Discovery and Optimization of Pyrimidone Indoline Amide PI3Kβ Inhibitors for the Treatment of Phosphatase and Tensin Homologue (PTEN)-Deficient Cancers

Abstract

Compelling molecular biology publications have reported the implication of phosphoinositide kinase PI3Kβ in PTEN-deficient cell line growth and proliferation. These findings supported a scientific rationale for the development of PI3Kβ-specific inhibitors for the treatment of PTEN-deficient cancers. This paper describes the discovery of 2-[2-(2,3-dihydro-indol-1-yl)-2-oxo-ethyl]-6-morpholin-4-yl-3H-pyrimidin-4-one (7) and the optimization of this new series of active and selective pyrimidone indoline amide PI3Kβ inhibitors. 2-[2-(2-Methyl-2,3-dihydro-indol-1-yl)-2-oxo-ethyl]-6-morpholin-4-yl-3H-pyrimidin-4-one (28), identified following a carefully designed methyl scan, displayed improved physicochemical and in vitro pharmacokinetic properties. Structural biology efforts enabled the acquisition of the first X-ray cocrystal structure of p110β with the selective inhibitor compound 28 bound to the ATP site. The nonplanar binding mode described herein is consistent with observed structure-activity relationship for the series. Compound 28 demonstrated significant in vivo activity in a UACC-62 xenograft model in mice, warranting further preclinical investigation. Following successful development, compound 28 entered phase I/Ib clinical trial in patients with advanced cancer.

Overcoming resistance to BRAF inhibitors

“…While in vitro studies clearly show the potential of using AKT, pan-PI3K or dual PI3K/mTOR inhibitors in combination with BRAF/MEK inhibitor, the translation into the clinical setting is troublesome due to enhanced systemic toxicities (124)(125)(126)(127)(128). The PI3K family of proteins is relevant in many physiological processes and malignant conditions but nevertheless this interest on the pathway is producing encouraging data advancing in the understanding of melanoma specific PI3K-signaling (129) and lately PI3Kβ isoform specific inhibitors are being developed and trialed in the context of PTEN mutant melanoma patients (130)(131)(132). Interestingly targeting the PI3K has not only been proposed as a strategy to overcome resistance to BRAF/MEK inhibitors, but also with the therapeutic goal of preventing the onset of MEK1/2 inhibitor resistance in BRAF-mutated melanoma (133).…”

Concomitant Inhibition of PI3Kβ and BRAF or MEK in PTEN-Deficient/BRAF-Mutant Melanoma Treatment: Preclinical Assessment of SAR260301 Oral PI3Kβ-Selective Inhibitor

“…Aiming to specifically target PTEN-deficient cancers and reduce adverse events, we undertook a PI3Kb isoform-specific discovery program and identified SAR260301 as a potent and highly selective PI3Kb inhibitor (9).…”

“…Enzymatic assays were performed using the PI3K homogeneous-time-resolved-fluorescence (HTRF) kit (Millipore) in 384-well format, as described previously (9). IC 50 values and 95% confidence intervals (CI) were calculated using a fourparameter logistic model (18) in Biost@t Speed internal software.…”

“…Female SCID mice (Charles River, France), [8][9][10] weeks, weighing at least 18 g, with free access to food and sterile water, were implanted subcutaneously with UACC-62 or WM-266.4 cells (3 Â 10 6 cells/animal). Drugs were administered orally to seven mice (median tumor size at start of treatment: 125-126 mm 3 for SAR260301/vemurafenib and 126-144 mm 3 for SAR260301/selumetinib).…”

“…Indeed, conditional knockout of PIK3CB, which encodes the p110b catalytic subunit, but not PIK3CA, has been reported to inhibit tumor growth and prevent formation of cancers induced by PTEN deficiency (6)(7)(8). Thus, PI3Kb-selective kinase inhibitors are being developed for the treatment of PTEN-deficient malignancies, including SAR260301, an agent discovered and characterized in our laboratory (9).…”