Bioisosteric Discovery of NPA101.3, a Second-Generation RET/VEGFR2 Inhibitor Optimized for Single-Agent Polypharmacology

Abstract

RET receptor tyrosine kinase is a driver oncogene in human cancer. We recently identified the clinical drug candidate Pz-1, which targets RET and VEGFR2. A key in vivo metabolite of Pz-1 is its less active demethylated pyrazole analogue. Using bioisosteric substitution methods, here, we report the identification of NPA101.3, lacking the structural liability for demethylation. NPA101.3 showed a selective inhibitory profile and an inhibitory concentration 50 (IC 50 ) of <0.003 μM for both RET and VEGFR2. NPA101.3 inhibited phosphorylation of all tested RET oncoproteins as well as VEGFR2 and proliferation of cells transformed by RET. Oral administration of NPA101.3 (10 mg/kg/day) completely prevented formation of tumors induced by RET/C634Y-transformed cells, while it weakened, but did not abrogate, formation of tumors induced by a control oncogene (HRAS/G12V). The balanced synchronous inhibition of both RET and VEGFR2, as well the resistance to demethylation, renders NPA101.3 a potential clinical candidate for RET-driven cancers.

Discovery of pyrazolo-thieno[3,2-d]pyrimidinylamino-phenyl acetamides as type-II pan-tropomyosin receptor kinase (TRK) inhibitors: Design, synthesis, and biological evaluation

“…4-(Methylsulfonyl)phenyl group was established as a bioisosteric group of methyl-pyrazole which can avoid the formation of de-methylation metabolite. [28] However, the resulting compounds 4l and 4m totally abolished the potency in the enzymatic assay. Although it is unexpected, the loss of the potency can be partially explained with potential steric clash between the bulky methylsulfonyl (4l) or trimethoxyl group (4m) with surrounding residues; because as observed in Figure 4B, the methyl-pyrazole of 4c was tightly surrounded by the solvent front residues.…”

“…As a part of our continuous effort on the development of kinase inhibitors, [25][26][27][28][29][30] especially TRKA inhibitors, [31] we recently screened a small in-house kinase compounds library, and compounds 1b and 2b were found to exhibit moderate TRKA inhibitory activity. Although thienopyrimidines derivatives had been reported having a variety of biological activities including anti-parasitic activity [32]; Bertrand et al, disclosed the co-crystal structure of EX429 with TRKA and TRKB, [33] but the medicinal chemistry effort towards the discovery of this compound remained unknown.…”

Recent progress on vascular endothelial growth factor receptor inhibitors with dual targeting capabilities for tumor therapy

“…It also remarkably inhibits the proliferation of RET-transformed Ba/F3 cells with IC 50 values in the low nanomolar concentration range. In vivo pieces of evidence proved that compound 93 completely prevented the formation of tumors induced by RET C634Y -transformed cells [147].…”

Discovery of N-Trisubstituted Pyrimidine Derivatives as Type I RET and RET Gatekeeper Mutant Inhibitors with a Novel Kinase Binding Pose

“…Over the last several years, our lab has been working at discovering RET kinase inhibitors. Pz-1, a clinical drug candidate from our lab with dual RET–VEGFR2 activity, and its second-generation derivative NPA101.3 were described. Recently we also reported a structure–activity relationship (SAR) study of pyrrolo­[2,3- d ]­pyrimidine-based ATP noncompetitive RET inhibitors .…”