Anna Kohlmann

Discovery of Brigatinib (AP26113), a Phosphine Oxide-Containing, Potent, Orally Active Inhibitor of Anaplastic Lymphoma Kinase

In the treatment of echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase positive (ALK+) non-small-cell lung cancer (NSCLC), secondary mutations within the ALK kinase domain have emerged as a major resistance mechanism to both first- and second-generation ALK inhibitors. This report describes the design and synthesis of a series of 2,4-diarylaminopyrimidine-based potent and selective ALK inhibitors culminating in identification of the investigational clinical candidate brigatinib. A unique structural feature of brigatinib is a phosphine oxide, an overlooked but novel hydrogen-bond acceptor that drives potency and selectivity in addition to favorable ADME properties. Brigatinib displayed low nanomolar IC50s against native ALK and all tested clinically relevant ALK mutants in both enzyme-based biochemical and cell-based viability assays and demonstrated efficacy in multiple ALK+ xenografts in mice, including Karpas-299 (anaplastic large-cell lymphomas [ALCL]) and H3122 (NSCLC). Brigatinib represents the most clinically advanced phosphine oxide-containing drug candidate to date and is currently being evaluated in a global phase 2 registration trial.

Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors.

Lactate dehydrogenase A (LDH-A) catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway. Cancer cells rely heavily on glycolysis instead of oxidative phosphorylation to generate ATP, a phenomenon known as the Warburg effect. The inhibition of LDH-A by small molecules is therefore of interest for potential cancer treatments. We describe the identification and optimization of LDH-A inhibitors by fragment-based drug discovery. We applied ligand based NMR screening to identify low affinity fragments binding to LDH-A. The dissociation constants (K(d)) and enzyme inhibition (IC(50)) of fragment hits were measured by surface plasmon resonance (SPR) and enzyme assays, respectively. The binding modes of selected fragments were investigated by X-ray crystallography. Fragment growing and linking, followed by chemical optimization, resulted in nanomolar LDH-A inhibitors that demonstrated stoichiometric binding to LDH-A. Selected molecules inhibited lactate production in cells, suggesting target-specific inhibition in cancer cell lines.

Ponatinib inhibits polyclonal drug-resistant KIT oncoproteins and shows therapeutic potential in heavily pretreated gastrointestinal stromal tumor (GIST) patients.

Purpose: KIT is the major oncogenic driver of gastrointestinal stromal tumors (GIST). Imatinib, sunitinib, and regorafenib are approved therapies; however, efficacy is often limited by the acquisition of polyclonal secondary resistance mutations in KIT, with those located in the activation (A) loop (exons 17/18) being particularly problematic. Here, we explore the KIT-inhibitory activity of ponatinib in preclinical models and describe initial characterization of its activity in patients with GIST. Experimental Design: The cellular and in vivo activities of ponatinib, imatinib, sunitinib, and regorafenib against mutant KIT were evaluated using an accelerated mutagenesis assay and a panel of engineered and GIST-derived cell lines. The ponatinib–KIT costructure was also determined. The clinical activity of ponatinib was examined in three patients with GIST previously treated with all three FDA-approved agents. Results: In engineered and GIST-derived cell lines, ponatinib potently inhibited KIT exon 11 primary mutants and a range of secondary mutants, including those within the A-loop. Ponatinib also induced regression in engineered and GIST-derived tumor models containing these secondary mutations. In a mutagenesis screen, 40 nmol/L ponatinib was sufficient to suppress outgrowth of all secondary mutants except V654A, which was suppressed at 80 nmol/L. This inhibitory profile could be rationalized on the basis of structural analyses. Ponatinib (30 mg daily) displayed encouraging clinical activity in two of three patients with GIST. Conclusion:Ponatinib possesses potent activity against most major clinically relevant KIT mutants and has demonstrated preliminary evidence of activity in patients with refractory GIST. These data strongly support further evaluation of ponatinib in patients with GIST. Clin Cancer Res; 20(22); 5745–55. ©2014 AACR.

Application of MM-GB/SA and WaterMap to SRC Kinase Inhibitor Potency Prediction.

WaterMap and MM-GB/SA scoring methods were applied to an extensive congeneric series of small-molecule SRC inhibitors with high-quality enzyme data and well characterized binding modes to compare the performance of these scoring methods in this data set and to provide insight into the relative strengths of each method. Only minor conformational changes in SRC bound with representative DFG-in class of inhibitors were demonstrated in previous studies; thus, the protein flexibility that normally presents a challenge to pose and potency predictions was minimized in this model system. While WaterMap correctly recognized major trends in the SAR of this series, MM-GB/SA performed better in ranking the relative ligand affinities. The different scoring methods were further analyzed to determine which aspects of series SAR were more amenable to MM-GB/SA than WaterMap scoring.

Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery

Choline kinase α (ChoKα) is an enzyme involved in the synthesis of phospholipids and thereby plays key roles in regulation of cell proliferation, oncogenic transformation, and human carcinogenesis. Since several inhibitors of ChoKα display antiproliferative activity in both cellular and animal models, this novel oncogene has recently gained interest as a promising small molecule target for cancer therapy. Here we summarize our efforts to further validate ChoKα as an oncogenic target and explore the activity of novel small molecule inhibitors of ChoKα. Starting from weakly binding fragments, we describe a structure based lead discovery approach, which resulted in novel highly potent inhibitors of ChoKα. In cancer cell lines, our lead compounds exhibit a dose-dependent decrease of phosphocholine, inhibition of cell growth, and induction of apoptosis at low micromolar concentrations. The druglike lead series presented here is optimizable for improvements in cellular potency, drug target residence time, and pharmacokinetic parameters. These inhibitors may be utilized not only to further validate ChoKα as antioncogenic target but also as novel chemical matter that may lead to antitumor agents that specifically interfere with cancer cell metabolism.

Abstract 2644: AP32788, a potent, selective inhibitor of EGFR and HER2 oncogenic mutants, including exon 20 insertions, in preclinical models

In non-small cell lung cancer (NSCLC), multiple classes of activating mutations have been identified in EGFR and HER2 that vary widely in their sensitivity to available tyrosine kinase inhibitors (TKIs). Erlotinib, gefitinib, and afatinib are approved for use in patients with the most common forms of EGFR activating mutations (ie, exon 19 deletions or L858R substitutions). However, no TKIs are approved for patients with EGFR activated by any other mutation, including exon 20 insertions or other uncommon substitutions, or for patients with any class of HER2 activating mutation (including exon 20 insertions). As inhibition of wild-type (WT) EGFR is associated with dose-limiting toxicities, a TKI that inhibits oncogenic EGFR and HER2 variants more potently than WT EGFR is more likely to be able to be dosed to efficacious levels. AP32788 is a potent inhibitor of all oncogenic forms of EGFR and HER2, including exon 20 insertions, with selectivity over WT EGFR. Activity of AP32788 and other TKIs was assessed by measuring viability of Ba/F3 cell lines engineered to express 20 mutant variants of EGFR (n = 14) or HER2 (n = 6): 4 EGFR variants containing a common activating mutation with or without a T790M resistance mutation, 8 EGFR/HER2 variants containing an exon 20 activating insertion (eg, EGFR ASV, HER2 YVMA), and 8 EGFR/HER2 variants containing other uncommon activating mutations (eg, EGFR G719A, HER2 G776V). Inhibition of WT EGFR was assessed by measuring effects on EGFR phosphorylation in cells (A431) that over-express WT EGFR. Consistent with their clinical activity, erlotinib and gefitinib generally only inhibited the 2 EGFR variants with common activating mutations more potently than WT EGFR (IC50s 71 and 56 nM, respectively), and afatinib generally only inhibited EGFR with common activating mutations or uncommon substitutions more potently than WT EGFR (IC50 4 nM). In contrast, AP32788 inhibited all 14 mutant variants of EGFR (IC50s 2.4-22 nM), and all 6 mutant variants of HER2 (IC50s 2.4-26 nM), more potently than it inhibited WT EGFR (IC50 35 nM), including all 8 variants with exon 20 activating insertions. In mice implanted with a patient-derived tumor containing an EGFR exon 20 activating insertion, or with engineered Ba/F3 cells containing a HER2 exon 20 activating insertion, once daily oral dosing of AP32788 induced regression of tumors at doses that were well tolerated (30-100 mg/kg). In vivo efficacy was associated with inhibition of EGFR signaling in the tumor. AP32788 potently inhibited all activated forms of EGFR and HER2 tested, including exon 20 insertions, more potently than WT EGFR, suggesting it may have the selectivity necessary to achieve efficacious levels of exposure in patients. A phase 1/2 clinical trial of AP32788 in NSCLC patients is planned. Citation Format: Francois Gonzalvez, Xiaotian Zhu, Wei-Sheng Huang, Theresa E. Baker, Yaoyu Ning, Scott D. Wardwell, Sara Nadworny, Sen Zhang, Biplab Das, Yongjin Gong, Matthew T. Greenfield, Hyun G. Jang, Anna Kohlmann, Feng Li, Paul M. Taslimi, Meera Tugnait, Yongjin Xu, Emily Y. Ye, Willmen W. Youngsaye, Stephan G. Zech, Yun Zhang, Tianjun Zhou, Narayana I. Narasimhan, David C. Dalgarno, William C. Shakespeare, Victor M. Rivera. AP32788, a potent, selective inhibitor of EGFR and HER2 oncogenic mutants, including exon 20 insertions, in preclinical models. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2644.

