Wenyue Hu

PF-06463922, an ALK/ROS1 Inhibitor, Overcomes Resistance to First and Second Generation ALK Inhibitors in Preclinical Models

We report the preclinical evaluation of PF-06463922, a potent and brain-penetrant ALK/ROS1 inhibitor. Compared with other clinically available ALK inhibitors, PF-06463922 displayed superior potency against all known clinically acquired ALK mutations, including the highly resistant G1202R mutant. Furthermore, PF-06463922 treatment led to regression of EML4-ALK-driven brain metastases, leading to prolonged mouse survival, in a superior manner. Finally, PF-06463922 demonstrated high selectivity and safety margins in a variety of preclinical studies. These results suggest that PF-06463922 will be highly effective for the treatment of patients with ALK-driven lung cancers, including those who relapsed on clinically available ALK inhibitors because of secondary ALK kinase domain mutations and/or brain metastases.

PF-06463922 is a potent and selective next-generation ROS1/ALK inhibitor capable of blocking crizotinib-resistant ROS1 mutations

Significance Overcoming resistance to targeted kinase inhibitors is a major clinical challenge in oncology. Development of crizotinib resistance through the emergence of a secondary ROS1 mutation, ROS1G2032R, was observed in patients with ROS1 fusion-positive lung cancer. In addition, a novel ROS1 fusion recently has been identified in glioblastoma. A new agent with robust activity against the ROS1G2032R mutation and with CNS activity is needed to address these unmet medical needs. Here we report the identification of PF-06463922, a ROS1/anaplastic lymphoma kinase (ALK) inhibitor, with exquisite potency against ROS1 fusion kinases, capable of inhibiting the ROS1G2032R mutation and FIG-ROS1–driven glioblastoma tumor growth in preclinical models. PF-06463922 demonstrated excellent therapeutic potential against ROS1 fusion-driven cancers, and it currently is undergoing phase I/II clinical trial investigation. Oncogenic c-ros oncogene1 (ROS1) fusion kinases have been identified in a variety of human cancers and are attractive targets for cancer therapy. The MET/ALK/ROS1 inhibitor crizotinib (Xalkori, PF-02341066) has demonstrated promising clinical activity in ROS1 fusion-positive non-small cell lung cancer. However, emerging clinical evidence has shown that patients can develop resistance by acquiring secondary point mutations in ROS1 kinase. In this study we characterized the ROS1 activity of PF-06463922, a novel, orally available, CNS-penetrant, ATP-competitive small-molecule inhibitor of ALK/ROS1. In vitro, PF-06463922 exhibited subnanomolar cellular potency against oncogenic ROS1 fusions and inhibited the crizotinib-refractory ROS1G2032R mutation and the ROS1G2026M gatekeeper mutation. Compared with crizotinib and the second-generation ALK/ROS1 inhibitors ceritinib and alectinib, PF-06463922 showed significantly improved inhibitory activity against ROS1 kinase. A crystal structure of the PF-06463922-ROS1 kinase complex revealed favorable interactions contributing to the high-affinity binding. In vivo, PF-06463922 showed marked antitumor activity in tumor models expressing FIG-ROS1, CD74-ROS1, and the CD74-ROS1G2032R mutation. Furthermore, PF-06463922 demonstrated antitumor activity in a genetically engineered mouse model of FIG-ROS1 glioblastoma. Taken together, our results indicate that PF-06463922 has potential for treating ROS1 fusion-positive cancers, including those requiring agents with CNS-penetrating properties, as well as for overcoming crizotinib resistance driven by ROS1 mutation.

