as a diverse panel of protein kinases. In several tumor cell lines, the compounds were able to inhibit the formation of PCho at a concentration in agreement with that required to achieve anti-proliferative activity. The most potent compounds were tested on a panel of 24 representative breast cancer cell lines which showed differential sensitivity towards ChoKα inhibition. Analysis of genomic (DNA and RNA) and proteomic (>50 markers) expression profiles of the breast cancer cell lines is ongoing to identify predictive biomarkers of response.
Conclusion: Medicinal chemistry expansion of a novel class of compounds identified by HTS allowed the development of potent ChoKα ATP-mimetic inhibitors able to modulate PCho levels in cells, which can be used to identify preferential sensitivity contexts. Medicinal chemistry activities are ongoing to further improve their potency and optimize their ADME/PK properties.
Citation Format: Paola Gnocchi, Francesca Quartieri, Alessandra Badari, Roberta Bosotti, Elena Casale, Emiliana Corti, Cinzia G. Cristiani, Ulisse Cucchi, Fabio Gasparri, Laura M. Gianellini, Laura M. Giorgini, Marisa Montemartini, Giuliana Mion, Marcella Nesi, Christian Orrenius, Claudia E. Re, Daniele Donati, Eduard R. Felder, Arturo Galvani, Antonella Isacchi. Identification and characterization of ATP-mimetic choline kinase inhibitors abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4790.
A novel series of PIM inhibitors was derived from a combined effort in natural product-inspired library generation and screening. The novel pyrrolo1,2-apyrazinones initial hits are inhibitors of PIM ...isoforms with IC50 values in the low micromolar range. The application of a rational optimization strategy, guided by the determination of the crystal structure of the complex in the kinase domain of PIM1 with compound 1, led to the discovery of compound 15a, which is a potent PIM kinases inhibitor exhibiting excellent selectivity against a large panel of kinases, representative of each family. The synthesis, structure–activity relationship studies, and pharmacokinetic data of compounds from this inhibitor class are presented herein. Furthermore, the cellular activities including inhibition of cell growth and modulation of downstream targets are also described.
Abstract
Maternal Embryonic Leucine zipper Kinase (MELK) is a serine-threonine kinase implicated in stem cell renewal, override of cell cycle checkpoints, pre-mRNA splicing and resistance to ...apoptosis, while MELK gene expression levels correlate inversely with poor prognosis in breast cancer, prostate cancer and glioblastoma patients. Moreover, recent findings underlie the oncogenic role of this kinase in triple negative breast cancer (TNBC), a category of high-grade, invasive tumors which lack expression of estrogen receptor (ER) and progesterone receptor (PR) and HER2 amplification and which is resistant to current cytotoxic and targeted therapies. Furthermore, they are highly heterogeneous with respect to genomic alterations, and common therapeutic targets are lacking, although substantial evidence implicates dysregulated kinase signaling.
Here, we describe the preclinical characterization of novel, potent and selective ATP-competitive MELK kinase inhibitors identified by means of high-throughput screening of the NMS proprietary compound collection. Leading compounds possess biochemical activity against MELK in the nanomolar range with high selectivity against a panel of 60 further kinases representative of the human kinome. Amongst human tumor cell lines tested in 2-dimensional colony outgrowth assays, marked sensitivity was observed in breast cancer cell lines, with sub-micromolar anti-proliferative activity. This effect was accompanied by dose-dependent induction of apoptosis and by modulation of cellular biomarkers, consistent with a MELK-dependent mechanism of action.
Overall, these data provide further evidence that MELK is a promising biological target for the development of novel anticancer therapies.
Citation Format: Patrizia Carpinelli, Marisa Montemartini, Nadia Amboldi, Dario Ballinari, Sabrina Cribioli, Marina Ciomei, Riccardo Colombo, Stefania Re Depaolini, Nilla Avanzi, Giulia Canevari, Walter Ceccarelli, Helena Posteri, Maria Gabriella Brasca, Daniele Donati, Eduard Rudolf Felder, Antonella Isacchi, Arturo Galvani, Alessia Montagnoli. Novel and selective MELK kinase inhibitors active in breast cancer cell lines. abstract. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3795.
The crystal structure of tyrosine aminotransferase
(TAT) from the parasitic protozoan Trypanosoma cruzi,
which belongs to the aminotransferase subfamily Iγ,
has been determined at 2.5 Å resolution ...with the
R-value R = 15.1%. T. cruzi
TAT shares less than 15% sequence identity with aminotransferases
of subfamily Iα but shows only two larger topological
differences to the aspartate aminotransferases (AspATs).
First, TAT contains a loop protruding from the enzyme surface
in the larger cofactor-binding domain, where the AspATs
have a kinked α-helix. Second, in the smaller substrate-binding
domain, TAT has a four-stranded antiparallel β-sheet
instead of the two-stranded β-sheet in the AspATs.
The position of the aromatic ring of the pyridoxal-5′-phosphate
cofactor is very similar to the AspATs but the phosphate
group, in contrast, is closer to the substrate-binding
site with one of its oxygen atoms pointing toward the substrate.
Differences in substrate specificities of T. cruzi
TAT and subfamily Iα aminotransferases can be attributed
by modeling of substrate complexes mainly to this different
position of the cofactor-phosphate group. Absence of the
arginine, which in the AspATs fixes the substrate side-chain
carboxylate group by a salt bridge, contributes to the
inability of T. cruzi TAT to transaminate acidic
amino acids. The preference of TAT for tyrosine is probably
related to the ability of Asn17 in TAT to form a hydrogen
bond to the tyrosine side-chain hydroxyl group.
Rat liver and Trypanosoma cruzi tyrosine aminotransferases (TATs) share over 40% sequence identity, but differ in their substrate specificities. To explore the molecular features related to these ...differences, comparative mutagenesis studies were conducted on full length T. cruzi TAT and N‐terminally truncated rat TAT recombinant enzymes. The functionality of Arg315 and Arg417 in rat TAT was investigated for comparison with the conserved Arg292 and Arg386 in aspartate and bacterial aromatic aminotransferases (ASATs and ARATs). The rat TAT Arg315Lys variant remained fully active indicating that, as in T. cruzi TAT and contrary to subfamily Iα aminotransferases, this residue is not critical for activity. In contrast, the Arg417Gln variant was inactive. The catalytic relevance of the putative rat TAT active site residues Asn54 and Arg57, which are strictly conserved in TATs (Asn17 and Arg20 in T. cruzi TAT) but differ in ASATs and ARATs, was also explored. The substitutions Arg57Ala and Arg57Gln abolished enzymatic activity of these mutants. In both variants, spectral studies demonstrated that aromatic but not dicarboxylic substrates could efficiently bind in the active site. Thus, Arg57 appears to be functionally equivalent to Arg292 of ASATs and ARATs. Asn54 also appears to be involved in the catalytic mechanism of rat TAT since its exchange for Ser lowered the kcat/Km ratios towards its substrates. Mutation of the analogous residues in T. cruzi TAT also lowered the catalytic efficiencies (kcat/Km) of the variants substantially. The results imply that the mamalian TAT is more closely related to the T. cruzi TAT than to ASATs and ARATs.
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