Michele Modugno

Crystal Structure of the T315I Abl Mutant in Complex with the Aurora Kinases Inhibitor PHA-739358

Mutations in the kinase domain of Bcr-Abl are the most common cause of resistance to therapy with imatinib in patients with chronic myelogenous leukemia (CML). Second-generation Bcr-Abl inhibitors are able to overcome most imatinib-resistant mutants, with the exception of the frequent T315I substitution, which is emerging as a major cause of resistance to these drugs in CML patients. Structural studies could be used to support the drug design process for the development of inhibitors able to target the T315I substitution, but until now no crystal structure of the T315I Abl mutant has been solved. We show here the first crystal structure of the kinase domain of Abl T315I in complex with PHA-739358, an Aurora kinase inhibitor currently in clinical development for solid and hematologic malignancies. This compound inhibits in vitro the kinase activity of wild-type Abl and of several mutants, including T315I. The cocrystal structure of T315I Abl kinase domain provides the structural basis for this activity: the inhibitor associates with an active conformation of the kinase domain in the ATP-binding pocket and lacks the steric hindrance imposed by the substitution of threonine by isoleucine.

p53-dependent downregulation of metastasis-associated laminin receptor

Based on observations suggesting a role for the tumor suppressor protein p53 in regulating expression of the 67-kDa laminin receptor precursor, 37LRP, we analysed the 37LRP promoter activity in a wild-type p53 (wt p53) ovarian carcinoma cell line and in a cisplatin-resistant subline with mutated p53. We observed an increased promoter activity in wt p53 cells as compared to the mutated-p53 line when the first intron of the 37LRP gene was present in the reporter construct. Cotransfection experiments showed that the promoter is downregulated by both wt and mutated p53. Deletion analysis of the first intron localized an enhancer activity in the first 5′ 214 bp that upregulates both 37LRP and SV40 promoter activity and is repressed by both wt and mutant p53. Cotransfection, mutagenesis and gel-shift experiments identified a functional AP-2 cis-acting element in this intron region that is repressed by increased levels of both wt and mutated p53. Coimmunoprecipitation studies revealed AP-2 in physical association in vivo with both wt and mutated p53, indicating for the first time that interaction of p53 with AP-2 is involved in the repression mechanism and in the regulation of genes involved in cancer growth and progression.

Identification of a Phenylacylsulfonamide Series of Dual Bcl-2/Bcl-Xl Antagonists.

A series of phenylacylsulfonamides has been prepared as antagonists of Bcl-2/Bcl-xL. In addition to potent binding affinities for both Bcl-2 and Bcl-xL, these compounds were shown to induce classical markers of apoptosis in isolated mitochondria. Overall weak cellular potency was improved by the incorporation of polar functionality resulting in compounds with moderate antiproliferative activity.

Identification of Myb-binding protein 1A (MYBBP1A) as a novel substrate for aurora B kinase.

Aurora kinases are mitotic enzymes involved in centrosome maturation and separation, spindle assembly and stability, and chromosome condensation, segregation, and cytokinesis and represent well known targets for cancer therapy because their deregulation has been linked to tumorigenesis. The availability of suitable markers is of crucial importance to investigate the functions of Auroras and monitor kinase inhibition in in vivo models and in clinical trials. Extending the knowledge on Aurora substrates could help to better understand their biology and could be a source for clinical biomarkers. Using biochemical, mass spectrometric, and cellular approaches, we identified MYBBP1A as a novel Aurora B substrate and serine 1303 as the major phosphorylation site. MYBBP1A is phosphorylated in nocodazole-arrested cells and is dephosphorylated upon Aurora B silencing or by treatment with Danusertib, a small molecule inhibitor of Aurora kinases. Furthermore, we show that MYBBP1A depletion by RNA interference causes mitotic progression delay and spindle assembly defects. MYBBP1A has until now been described as a nucleolar protein, mainly involved in transcriptional regulation. The results presented herein show MYBBP1A as a novel Aurora B kinase substrate and reveal a not yet recognized link of this nucleolar protein to mitosis.

Pyrazole and pyrimidine phenylacylsulfonamides as dual Bcl-2/Bcl-xL antagonists.