Spectrum and Degree of CDK Drug Interactions Predicts Clinical Performance

Therapeutically targeting aberrant intracellular kinase signaling is attractive from a biological perspective but drug development is often hindered by toxicities and inadequate efficacy. Predicting drug behaviors using cellular and animal models is confounded by redundant kinase activities, a lack of unique substrates, and cell-specific signaling networks. Cyclin-dependent kinase (CDK) drugs exemplify this phenomenon because they are reported to target common processes yet have distinct clinical activities. Tumor cell studies of ATP-competitive CDK drugs (dinaciclib, AG-024322, abemaciclib, palbociclib, ribociclib) indicate similar pharmacology while analyses in untransformed cells illuminates significant differences. To resolve this apparent disconnect, drug behaviors are described at the molecular level. Nonkinase binding studies and kinome interaction analysis (recombinant and endogenous kinases) reveal that proteins outside of the CDK family appear to have little role in dinaciclib/palbociclib/ribociclib pharmacology, may contribute for abemaciclib, and confounds AG-024322 analysis. CDK2 and CDK6 cocrystal structures with the drugs identify the molecular interactions responsible for potency and kinase selectivity. Efficient drug binding to the unique hinge architecture of CDKs enables selectivity toward most of the human kinome. Selectivity between CDK family members is achieved through interactions with nonconserved elements of the ATP-binding pocket. Integrating clinical drug exposures into the analysis predicts that both palbociclib and ribociclib are CDK4/6 inhibitors, abemaciclib inhibits CDK4/6/9, and dinaciclib is a broad-spectrum CDK inhibitor (CDK2/3/4/6/9). Understanding the molecular components of potency and selectivity also facilitates rational design of future generations of kinase-directed drugs. Mol Cancer Ther; 15(10); 2273–81. ©2016 AACR.

Design and Synthesis of Pyridone-Containing 3,4-Dihydroisoquinoline-1(2H)-ones as a Novel Class of Enhancer of Zeste Homolog 2 (EZH2) Inhibitors

A new enhancer of zeste homolog 2 (EZH2) inhibitor series comprising a substituted phenyl ring joined to a dimethylpyridone moiety via an amide linkage has been designed. A preferential amide torsion that improved the binding properties of the compounds was identified for this series via computational analysis. Cyclization of the amide linker resulted in a six-membered lactam analogue, compound 18. This transformation significantly improved the ligand efficiency/potency of the cyclized compound relative to its acyclic analogue. Additional optimization of the lactam-containing EZH2 inhibitors focused on lipophilic efficiency (LipE) improvement, which provided compound 31. Compound 31 displayed improved LipE and on-target potency in both biochemical and cellular readouts relative to compound 18. Inhibitor 31 also displayed robust in vivo antitumor growth activity and dose-dependent de-repression of EZH2 target genes.

Mitotic Checkpoint Kinase Mps1 Has a Role in Normal Physiology which Impacts Clinical Utility

Cell cycle checkpoint intervention is an effective therapeutic strategy for cancer when applied to patients predisposed to respond and the treatment is well-tolerated. A critical cell cycle process that could be targeted is the mitotic checkpoint (spindle assembly checkpoint) which governs the metaphase-to-anaphase transition and insures proper chromosomal segregation. The mitotic checkpoint kinase Mps1 was selected to explore whether enhancement in genomic instability is a viable therapeutic strategy. The basal-a subset of triple-negative breast cancer was chosen as a model system because it has a higher incidence of chromosomal instability and Mps1 expression is up-regulated. Depletion of Mps1 reduces tumor cell viability relative to normal cells. Highly selective, extremely potent Mps1 kinase inhibitors were created to investigate the roles of Mps1 catalytic activity in tumor cells and normal physiology (PF-7006, PF-3837; K i<0.5 nM; cellular IC50 2–6 nM). Treatment of tumor cells in vitro with PF-7006 modulates expected Mps1-dependent biology as demonstrated by molecular and phenotypic measures (reduced pHH3-Ser10 levels, shorter duration of mitosis, micro-nucleation, and apoptosis). Tumor-bearing mice treated with PF-7006 exhibit tumor growth inhibition concomitant with pharmacodynamic modulation of a downstream biomarker (pHH3-Ser10). Unfortunately, efficacy only occurs at drug exposures that cause dose-limiting body weight loss, gastrointestinal toxicities, and neutropenia. Mps1 inhibitor toxicities may be mitigated by inducing G1 cell cycle arrest in Rb1-competent cells with the cyclin-dependent kinase-4/6 inhibitor palbociclib. Using an isogenic cellular model system, PF-7006 is shown to be selectively cytotoxic to Rb1-deficient cells relative to Rb1-competent cells (also a measure of kinase selectivity). Human bone marrow cells pretreated with palbociclib have decreased PF-7006-dependent apoptosis relative to cells without palbociclib pretreatment. Collectively, this study raises a concern that single agent therapies inhibiting Mps1 will not be well-tolerated clinically but may be when combined with a selective CDK4/6 drug.