Abstract 2827: Discovery of AP26113, a potent, orally active inhibitor of anaplastic lymphoma kinase and clinically relevant mutants

Phosphorus, despite its abundance in the human body, is rarely found in drug molecules, with clinical utility limited to a few phosphonic or bisphosponic acid-based medicines and several phosphonate or phosphate-containing prodrugs. Concerns about poor cell penetration, low oral bioavailability, or biological instability have limited application of these functional classes in drug design. In our efforts to discover pharmaceuticals with novel functionality, we introduced a neutral, stable phosphine oxide moiety as a unique hydrogen-bond acceptor in the design of anaplastic lymphoma kinase (ALK) inhibitors. ALK is a receptor tyrosine kinase first identified as a chromosomal rearrangement (NPM-ALK fusion gene) in anaplastic large cell lymphoma (ALCL) and subsequently detected as an alternate fusion oncogene (EML4-ALK) in a subset of non-small cell lung cancers (NSCLC). Crizotinib, the first approved ALK inhibitor, has demonstrated impressive clinical benefit in EML4-ALK (ALK+) NSCLC patients. Drug resistance, however, emerges rapidly and point mutations within the kinase domain have been identified as a major resistance mechanism. With the specific objective to identify more potent ALK inhibitors with pan-inhibitory activity against crizotinib-resistant ALK mutants, we designed and tested a series of phosphine oxide-based compounds culminating in the identification of the clinical candidate AP26113. AP26113 exhibited 10-fold greater potency than crizotinib against ALK-positive ALCL and NSCLC cell lines, and effectively inhibited clinically relevant crizotinib-resistant mutants. AP26113 displayed ∼100-fold increased selectivity for ALK-positive cells over ALK-negative cell lines while maintaining selectivity over insulin receptor tyrosine kinase receptors. Consistent with the in vitro profile, AP26113 demonstrated oral efficacy in multiple ALK+ mouse models including Karpas-299 (ALCL), H3122 (NSCLC), and Ba/F3 cells expressing crizotinib resistant mutants including G1269S and L1196M. Finally, AP26113 exhibited excellent drug-like properties including high cell permeability and solubility, moderate cross-species protein binding, and inactivity toward major cytochrome P450 iso-enzymes and hERG ion channels. Medicinal chemistry efforts leading to the discovery of this potent pan-ALK inhibitor, including design strategy, chemical series evolution, and DMPK optimization will be presented. AP26113 is currently in a global phase 2 registration trial (NCT02094573) in patients with locally advanced or metastatic NSCLC who test positive for the ALK oncogene and were previously treated with crizotinib. Citation Format: Wei-Sheng Huang, Feng Li, Lisi Cai, Yongjin Xu, Sen Zhang, Scott D. Wardwell, Yaoyu Ning, Anna Kohlmann, Tianjun Zhou, Emily Y. Ye, Xiaotian Zhu, Narayana I. Narasimhan, Tim Clackson, Victor M. Rivera, David Dalgarno, William C. Shakespeare. Discovery of AP26113, a potent, orally active inhibitor of anaplastic lymphoma kinase and clinically relevant mutants. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2827. doi:10.1158/1538-7445.AM2015-2827

Abstract A98: An in vitro mutagenesis screen identifies L1951R and G2032R as drug-resistant mutants of CD74-ROS1.

