Supplementary Methods Supplementary References Supplementary Figure 1. Effect of acquired resistance mutations on TRK inhibitor activity. Supplementary Figure 2. Further characterization of LOXO-195 inhibitory activity against acquired resistance mutations. Supplementary Figure 3. LOXO-195 is selectively cytotoxic to TRK-fusion cell lines. Supplementary Figure 4. Identification of a clonal NTRK1 (TRKA)-G595R mutation after larotrectinib treatment. Supplementary Table 1. LOXO-195 ADME properties. Supplementary Table 2. Selectivity of LOXO-195 for 228 kinases. Supplementary Table 3. Summary of LOXO-195 PK parameters for each patient during intra-patient dose escalation.

Abstract Although approved BRAF inhibitors have transformed the treatment of patients with certain BRAF V600 mutant cancers, their long-term efficacy is thought to be limited by poor brain penetration. As a result, disease progression in the brain is a significant cause of morbidity and mortality. PF-07284890 (ARRY-461) is an orally bioavailable, brain penetrant, potent, small molecule inhibitor targeting BRAF V600 mutant tumors and is in clinical development in patients with BRAF V600 metastatic melanoma with progression to the brain. In biochemical in vitro studies, PF-07284890 inhibits BRAF and CRAF with IC50's of 5.8 and 4.1 nM, respectively. Additionally, PF-07284890 inhibits the clinically relevant kinase domain BRAF V600 mutants (V600E and V600K) (IC50 = 24-25 nM). In cell-based systems, PF-07284890 potently inhibits phosphorylation of ERK, a downstream marker of BRAF inhibition, and potently inhibits proliferation of BRAF V600E/K mutant melanoma cell lines (IC50 18-38 nM). PF-07284890 was designed to distribute to the brain and, as such, in vitro experiments indicate that PF-07284890 has high cellular membrane permeability and is not a substrate for human P glycoprotein (P-gp). After oral administration of PF-07284890 to mice and rats, PF-07284890 distributes to the brain where the free fraction adjusted exposure in the brain was approximately proportional to the free fraction adjusted exposure in plasma (i.e., Cbrain,u/Cplasma,u approaches 1.0). In vivo, PF-07284890 inhibits phosphorylation of ERK in A375 BRAF V600E tumors, achieving maximal target inhibitions at a dose of 10 mg/kg. PF-07284890 has been evaluated for its ability to control BRAF V600E cell line and patient-derived melanoma xenograft tumor growth in nude mice when implanted both subcutaneously and intracranially. Dose-related tumor growth inhibition was demonstrated at dose levels ranging from 1 to 30 mg/kg, BID in both subcutaneous and intracranial xenograft models. In all models, regardless of tumor location, maximal efficacy was observed in dose ranges of 10-30 mg/kg BID. In the intracranial A375-luc BRAF V600E melanoma xenograft model, significant and durable tumor regressions were seen at doses of 10 and 30 mg/kg/day which translated to a profound survival benefit in animals receiving PF-07284890 (median survival > 55 days post-implantation) compared to control animals (median survival = 15 days). GLP safety studies demonstrated a good safety profile for PF-07284890. PF-07284890 is fully brain penetrant, with the potential to address this key unmet medical need and thereby defines a new class of brain penetrant, potent and selective BRAF inhibitors. Citation Format: Karyn Bouhana, Deborah Anderson, Walter DeWolf, Suzy Brown, Lance Williams, Li Ren, David Moreno, Ross Wallace, Jay Brad Fell, Dylan Hartley, Patrice Lee. Nonclinical development of PF-07284890 (ARRY-461), a potent, brain-penetrant, small molecule inhibitor of BRAF V600-mutation-driven tumors in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1473.

Glucose flux through glucokinase (GK) controls insulin release from the pancreas in response to high levels of glucose. Flux through GK is also responsible for reducing hepatic glucose output. Since many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, identifying compounds that can activate GK could provide a therapeutic benefit. Herein we report the further structure activity studies of a novel series of glucokinase activators (GKA). These studies led to the identification of pyridine 72 as a potent GKA that lowered post-prandial glucose in normal C57BL/6J mice, and after 14d dosing in ob/ob mice.

Abstract Larotrectinib, a selective TRK tyrosine kinase inhibitor (TKI), has demonstrated histology-agnostic efficacy in patients with TRK fusion–positive cancers. Although responses to TRK inhibition can be dramatic and durable, duration of response may eventually be limited by acquired resistance. LOXO-195 is a selective TRK TKI designed to overcome acquired resistance mediated by recurrent kinase domain (solvent front and xDFG) mutations identified in multiple patients who have developed resistance to TRK TKIs. Activity against these acquired mutations was confirmed in enzyme and cell-based assays and in vivo tumor models. As clinical proof of concept, the first 2 patients with TRK fusion–positive cancers who developed acquired resistance mutations on larotrectinib were treated with LOXO-195 on a first-in-human basis, utilizing rapid dose titration guided by pharmacokinetic assessments. This approach led to rapid tumor responses and extended the overall duration of disease control achieved with TRK inhibition in both patients. Significance: LOXO-195 abrogated resistance in TRK fusion–positive cancers that acquired kinase domain mutations, a shared liability with all existing TRK TKIs. This establishes a role for sequential treatment by demonstrating continued TRK dependence and validates a paradigm for the accelerated development of next-generation inhibitors against validated oncogenic targets. Cancer Discov; 7(9); 963–72. ©2017 AACR. See related commentary by Parikh and Corcoran, p. 934. This article is highlighted in the In This Issue feature, p. 920

Glucokinase (GK) catalyzes the phosphorylation of glucose to glucose-6-phosphate. We present the structure-activity relationships leading to the discovery of AM-2394, a structurally distinct GKA. AM-2394 activates GK with an EC50 of 60 nM, increases the affinity of GK for glucose by approximately 10-fold, exhibits moderate clearance and good oral bioavailability in multiple animal models, and lowers glucose excursion following an oral glucose tolerance test in an ob/ob mouse model of diabetes.