Abstract A277: PF-06463922, a novel ROS1/ALK inhibitor, demonstrates sub-nanomolar potency against oncogenic ROS1 fusions and capable of blocking the resistant ROS1G2032R mutant in preclinical tumor models.

The oncogenic ROS1 gene fusion ( Fig-ROS1 ) was first identified in glioblastoma cells over two decades ago. Recently, ROS1 gene rearrangements were further discovered in a variety of human cancers, including lung adenocarcinoma, cholangiocarcinoma, ovarian cancer, gastric adenocarcinoma, colorectal cancer, inflammatory myofibroblastic tumor, angiosarcoma, and epithelioid hemangioendothelioma, providing additional evidence for ROS1 as an attractive cancer target. The 1st generation Met/ALK/ROS1 inhibitor XALKORI ® (crizotinib) has demonstrated promising clinical response in ROS1 fusion positive NSCLC. But similar to what was seen with acquired ALK secondary resistant mutations in XALKORI refractory patients, a ROS1 kinase domain mutant–ROS1G2032R has been identified in a ROS1 positive NSCLC patient who developed resistance to XALKORI. Therefore, there is an urgent need to develop agents that can overcome this type of resistance. PF-06463922 is a novel, orally available, ATP-competitive small molecule inhibitor of ROS1/ALK with exquisite potency against ROS1 kinase. PF-06463922 inhibited the catalytic activity of recombinant ROS1 with a mean Ki of < 0.005 nM, and inhibited ROS1 autophosphorylation at IC50 values ranging from 0.1 nM to 1 nM cross a panel of cell lines harboring oncogenic ROS1 fusion variants including CD74-ROS1, SLC34A2-ROS1 and Fig-ROS1. PF-06463922 also inhibited cell proliferation and induced cell apoptosis at sub- to low-nanomolar concentrations in the HCC78 human NSCLC cells harboring SLC34A2-ROS1 fusions and the BaF3-CD74-ROS1 cells expressing human CD74-ROS1. In the BaF3 cells engineered to express the XALKORI resistant CD74-ROS1G2032R mutant, PF-06463922 demonstrated nanomolar potency against either ROS1G2032R cellular activity or cell proliferation. In vivo, PF-06463922 demonstrated marked cytoreductive antitumor efficacy at low nanomolar concentration in the NIH3T3 xenograft models expressing human CD74-ROS1 and Fig-ROS1. The antitumor efficacy of PF-06463922 was dose dependent and strongly correlated to inhibition in ROS1 phosphorylation and the downstream signaling molecules pSHP1, pSHP2 and pErk1/2, as well as inhibition of the cell cycle protein Cyclin D1 in tumors. To our knowledge, PF-06463922 is the first reported ROS1 inhibitor that is capable of blocking the resistant ROS1G2032R mutant at predicted pharmacologically relevant concentrations. Our data indicate that PF-06463922 has great potential for treating ROS1 fusion positive cancers including those from patients who relapsed from XALKORI therapy due to acquired ROS1G2032Rmutation. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A277. Citation Format: Helen Y. Zou, Lars R. Engstrom, Qiuhua Li, Melissa West Lu, Ruth Wei Tang, Hui Wang, Konstantinos Tsaparikos, Sergei Timofeevski, Justine Lam, Shinji Yamazaki, Wenyue Hu, Hovhannes Gukasyan, Nathan Lee, Ted W. Johnson, Valeria Fantin, Tod Smeal. PF-06463922, a novel ROS1/ALK inhibitor, demonstrates sub-nanomolar potency against oncogenic ROS1 fusions and capable of blocking the resistant ROS1G2032R mutant in preclinical tumor models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A277.

