From Type†I to Type†II: Design, Synthesis, and Characterization of Potent Pyrazin-2-ones as DFG-Out Inhibitors of PDGFRß.

Reversible protein kinase inhibitors that bind in the ATP cleft can be classified as type I or type II binders. Of these, type I inhibitors address the active form, whereas type II inhibitors typically lock the kinase in an inactive form. At the molecular level, the conformation of the flexible activation loop holding the key DFG motif controls access to the ATP site, thereby determining an active or inactive kinase state. Accordingly, type I and type II kinase inhibitors bind to so-called DFG-in or DFG-out conformations, respectively. Based on our former study on highly selective platelet-derived growth factor receptorâ€…ß (PDGFRß) pyrazin-2-one type I inhibitors, we expanded this scaffold toward the deep pocket, yielding the highly potent and effective type II inhibitor 5 (4-[(4-methylpiperazin-1-yl)methyl]-N-[3-[[6-oxo-5-(3,4,5-trimethoxyphenyl)-1H-pyrazin-3-yl]methyl]phenyl]benzamide). In vitro characterization, including selectivity panel data from activity-based assays (300 kinases) and affinity-based assays (97 kinases) of these PDGFRß type I (1; 5-(4-hydroxy-3-methoxy-phenyl)-3-(3,4,5-trimethoxyphenyl)-1H-pyrazin-2-one) and II (5) inhibitors showing the same pyrazin-2-one chemotype are compared. Implications are discussed regarding the data for selectivity and efficacy of type I and type II ligands.

Optimization of potent DFG-in inhibitors of platelet derived growth factor receptorß (PDGF-Rß) guided by water thermodynamics.

In this study we report on the hit optimization of substituted 3,5-diaryl-pyrazin-2(1H)-ones toward potent and effective platelet-derived growth factor receptor (PDGF-R) ß-inhibitors. Originally, the 3,5-diaryl-pyrazin-2-one core was derived from the marine sponge alkaloid family of hamacanthins. In our first series compound 2 was discovered as a promising hit showing strong activity against PDGF-Rß in the kinase assay (IC50 = 0.5 µM). Furthermore, 2 was shown to be selective for PDGF-Rß in a panel of 24 therapeutically relevant protein kinases. Molecular modeling studies on a PDGF-Rß homology model using prediction of water thermodynamics suggested an optimization strategy for the 3,5-diaryl-pyrazin-2-ones as DFG-in binders by using a phenolic OH function to replace a structural water molecule in the ATP binding site. Indeed, we identified compound 38 as a highly potent inhibitor with an IC50 value of 0.02 µM in a PDGF-Rß enzymatic assay also showing activity against PDGF-R dependent cancer cells.

Marine derived hamacanthins as lead for the development of novel PDGFRß protein kinase inhibitors.

In this study, we report on pyrazin-2(1H)-ones as lead for the development of potent adenosine triphosphate (ATP) competitive protein kinase inhibitors with implications as anti-cancer drugs. Initially, we identified the pyrazin-2(1H)-one scaffold from hamacanthins (deep sea marine sponge alkaloids) by Molecular Modeling studies as core binding motif in the ATP pocket of receptor tyrosine kinases (RTK), which are validated drug targets for the treatment of various neoplastic diseases. Structure-based design studies on a human RTK member PDGFR (platelet-derived growth factor receptor) suggested a straight forward lead optimization strategy. Accordingly, we focused on a Medicinal Chemistry project to develop pyrazin-2(1H)-ones as optimized PDGFR binders. In order to reveal Structure-Activity-Relationships (SAR), we established a flexible synthetic route via microwave mediated ring closure to asymmetric 3,5-substituted pyrazin-2(1H)-ones and produced a set of novel compounds. Herein, we identified highly potent PDGFR binders with IC50 values in an enzymatic assay below µM range, and possessing significant activity against PDGFR dependent cancer cells. Thus, marine hamacanthin-derived pyrazin-2(1H)-ones showing interesting properties as lead for their further development towards potent PDGFR-inhibitors.

Weekly paclitaxel plus trastuzumab in metastatic breast cancer pretreated with anthracyclines--a phase II multipractice study.

BACKGROUND: The 3-weekly combination of trastuzumab and paclitaxel has been approved for the treatment of advanced breast cancer based on a large pivotal study. However, mono and combination chemotherapy trials suggest that weekly paclitaxel has a better therapeutic index, especially in the palliative setting. The present trial examined the efficacy and safety of weekly paclitaxel over a limited duration combined with continued trastuzumab in HER2+ patients. METHODS: Patients with histologically confirmed metastatic breast cancer overexpressing HER2 were eligible if pretreated with anthracycline in either the adjuvant or palliative setting. Treatment consisted of weekly trastuzumab (2 mg/kg/week for up to one year after a loading dose of 4 mg/kg in week 1) and paclitaxel (90 mg/m², administered in weeks 1-6 and 8-13). RESULTS: Twenty-seven German centers enrolled 121 patients. The median number of metastatic sites was two (range 1-5); 38% of patients had received chemotherapy for advanced disease. After a median 42 weeks of trastuzumab treatment, limited by disease progression in roughly half the patients, a best objective response rate (complete response + partial response) of 76% was achieved, including complete remissions in 29%. 74% of patients lived without tumor progression at six months. Median progression-free and overall survival were 9.4 (95% confidence interval [CI]: 8.1-11.3) and 22 months (95% CI: 17-46). After alopecia, Common Toxicity Criteria grade ≥2 toxicity was predominantly hematological (leukopenia [31%] and anemia [41%]); however, thrombocytopenia occurred in only 5%. Neurotoxicity was remarkably low. Two cardiac events (grades 2 and 3) were presumed treatment-related. CONCLUSIONS: Weekly paclitaxel plus trastuzumab allows an increased dose density and offers an attractive and effective alternative to the conventional schedule. Limiting the duration of cytotoxic therapy to 3 months seems to be an option to reduce neurotoxicity without impairing long-term outcome.

7-[4-(4-Fluoro-phen-yl)-2-methyl-sulfanyl-1H-imidazol-5-yl]tetra-zolo[1,5-a]pyridine.

The crystal structure of the title compound, C(15)H(11)FN(6)S, forms a three-dimensional network stabilized by π-π inter-actions between the imidazole core and the tetra-zole ring of the tetra-zolopyridine-unit; the centroid-centroid distance is 3.627 (1) Å. The crystal structure also displays bifurcated N-H⋯(N,N) hydrogen bonding and C-H⋯F inter-actions. The former involve the NH H atom of the imidazole core and the tetra-zolopyridine N atoms, while the latter involve a methyl H atom, of the methyl-sulfanyl group, and the 4-fluoro-phenyl F atom. In the mol-ecule, the imidazole ring makes dihedral angles of 40.45 (9) and 17.09 (8)°, respectively, with the 4-fluoro-phenyl ring and the tetra-zolopyridine ring mean plane.

2-[(1-Methyl-1H-pyrrol-2-yl)carbonyl-meth-yl]isoindoline-1,3-dione.

The asymmetric unit of the title compound, C(15)H(12)N(2)O(3), contains two almost identical mol-ecules forming an nearly C(2-)symmetric dimeric pattern. The dihedral angles between the pyrrole ring and the phthalimide unit are 82.95 (8) and 86.57 (8)° for the two mol-ecules. Within such a dimer, the phthalimide units of the two mol-ecules form a dihedral angle of 1.5 (5)°.