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.

Class IA PI3K pathway activation resulting from PTEN deficiency has been associated with lack of sensitivity of melanoma to BRAF kinase inhibitors. Although previous studies have shown synergistic activity when pan-PI3K inhibitors were combined with MAPK inhibitors in the treatment of melanoma exhibiting concurrent genetic abnormalities, overlapping adverse events in patients limit optimal dosing and clinical application. With the aim of specifically targeting PTEN-deficient cancers and minimizing the potential for on-target toxicity when inhibiting multiple PI3K isoforms, we developed a program to discover PI3Kb-selective kinase inhibitors and identified SAR260301 as a potent PI3Kb-selective, orally available compound, which is now in clinical development. Herein, we provide a detailed biological characterization of SAR260301, and show that this compound has outstanding biochemical and cellular selectivity for the PI3Kb isoform versus the a, d, and g isoforms and a large panel of protein and lipid kinases. We demonstrate that SAR260301 blocks PI3K pathway signaling preferentially in PTEN-deficient human tumor models, and has synergistic antitumor activity when combined with vemurafenib (BRAF inhibitor) or selumetinib (MEK inhibitor) in PTEN-deficient/BRAF-mutated human melanoma tumor models. Combination treatments were very well tolerated, suggesting the potential for a superior safety profile at optimal dosing using selective compounds to inhibit multiple signaling pathways. Together, these experiments provide a preclinical proof-of-concept for safely combining inhibitors of PI3Kb and BRAF or MEK kinase modulators to improve antitumor activity in PTEN-deficient/BRAF-mutant melanoma, and support the evaluation of SAR260301-based combinations in clinical studies. Mol Cancer Ther; 15(7); 1460-71. Ó2016 AACR.

The PI3K/mTOR pathway is involved in promoting tumor cell proliferation, survival and metastasis. The development of new anticancer therapies targeting different components of this pathway has been motivated by the identification of somatic PIK3CA missense mutations as well as the high frequency of loss of negative regulatory proteins such as the tumor suppressor PTEN. In this last case, the abnormal activation of downstream effectors is mediated by PI3Kβ. PTEN deficiency has also been reported to be involved in the resistance to a variety of anticancer therapies. The preceding findings support investigation into selective modulators of the lipid kinase activity of p110β as agents for the treatment of PTEN-deficient tumors, with potentially reduced on-target adverse events described for pan-PI3K inhibitors currently undergoing clinical trials. SAR260301 is a selective PI3Kβ lipid kinase inhibitor that has demonstrated higher potency in vitro on p110β (IC50= 52 nM) than on p110δ and p110α isoforms and no or weak activity against p110γ, mTOR and a wide range of protein kinases (>400 enzymes). The potency and selectivity against the intended target was further confirmed in mechanistic cellular models (IC50 = 32 nM, p110β; 26- and 88-fold selective over p110δ and p110α, respectively). Moreover, SAR260301 also modulates pAkt levels exclusively in PTEN-deficient tumor cell lines with IC50 values ranging from 39 to 310 nM and from 20 to 209 nM for pAkt-S473 and pAkt-T308, respectively. When administered orally, the compound shows dose and time-dependent inhibition of the PI3K pathway in human PTEN-deficient tumor xenografts in mice. In these models, target engagement correlates with compound exposure and is associated with good tolerability. The MAPK pathway also plays an important role in cancer and is often constitutively and simultaneously activated with the PI3K pathway. Furthermore, PTEN loss has been shown to correlate with resistance to MAPK inhibitors. Preclinical data evidencing the ability of SAR260301 to modulate pAkt levels in genetic contexts where PTEN deficiency co-exists with MAPK pathway activation, as well as the effects of combining SAR260301 with MAPK inhibitors will also be presented. The foregoing studies support ongoing Phase I clinical investigation of SAR260301 in patients with PTEN-deficient malignancies. Citation Format: Angela Virone-Oddos, Hélène Bonnevaux, Olivier Lemaitre, Loic Vincent, Franck Halley, Brigitte Demers, Véronique Charrier, Olivier Courtin, Stéphane Guérif, Laurent Besret, Pierre-Yves Abecassis, Sylvaine Cartot-Cotton, Gary Emmons, Alan Roberts, David Compton, Bin Wu, Laurent Schio, Christoph Lengauer, Carlos Garcia-Echeverria. Discovery and characterization of SAR260301, a novel PI3Kβ-selective inhibitor in clinical development for the treatment of PTEN-deficient tumors . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3258. doi:10.1158/1538-7445.AM2013-3258

The TGF-β signaling mediator SMAD4 is frequently mutated or deleted in colorectal and pancreatic cancers. SMAD4 acts as a tumor suppressor and its loss is associated with poorer patient outcomes. The purpose of this study was to find synthetic lethal interactions with SMAD4 deficiency in order to find novel therapeutic strategies for the treatment of patients with SMAD4-deficient colorectal or pancreatic cancers. Using pooled lentiviral sgRNA libraries, we conducted genome-wide loss-of-function screens in Cas9-expressing colorectal and pancreatic cancer cells harboring altered or wild-type SMAD4. The small GTPase protein RAB10 was identified and validated as a susceptibility gene in SMAD4-altered colorectal and pancreatic cancer cells. Rescue assays showed that RAB10 re-introduction reversed the anti-proliferative effects of RAB10 KO in SMAD4 negative cell lines. Further investigation is necessary to shed light on the mechanism by which RAB10 inhibition decreases cell proliferation of SMAD4-negative cells.

<p>Supplementary Tables S1. Table S1 describes the inhibitory activity of SAR260301 on AKT phosphorylation (Ser473 and Thr308) in a panel of tumor cell lines with different genetic abnormalities that are reported. Supplementary Figures S1-S4. Figure S1 illustrates the selectivity of SAR260301 against VPS34 in cellular setting: Figure S1A describes the activity of SAR260301 on VPS34 kinase function in GFP-FYVE cellular assay; Figure S1B describes the activity of SAR260301 on autophagy in GFP-LC3 cellular assays. Figure S2 describes the inhibitory activity of SAR260301 on the phosphorylation of AKT downstream effectors PRAS40 and S6RP in PC3 cell line, as a function of time. Figure S3 describes the in vitro antitumor activity of SAR260301: Figure S3A describes the antiproliferative activity of SAR260301on MEF-3T3-myr p110β cells. Figure S3B describes the antiproliferative activity of SAR260301on PC3 cells. Figure S3C describes the activity of SAR260301on PC3 cell death. Figure S3D describes the activity of SAR260301on LnCaP cell apoptosis. Figure S4 is a scheme describing the rationale for combining inhibitors of PI3K� and MAPK.</p>

<p>Map of the plasmids to express inducible SMAD4 and Cas9</p>

<p>Behavior of sgRNAs targeting essential and nonessential genes in the screen samples.</p>

<p>QCsummary</p>