5-Butyl-1,4-diphenyl pyrazole and 2-amino-5-chloro pyrimidine acylsulfonamides were developed as potent dual antagonists of Bcl-2 and Bcl-xL. Compounds were optimized for binding to the I88, L92, I95, and F99 pockets normally occupied by pro-apoptotic protein Bim. An X-ray crystal structure confirmed the proposed binding mode. Observation of cytochrome c release from isolated mitochondria in MV-411 cells provides further evidence of target inhibition. Compounds demonstrated submicromolar antiproliferative activity in Bcl-2/Bcl-xL dependent cell lines.

Optimization of Diarylthiazole B-Raf Inhibitors: Identification of a Compound Endowed with High Oral Antitumor Activity, Mitigated Herg Inhibition, and Low Paradoxical Effect.

Aberrant activation of the mitogen‐activated protein kinase (MAPK)‐mediated pathway components, RAF‐MEK‐ERK, is frequently observed in human cancers and clearly contributes to oncogenesis. As part of a project aimed at finding inhibitors of B‐Raf, a key player in the MAPK cascade, we originally identified a thiazole derivative endowed with high potency and selectivity, optimal in vitro ADME properties, and good pharmacokinetic profiles in rodents, but that suffers from elevated hERG inhibitory activity. An optimization program was thus undertaken, focused mainly on the elaboration of the R1 and R2 groups of the scaffold. This effort ultimately led to N‐(4‐{2‐(1‐cyclopropylpiperidin‐4‐yl)‐4‐[3‐(2,5‐difluorobenzenesulfonylamino)‐2‐fluorophenyl]thiazol‐5‐yl}‐pyridin‐2‐yl)acetamide (20), which maintains favorable in vitro and in vivo properties, but lacks hERG liability. Besides exhibiting potent antiproliferative activity against only cell lines bearing B‐Raf V600E or V600D mutations, compound 20 also intriguingly shows a weaker “paradoxical” activation of MEK in non‐mutant B‐Raf cells than other known B‐Raf inhibitors. It also demonstrates very good efficacy in vivo against the A375 xenograft melanoma model (tumor volume inhibition >90 % at 10 mg kg−1); it is therefore a suitable candidate for preclinical development.

Abstract 2851: Preclinical characterization of NMS-P648, a novel and potent PARP-1/-3 inhibitor

PARP-1 and PARP-2 are nuclear enzymes activated by DNA strand breaks and are involved in recruitment of DNA repair proteins to sites of damage. PARP-1 and PARP-2 share partially overlapping functions, as shown by the embryonic lethality of double knockout mice compared to animals with single ablation either gene, which are viable. Despite this partial functional redundancy, PARP-1, but not PARP-2, inhibition has been shown to be synthetically lethal with defects in homologous recombination such as BRCA gene mutations. All PARP inhibitors that are currently under clinical investigation inhibit both PARP-1 and PARP-2, due to the high sequence similarity between the catalytic domains of the two enzymes. A third member of the family, PARP-3, has lower homology with PARP-1 and -2 and is much less well characterized, although it is known that its activity is stimulated by double strand breaks and that it promotes DNA repair through an error prone repair pathway, non-homologous end joining (NHEJ). PARP-3 inhibition is thus presumed to be synthetically lethal with other, alternative DNA repair pathway deficiencies. We report preclinical characterization of NMS-P648, a selective PARP-1/-3 inhibitor, with a dissociation constants (K D ), of 0.9 nM on PARP-1 and with greater than four hundred-fold less affinity for PARP-2, as assessed by direct binding assay. In cells, NMS-P648 inhibits hydrogen peroxide induced poly ADP-ribose (PAR) synthesis with an IC 50 of 1 nM, confirming expected mechanism of action and indicating that inhibition of PARP-2 is not required for this process. NMS-P648 has favourable ADME properties, including stability in liver microsome incubation assays, low efflux ratio in the CACO2 assay and an excellent pharmacokinetic profile, with complete oral bioavailability and exposure levels that increase proportionally with dose. Testing NMS-P648 on a panel of more than 100 human tumor cell lines using a 2D colony forming assay format revealed that 7 cell lines were highly sensitive to the compound (IC 50 Citation Format: Alessia Montagnoli, Gianluca Papeo, Sonia Rainoldi, Alessandra Cirla, Antonella Ciavolella, Clara Albanese, Michele Modugno, Roberta Bosotti, Alessio Somaschini, Giovanni Carapezza, Rosita Lupi, Dario Ballinari, Marina Ciomei, Enrico Pesenti, Daniele Donati, Antonella Isacchi, Arturo Galvani. Preclinical characterization of NMS-P648, a novel and potent PARP-1/-3 inhibitor. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2851. doi:10.1158/1538-7445.AM2015-2851