Crizotinib Reduces the Rate of Dark Adaptation in the Rat Retina Independent of ALK Inhibition

Crizotinib (Xalkori) is a tyrosine kinase inhibitor of both anaplastic lymphoma kinase (ALK) and mesenchymal-epithelial transition factor (c-Met). Though not predicted from standard nonclinical toxicological evaluation, visual disturbance became a frequently observed adverse event in humans. To understand the possible mechanism of this vision effect, an in vivo electroretinogram (ERG) study was conducted to assess retinal functional changes following oral administration of crizotinib. Immunohistochemical (IHC) staining of ALK and c-Met in the neural retinas of human, non-human primate, dog, rat, and mouse was used to aid in the animal model selection. ALK IHC staining was identified predominantly in the ganglion cell and inner nuclear layers of most species evaluated, in the inner plexiform layer in human and rodent, and in the nerve fiber layer in human and rat only. There was no apparent staining of any layer of the neural retina for c-Met in any of the species evaluated. ERG measurements identified a significant reduction in b-wave amplitude during the initial phase of dark adaptation in the crizotinib-treated rats. ERGs were also taken following oral administration of PF-06463922 (an ALK-selective inhibitor), for an understanding of potential kinase involvement. ERG effects were not observed in PF-06463922-treated animals when comparable exposures in the vitreous humor were achieved. Collectively, our results suggest that the ERG b-wave amplitude decreases during dark adaption following crizotinib administration may be related to signaling changes within the retina in rats, likely independent of ALK inhibition.

Epithelial Tissue Hyperplasia Induced by the RAF Inhibitor PF-04880594 is Attenuated by a Clinically Well-Tolerated Dose of the MEK Inhibitor PD-0325901

Clinical trials of selective RAF inhibitors in patients with melanoma tumors harboring activated BRAFV600E have produced very promising results, and a RAF inhibitor has been approved for treatment of advanced melanoma. However, about a third of patients developed resectable skin tumors during the course of trials. This is likely related to observations that RAF inhibitors activate extracellular signal–regulated kinase (ERK) signaling, stimulate proliferation, and induce epithelial hyperplasia in preclinical models. Because these findings raise safety concerns about RAF inhibitor development, we further investigated the underlying mechanisms. We showed that the RAF inhibitor PF-04880594 induces ERK phosphorylation and RAF dimerization in those epithelial tissues that undergo hyperplasia. Hyperplasia and ERK hyperphosphorylation are prevented by treatment with the mitogen-activated protein/extracellular signal–regulated kinase (MEK) inhibitor PD-0325901 at exposures that extrapolate to clinically well-tolerated doses. To facilitate mechanistic and toxicologic studies, we developed a three-dimensional cell culture model of epithelial layering that recapitulated the RAF inhibitor–induced hyperplasia and reversal by MEK inhibitor in vitro. We also showed that PF-04880594 stimulates production of the inflammatory cytokine interleukin 8 in HL-60 cells, suggesting a possible mechanism for the skin flushing observed in dogs. The complete inhibition of hyperplasia by MEK inhibitor in epithelial tissues does not seem to reduce RAF inhibitor efficacy and, in fact, allows doubling of the PF-04880594 dose without toxicity usually associated with such doses. These findings indicated that combination treatment with MEK inhibitors might greatly increase the safety and therapeutic index of RAF inhibitors for the treatment of melanoma and other cancers. Mol Cancer Ther; 11(10); 2274–83. ©2012 AACR.

Evaluation of miR-216a and miR-217 as Potential Biomarkers of Acute Exocrine Pancreatic Toxicity in Rats:

Detecting and monitoring exocrine pancreatic damage during nonclinical and clinical testing is challenging because classical biomarkers amylase and lipase have limited sensitivity and specificity. Novel biomarkers for drug-induced pancreatic injury are needed to improve safety assessment and reduce late-stage attrition rates. In a series of studies, miR-216a and miR-217 were evaluated as potential biomarkers of acute exocrine pancreatic toxicity in rats. Our results revealed that miR-216a and miR-217 were almost exclusively expressed in rat pancreas and that circulating miR-216a and miR-217 were significantly increased in rats following administration of established exocrine pancreatic toxicants caerulein (CL) and 1-cyano-2-hydroxy-3-butene (CHB) as well as in rats administered a proprietary molecule known to primarily affect the exocrine pancreas. Conversely, neither microRNA was increased in rats administered a proprietary molecule known to cause a lesion at the pancreatic endocrine–exocrine interface (EEI) or in rats administered an established renal toxicant. Compared with amylase and lipase, increases in miR-216a and miR-217 were of greater magnitude, persisted longer, and/or correlated better with microscopic findings within the exocrine pancreas. Our findings demonstrate that in rats, miR-216a and miR-217 are sensitive and specific biomarkers of acute exocrine pancreatic toxicity that may add value to the measurement of classical pancreatic biomarkers.

