gne-617 and Neoplasms

NAMPT inhibitors may show potential as therapeutics for oncology. Throughout our NAMPT inhibitor program, we found that exposed pyridines or related heterocyclic systems in the left-hand portion of the inhibitors are necessary pharmacophores for potent cellular NAMPT inhibition. However, when combined with a benzyl group in the center of the inhibitors, such pyridine-like moieties also led to consistent and potent inhibition of CYP2C9. In an attempt to reduce CYP2C9 inhibition, a parallel synthesis approach was used to identify central benzyl group replacements with increased Fsp3. A spirocyclic central motif was thus discovered that was combined with left-hand pyridines (or pyridine-like systems) to provide cellularly potent NAMPT inhibitors with minimal CYP2C9 inhibition. Further optimization of potency and ADME properties led to the discovery of compound 68, a highly potent NAMPT inhibitor with outstanding efficacy in a mouse tumor xenograft model and lacking measurable CYP2C9 inhibition at the concentrations tested.

Topics: Animals; Antineoplastic Agents; Cell Line, Tumor; Cytochrome P-450 CYP2C9; Cytochrome P-450 CYP2C9 Inhibitors; Drug Discovery; Enzyme Inhibitors; Female; Humans; Mice; Mice, Nude; Models, Molecular; Neoplasms; Nicotinamide Phosphoribosyltransferase; Pyridines

Herein we report the optimization efforts to ameliorate the potent CYP3A4 time-dependent inhibition (TDI) and low aqueous solubility exhibited by a previously identified lead compound from our NAMPT inhibitor program (1, GNE-617). Metabolite identification studies pinpointed the imidazopyridine moiety present in 1 as the likely source of the TDI signal, and replacement with other bicyclic systems was found to reduce or eliminate the TDI finding. A strategy of reducing the number of aromatic rings and/or lowering cLogD7.4 was then employed to significantly improve aqueous solubility. These efforts culminated in the discovery of 42, a compound with no evidence of TDI, improved aqueous solubility, and robust efficacy in tumor xenograft studies.

Topics: Animals; Binding Sites; Cell Line, Tumor; Cell Membrane Permeability; Cell Proliferation; Crystallography, X-Ray; Cytochrome P-450 CYP3A; Cytochrome P-450 CYP3A Inhibitors; Dogs; Enzyme Inhibitors; Female; Half-Life; Humans; Kinetics; Madin Darby Canine Kidney Cells; Mice; Mice, Nude; Molecular Dynamics Simulation; Neoplasms; Nicotinamide Phosphoribosyltransferase; Protein Binding; Protein Structure, Tertiary; Pyrimidines; Solubility; Structure-Activity Relationship; Thermodynamics; Transplantation, Heterologous; Water

We sought to identify predictive biomarkers for a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor.. We use a NAMPT inhibitor, GNE-617, to evaluate nicotinic acid rescue status in a panel of more than 400 cancer cell lines. Using correlative analysis and RNA interference (RNAi), we identify a specific biomarker for nicotinic acid rescue status. We next determine the mechanism of regulation of expression of the biomarker. Finally, we develop immunohistochemical (IHC) and DNA methylation assays and evaluate cancer tissue for prevalence of the biomarker across indications.. Nicotinate phosphoribosyltransferase (NAPRT1) is necessary for nicotinic acid rescue and its expression is the major determinant of rescue status. We demonstrate that NAPRT1 promoter methylation accounts for NAPRT1 deficiency in cancer cells, and NAPRT1 methylation is predictive of rescue status in cancer cell lines. Bisulfite next-generation sequencing mapping of the NAPRT1 promoter identified tumor-specific sites of NAPRT1 DNA methylation and enabled the development of a quantitative methylation-specific PCR (QMSP) assay suitable for use on archival formalin-fixed paraffin-embedded tumor tissue.. Tumor-specific promoter hypermethylation of NAPRT1 inactivates one of two NAD salvage pathways, resulting in synthetic lethality with the coadministration of a NAMPT inhibitor. NAPRT1 expression is lost due to promoter hypermethylation in most cancer types evaluated at frequencies ranging from 5% to 65%. NAPRT1-specific immunohistochemical or DNA methylation assays can be used on archival formalin paraffin-embedded cancer tissue to identify patients likely to benefit from coadministration of a Nampt inhibitor and nicotinic acid.

Topics: Biomarkers, Tumor; Cell Line, Tumor; Cytokines; DNA Methylation; Gene Expression Regulation, Neoplastic; Heterocyclic Compounds, 2-Ring; Humans; Neoplasms; Niacin; Nicotinamide Phosphoribosyltransferase; Pentosyltransferases; Promoter Regions, Genetic; Sulfones