Abstract 3754: Characterization of NMS-P285, a new highly selective and potent BRAF inhibitor

Aberrant activation of the MAPK-mediated pathway components, RAF-MEK-ERK, is frequently found in human cancers and clearly contributes to oncogenesis. In particular, one of the three isoforms of RAF, BRAF, presents activating somatic mutations in 60% of melanomas, 50% of thyroid cancers, 10% of colon and 20% ovarian carcinomas. The most common BRAF mutation, substitution of glutamic acid for valine at position 600 within the activation segment of the kinase domain, accounts for 90% of mutated BRAF cases, and results in elevated kinase activity with consequent enhanced promotion of cell survival and proliferation. BRAF selective inhibitors as vemurafenib and dabrafenib have recently shown excellent results in patients with advanced melanoma expressing BRAF V600E mutant form. Here we describe the in vitro and in vivo properties of a novel potent and selective BRAF inhibitor belonging to the arylthiazole class of compounds. This, NMS-P285, is a potent inhibitor of both wild-type and mutated BRAF, with no cross-reactivity in a panel of 61 kinases. This compound occupies the ATP-binding pocket of the activated form of the enzyme (DFG motif in), partly filling the kinase back pocket, (i.e. type I ½ inhibitors). NMS-P285 has an antiproliferative activity in the low nanomolar range only against cell lines bearing BRAF V600E or V600D mutations. Its mechanism of action is confirmed: a strong inhibition of MAPK pathway was observed in BRAF mutated cells whereas in non-BRAF mutated cells MEK activation was not observed. NMS-P285 possesses a favourable in vitro ADME profile and a very good preliminary PK in mouse. When orally administered to mice with BRAF mutated human xenograft tumors, NMS-P285 resulted more potent than both vemurafenib and dabrafenib demonstrating high antitumor activity with strong and persistent tumor regression observed in all mice. Mechanism of action was demonstrated also ex vivo in A375 bearing mice: MAPK pathway resulted to be completely inhibited up to 6 hours after a single treatment at 30 mg/kg. In conclusion, NMS-P285 is a candidate suitable for preclinical development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3754. doi:1538-7445.AM2012-3754

Abstract 2522: Identification and characterization of new highly selective and potent BRAF inhibitors

Aberrant activation of the MAPK-mediated pathway components, RAF-MEK-ERK, is frequently found in human cancers and clearly contributes to oncogenesis. In particular, one of the three isoforms of RAF, BRAF, presents activating somatic mutations in 70% of melanomas, 50% of thyroid cancers, 10% of colon and 20% ovarian carcinomas. The most common BRAF mutation, substitution of glutamic acid for valine at position 600 within the activation segment of the kinase domain, accounts for 90% of mutated BRAF cases, and results in elevated kinase activity with consequent enhanced promotion of cell survival and proliferation. Here we describe the in vitro and in vivo properties of a novel class of potent and selective BRAF inhibitors. Starting from a series of arylpyrazole derivatives that were found to be active against wild-type and mutated BRAF, an expansion and optimization program was undertaken. This led to the identification of both inhibitors of the active conformation and inhibitors of the inactive conformation of the enzyme, as confirmed by co-crystallography studies. Among the former category, a sub-series endowed with high potency and selectivity was identified, with compounds possessing low nM affinity for BRAF V600E and negligible cross-reactivity against a panel of 44 kinases. Members of this sub-series inhibited 72-hour proliferation of cell lines harboring the BRAF V600E mutation with IC 50 s below 100 nM and with greater than 100-fold selectivity compared to lines with wild-type BRAF. Consistent with this observation, inhibition of the MAPK signal transduction pathway was highly selective for cell lines with mutated BRAF. Biochemical profile, potency in cell proliferation assays, and cellular mechanism of action compared favorably among the sub-series to a reference BRAF inhibitor, PLX-4720, tested in parallel. The most potent compounds (e.g. NMS-P730 and NMS-P383) were selected for in vivo evaluation. In vivo, potent tumor growth inhibition was observed in the A375 xenograft model following oral administration, with no overt toxicity, and with corresponding modulation of the MAPK pathway, consistent with expected mechanism of action. Selection of candidates most suitable for further development is underway. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2522.