Abstract C253: PF-06463922, a novel brain-penetrating small molecule inhibitor of ALK/ROS1 with potent activity against a broad spectrum of ALK resistant mutations in preclinical models in vitro and in vivo.

Oncogenic fusions of Anaplastic Lymphoma Kinase (ALK) define a subset of human lung adenocarcinomas. The 1st generation ALK inhibitor XALKORI ® (crizotinib) demonstrated impressive clinical benefit in ALK-fusion positive lung cancers and was approved by the FDA for the treatment of ALK-fusion positive NSCLC in 2011. However, as seen with most kinase inhibitors, patients treated with XALKORI eventually developed resistance to therapy. Acquired ALK kinase domain mutations and brain metastases are significant contributors to the relapse after XALKORI therapy. To date, multiple types of ALK kinase domain mutations have been identified in XALKORI refractory patients including ALKG1269A, ALKL1196M, ALKC1156Y, ALKL1152R, ALKF1174L, ALKS1206Y, ALK1151Tins and ALKG1202R, accounting for about 1/3 of patient samples tested. Currently, a number of 2nd generation ALK inhibitors are under development aiming to overcome XALKORI resistant mutations. Even though in preclinical models, some ALK mutants such as ALKG1202R and ALK1151Tins confer high-levels of resistance to almost all of the 2nd generation ALK inhibitors tested. Here we report PF-06463922, a novel ATP competitive small molecule inhibitor of ALK/ROS1, with potent and selective inhibitory activity against all known acquired XALKORI resistant mutations identified in patients. PF-06463922 is also capable of penetrating the blood brain barrier in preclinical animal models. In vitro, PF-06463922 demonstrated potent inhibition in catalytic activities of ALK and 8 different ALK mutant kinases in recombinant enzyme and cell based assays (cell IC50s = 1 to 65 nM). PF-06463922 also showed potent growth inhibitory activity and induced apoptosis in the NSCLC cells harboring either non-mutant ALK or mutant ALK fusions (IC50s = 1 to 30 nM). In vivo, PF-06463922 demonstrated marked cytoreductive activity in mice bearing tumor xenografts that express EML4-ALK, EML4-ALKL1196M, EML4-ALKG1269A, EML4-ALKG1202R or NPM-ALK at low nM free plasma concentrations. These effects were associated with significant inhibition in cellular Ki67 and increased cleaved-caspase3 levels in tumors. In addition, PF-06463922 achieved brain exposure of 20-30% of its plasma levels in mice, and significantly regressed the brain tumors and prolonged survival of mice bearing orthotopic EML4-ALK and EML4-ALKL1196M positive brain tumor implants. The antitumor efficacy of PF-06463922 was dose dependent and strongly correlated with inhibition of ALK phosphorylation and downstream signaling. Our data indicate that PF-06463922 is the most potent ALK inhibitor reported to date (to our knowledge, against both non-mutant or mutant ALK in cell assays), and it demonstrates great potential for treating ALK fusion positive cancers including patients who relapsed from XALKORI therapy due to various ALK kinase domain mutations and/or brain metastases. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C253. Citation Format: Helen Y. Zou, Lars R. Engstrom, Qiuhua Li, Melissa West Lu, Ruth Wei Tang, Hui Wang, Konstantinos Tsaparikos, Jinwei Wang, Sergei Timofeevski, Dac M. Dinh, Hieu Lam, Justine Lam, Shinji Yamazaki, Wenyue Hu, Timothy Affolter, Patrick B. Lappin, Hovhannes Gukasyan, Nathan Lee, Jennifer M. Tursi, Ted W. Johnson, Valeria Fantin, Tod Smeal. PF-06463922, a novel brain-penetrating small molecule inhibitor of ALK/ROS1 with potent activity against a broad spectrum of ALK resistant mutations in preclinical models in vitro and in vivo. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C253.