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

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 PI3Kβ-selective kinase inhibitors and identified SAR260301 as a potent PI3Kβ-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 PI3Kβ isoform versus the α, δ, and γ 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 PI3Kβ 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. ©2016 AACR.

[1]  S. Barry,et al.  High Efficacy of Combination Therapy Using PI3K/AKT Inhibitors with Androgen Deprivation in Prostate Cancer Preclinical Models. , 2015, European urology.

[2]  J. Engelman,et al.  Measurement of PIP3 levels reveals an unexpected role for p110β in early adaptive responses to p110α-specific inhibitors in luminal breast cancer. , 2015, Cancer cell.

[3]  Simon T Barry,et al.  Feedback suppression of PI3Kα signaling in PTEN-mutated tumors is relieved by selective inhibition of PI3Kβ. , 2015, Cancer cell.

[4]  M. Mathieu,et al.  A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy. , 2014, Nature chemical biology.

[5]  S. Barry,et al.  Inhibition of PI3Kβ Signaling with AZD8186 Inhibits Growth of PTEN-Deficient Breast and Prostate Tumors Alone and in Combination with Docetaxel , 2014, Molecular Cancer Therapeutics.

[6]  P. Fox,et al.  Complete Loss of PTEN Protein Expression Correlates with Shorter Time to Brain Metastasis and Survival in Stage IIIB/C Melanoma Patients with BRAFV600 Mutations , 2014, Clinical Cancer Research.

[7]  D. Erdmann,et al.  Characterization of the Novel and Specific PI3Kα Inhibitor NVP-BYL719 and Development of the Patient Stratification Strategy for Clinical Trials , 2014, Molecular Cancer Therapeutics.

[8]  Jean-Pierre Marquette,et al.  Discovery and optimization of pyrimidone indoline amide PI3Kβ inhibitors for the treatment of phosphatase and tensin homologue (PTEN)-deficient cancers. , 2014, Journal of medicinal chemistry.

[9]  L. Kwong,et al.  Navigating the Therapeutic Complexity of PI3K Pathway Inhibition in Melanoma , 2013, Clinical Cancer Research.

[10]  K. Nathanson,et al.  Tumor Genetic Analyses of Patients with Metastatic Melanoma Treated with the BRAF Inhibitor Dabrafenib (GSK2118436) , 2013, Clinical Cancer Research.

[11]  R. Sullivan,et al.  MAP kinase signaling and inhibition in melanoma , 2013, Oncogene.

[12]  J. Tabernero,et al.  Development of PI3K inhibitors: lessons learned from early clinical trials , 2013, Nature Reviews Clinical Oncology.

[13]  J. Nicolas,et al.  Preparation and optimization of new 4-(morpholin-4-yl)-(6-oxo-1,6-dihydropyrimidin-2-yl)amide derivatives as PI3Kβ inhibitors. , 2012, Bioorganic & medicinal chemistry letters.

[14]  John Wang,et al.  Sensitivity to the MEK inhibitor E6201 in melanoma cells is associated with mutant BRAF and wildtype PTEN status , 2012, Molecular Cancer.

[15]  G. Schwartz,et al.  Impact of Combined mTOR and MEK Inhibition in Uveal Melanoma Is Driven by Tumor Genotype , 2012, PloS one.

[16]  J. Nicolas,et al.  Discovery and optimization of new benzimidazole- and benzoxazole-pyrimidone selective PI3Kβ inhibitors for the treatment of phosphatase and TENsin homologue (PTEN)-deficient cancers. , 2012, Journal of medicinal chemistry.

[17]  N. Gray,et al.  Functional characterization of an isoform-selective inhibitor of PI3K-p110β as a potential anticancer agent. , 2012, Cancer discovery.

[18]  T. Gilmer,et al.  Combinations of BRAF, MEK, and PI3K/mTOR Inhibitors Overcome Acquired Resistance to the BRAF Inhibitor GSK2118436 Dabrafenib, Mediated by NRAS or MEK Mutations , 2012, Molecular Cancer Therapeutics.

[19]  S. Woodman,et al.  Role and therapeutic potential of PI3K‐mTOR signaling in de novo resistance to BRAF inhibition , 2012, Pigment cell & melanoma research.