NSCLC can be divided into a series of genomically-defined subsets, each generally containing a distinct molecular driver. The development of drugs that specifically target drivers such as mutant EGFR (erlotinib) and ALK fusions (crizotinib) has proven to be an effective therapeutic strategy. Despite these treatment advances, drug resistance inevitably occurs via a variety of mechanisms. Drug resistant point mutations of the driver oncogene are a common occurrence, with gatekeeper mutants often being problematic. ROS1 is rearranged in approximately 1.5% of NSCLC patients and is sensitive to crizotinib. Since ALK and ROS1 are structurally related, we generated Ba/F3 cells lines expressing CD74-ROS1 and tested their sensitivity to key ALK- targeted inhibitors currently in clinical testing. Crizotinib, AP26113, LDK378, and ASP3026 inhibited the viability of CD74-ROS1 expressing cells with IC50s significantly below their clinically-achievable plasma concentrations while CH5424802 was inactive thus highlighting that co-optimization of ROS1 activity is not a universal property of all ALK inhibitors. To investigate potential drug resistant mutant liabilities associated with each inhibitor, we performed a large scale mutagenesis screen, coupled with next generation sequencing, in Ba/F3 CD74-ROS1 cells exposed to increasing concentrations of each inhibitor. From our screens we identified a number of candidate mutants spanning the kinase domain of ROS1. L1951R and G2032R were the most frequent mutants in each screen, but mutation of the ROS1 gatekeeper residue (L2026) was not observed. To confirm the degree of resistance imparted by each mutant, we engineered CD74-ROS1 Ba/F3 cells to express the key ROS1 mutants identified and determined their sensitivities to crizotinib, AP26113, LDK378 and ASP3026. In addition to their frequent occurrence in our screens, L1951R and G2032R also conferred the highest degree of resistance (>50-fold) to each inhibitor. A ROS1 structural homology model indicates that L1951 and G2032 form part of the ATP-binding pocket of ROS1, and mutation of either residue to the larger amino acid arginine negatively impacts inhibitor activity without affecting the ability of CD74-ROS1 to transform cells. Interestingly, the analogous G2032R mutant in ALK (G1202R) has been observed as a clinical resistance mechanism induced by crizotinib, but remains sensitive to AP26113 (IC50 379 nM) in preclinical studies. In conclusion, we have demonstrated that crizotinib, AP26113, LDK378, and ASP3026 inhibit ROS1 activity. However, L1951R and G2032R ROS1 mutants are particularly resistant to each inhibitor. These preclinical data are supported by the recent identification of a G2032R mutant in a ROS1 patient who acquired resistance to crizotinib treatment, suggesting that generation of a ROS1-targeted compound that potently inhibits L1951R and G2032R mutants will ultimately be needed. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A98. Citation Format: Rana Anjum, Sadanand Vodala, Anna Kohlmann, Victor M. Rivera, Andrew P. Garner. An in vitro mutagenesis screen identifies L1951R and G2032R as drug-resistant mutants of CD74-ROS1. [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 A98.

Abstract 3236: Small molecule inhibitors of choline kinase lead to reduced phosphocholine levels and induction of apoptosis in cancer cells

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Choline Kinase (ChoK) catalyzes the synthesis of phosphocholine (pCho) as the first step in the Kennedy pathway towards synthesis of the major membrane phospholipid, phosphatidylcholine. Increased phosphorylation of choline is a hallmark of the malignant phenotype and ChoK over-expression (primarily ChoKβ) has been reported in a variety of human cancers including breast, lung, colorectal and prostate. These observations have recently motivated efforts to develop anti-cancer agents targeting ChoK. Here we summarize our efforts to further validate ChoKα as an oncogenic target by characterizing its tumorigenic potential and exploring the activity of novel small molecule inhibitors. We transduced the ChoKα gene into HEK293 cells to examine the effects of ChoK expression in vitro and in vivo. Under reduced serum conditions, over-expression of ChoK promoted cell growth, increased phospho-ERK and phospho-AKT levels, and reduced p21 levels. ChoKα, but not vector-expressing cells, formed tumors in immune-compromised mice and ChoKα expression levels were positively associated with tumor growth rates. Together, these data suggest that ChoK maintains proliferative pathways in the absence of growth factors, and itself provides an oncogenic driver capable of inducing tumor growth in the absence of other transforming mutations. Recently we identified a novel chemical series that inhibits ChoKα in both enzymatic and cellular assays. The binding of these inhibitors to ChoK protein was confirmed in surface plasmon resonance experiments. A representative member of this lead series, compound A, was characterized in more detail and demonstrated potent enzyme inhibition against ChoKα with an IC50 of 70 nM. Compound A also inhibited the growth of ChoKα -expressing breast cancer lines, MDA-MB-468 and MDA-MB-415, with GI50s of 7 and 2 uM respectively. In contrast, compound A exhibited much lower activity against the non-transformed breast epithelial cell line MCF-12A, with a GI50 >40 uM. Consistent with its effects on cell growth, pCho levels in MDA-MB-415 cells, as measured by NMR, were dose-dependently inhibited up to ∼80% by 24 hours with an IC50 of ∼750 nM. In MDA-MB-415 cells, but not MCF-12A cells, levels of apoptotic markers were increased at 24 hours with compound concentrations β5 uM. In summary, we demonstrated that small molecule inhibition of ChoK results in a dose-dependent decrease of pCho levels, inhibition of proliferation and induction of apoptosis in ChoKα expressing breast cancer cells. We established that exogenous expression of ChoKα in HEK293 cells drives both oncogenic transformation and constitutive activation of proliferative signaling pathways. Taken together, these data further validate ChoKα as a potential therapeutic target in cancer and support the continued investigation into the utility of ChoKα inhibitors as anti-oncogenic agents. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3236. doi:1538-7445.AM2012-3236