[20]  B. Taylor,et al.  Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600EBRAF , 2012, Oncogene.

[21]  P. Mischel,et al.  Reversing Melanoma Cross-Resistance to BRAF and MEK Inhibitors by Co-Targeting the AKT/mTOR Pathway , 2011, PloS one.

[22]  N. Gray,et al.  In situ kinase profiling reveals functionally relevant properties of native kinases. , 2011, Chemistry & biology.

[23]  V. Sondak,et al.  Abstract 5370: PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression , 2011 .

[24]  D. Rimm,et al.  Vertical Targeting of the Phosphatidylinositol-3 Kinase Pathway as a Strategy for Treating Melanoma , 2010, Clinical Cancer Research.

[25]  Damien Kee,et al.  Acquired resistance to BRAF inhibitors mediated by a RAF kinase switch in melanoma can be overcome by cotargeting MEK and IGF-1R/PI3K. , 2010, Cancer cell.

[26]  Prahlad T. Ram,et al.  Basal and treatment-induced activation of AKT mediates resistance to cell death by AZD6244 (ARRY-142886) in Braf-mutant human cutaneous melanoma cells. , 2010, Cancer research.

[27]  Victor G Prieto,et al.  Integrated Molecular and Clinical Analysis of AKT Activation in Metastatic Melanoma , 2009, Clinical Cancer Research.

[28]  R. DePinho,et al.  BRafV600E cooperates with Pten silencing to elicit metastatic melanoma , 2009, Nature Genetics.

[29]  L. Zhao,et al.  Class I PI3K in oncogenic cellular transformation , 2008, Oncogene.

[30]  P. Musiani,et al.  Phosphoinositide 3-Kinase p110β Activity: Key Role in Metabolism and Mammary Gland Cancer but Not Development , 2008, Science Signaling.

[31]  Alice T. Loo,et al.  PTEN-deficient cancers depend on PIK3CB , 2008, Proceedings of the National Academy of Sciences.

[32]  M. Loda,et al.  Essential roles of PI(3)K–p110β in cell growth, metabolism and tumorigenesis , 2008, Nature.

[33]  Suzanne Schubbert,et al.  Hyperactive Ras in developmental disorders and cancer , 2007, Nature Reviews Cancer.

[34]  C. Garbe,et al.  Combined targeting of MAPK and AKT signalling pathways is a promising strategy for melanoma treatment , 2007, The British journal of dermatology.

[35]  Kathylynn Saboda,et al.  Inhibition of phosphatidylinositol-3-kinase and mitogen-activated protein kinase kinase 1/2 prevents melanoma development and promotes melanoma regression in the transgenic TPRas mouse model , 2006, Molecular Cancer Therapeutics.

[36]  Ji Luo,et al.  The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism , 2006, Nature Reviews Genetics.

[37]  Luc Bijnens,et al.  Design and Analysis of Drug Combination Experiments , 2005, Biometrical journal. Biometrische Zeitschrift.

[38]  L. Wodicka,et al.  A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.

[39]  J. Ptak,et al.  High Frequency of Mutations of the PIK3CA Gene in Human Cancers , 2004, Science.

[40]  F. Haluska,et al.  PTEN signaling pathways in melanoma , 2003, Oncogene.

[41]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[42]  Lewis C Cantley,et al.  The phosphoinositide 3-kinase pathway. , 2002, Science.

[43]  L. Cantley,et al.  New insights into tumor suppression: PTEN suppresses tumor formation by restraining the phosphoinositide 3-kinase/AKT pathway. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[44]  F. Haluska,et al.  Identification of PTEN/MMAC1 alterations in uncultured melanomas and melanoma cell lines , 1998, Oncogene.

[45]  G. Mills,et al.  MMAC1/PTEN mutations in primary tumor specimens and tumor cell lines. , 1997, Cancer research.

[46]  D. Ratkowsky,et al.  Choosing near-linear parameters in the four-parameter logistic model for radioligand and related assays. , 1986, Biometrics.

[47]  Michael A Davies,et al.  The role of the PI3K-AKT pathway in melanoma. , 2012, Cancer journal.

[48]  Robert A. Copeland,et al.  Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis , 1996 .