Two 1-(4-aryl-5-alkyl-pyridin-2-yl)-3-methylurea glucokinase activators were identified with robust in vivo efficacy. These two compounds possessed higher solubilities than the previously identified triaryl compounds (i.e., AM-2394). Structure-activity relationship studies are presented along with relevant pharmacokinetic and in vivo data.

Glucokinase (GK) activators represent a class of type 2 diabetes therapeutics actively pursued due to the central role that GK plays in regulating glucose homeostasis. Herein we report a novel C5-alkyl-2-methylurea-substituted pyridine series of GK activators derived from our previously reported thiazolylamino pyridine series. Our efforts in optimizing potency, enzyme kinetic properties, and metabolic stability led to the identification of compound 26 (AM-9514). This analogue showed a favorable combination of in vitro potency, enzyme kinetic properties, acceptable pharmacokinetic profiles in preclinical species, and robust efficacy in a rodent PD model.

Glucokinase (GK) is the rate-limiting step for insulin release from the pancreas in response to high levels of glucose. Flux through GK also contributes to reducing hepatic glucose output. Since many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, identifying compounds that can allosterically activate GK may address this issue. Herein we report the identification and initial optimization of a novel series of glucokinase activators (GKAs). Optimization led to the identification of 33 as a compound that displayed activity in an oral glucose tolerance test (OGTT) in normal and diabetic mice.

Glucokinase (GK) is a hexokinase isozyme that catalyzes the phosphorylation of glucose to glucose-6-phosphate. Glucokinase activators are being investigated as potential diabetes therapies because of their effects on hepatic glucose output and/or insulin secretion. Here, we have examined the efficacy and mechanisms of action of a novel glucokinase activator, GKA23. In vitro, GKA23 increased the affinity of rat and mouse glucokinase for glucose, and increased glucose uptake in primary rat hepatocytes. In vivo, GKA23 treatment improved glucose homeostasis in rats by enhancing beta cell insulin secretion and suppressing hepatic glucose production. Sub-chronic GKA23 treatment of mice fed a high-fat diet resulted in improved glucose homeostasis and lipid profile.

Glucose flux through glucokinase (GK) controls insulin release from the pancreas in response to high glucose concentrations. Glucose flux through GK also contributes to reducing hepatic glucose output. Because many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, compounds that can activate GK may serve as effective treatments for type 2 diabetes. Herein we report the identification and initial optimization of a novel series of allosteric glucokinase activators (GKAs). We discovered an initial thiazolylamino pyridine-based hit that was optimized using a structure-based design strategy and identified 26 as an early lead. Compound 26 demonstrated a good balance of in vitro potency and enzyme kinetic parameters and demonstrated blood glucose reductions in oral glucose tolerance tests in both C57BL/6J mice and high-fat fed Zucker diabetic fatty rats.

Abstract Increasing evidence suggests that interactions between tumor cells, stromal cells, macrophages and the extracellular matrix are pivotal to the processes of tumorigenesis, metastasis, and neovascularization. Macrophages within the tumor microenvironment are thought to facilitate cancer progression, making them intriguing targets for therapy. Colony stimulating factor 1 (CSF-1) and its receptor, cFMS, play a central role in the development of mononuclear phagocytes, recruitment of macrophages to tumors, and differentiation and function of osteoclasts. We have developed an orally active, selective small-molecule cFMS inhibitor for cFMS. This molecule inhibits cFMS cellular activity (IC50 = 9 nM) in vitro and inhibits cFMS phosphorylation in a transfected cell line grown in nude mice (ED50 = 3 mg/kg). Our compound also inhibits CSF-1-mediated osteoclast differentiation and function (IC50 values of = 4 nM and 58 nM, respectively). To further explore the potential of our selective inhibitor for the treatment of cancer, we evaluated anti-tumor activity in several preclinical models. We first explored the effect on the murine ovarian cancer cell line, ID8. ID8 cells injected intraperitoneally into nude mice form multiple peritoneal tumor deposits and abundant ascites. Macrophage infiltration in the ID8 ascites was markedly lowered in mice treated with a cFMS inhibitor. Using MCF-7, a human breast adenocarcinoma cell line that has been shown to produce M-CSF, a daily oral dose with 100 mg/kg of our inhibitor for 21 days significantly reduced tumor growth and was accompanied by a marked reduction in tumor-associated macrophages. These findings support the potential of a selective inhibitor of cFMS to favorably impact human cancers by modulating tumor-associated macrophage functions. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 551. doi:10.1158/1538-7445.AM2011-551

Abstract As a consequence of a variety of genetic lesions, the PI3K/Akt pathway is constitutively activated in a large proportion of human cancers. The mTOR kinase plays an important role in this pathway as the key component of two independent signaling complexes (TORC1 and TORC2) that are involved at two distinct levels in this signaling cascade. Accordingly, inhibition of mTOR kinase will abrogate signaling from both mTOR complexes and serve as an effective means of targeting this pathway. In addition, the activity of the TORC1 complex is often aberrantly activated in a PI3K-independent manner to allow tumor cells to survive and proliferate despite the many negative influences of the tumor microenvironment such as hypoxia and limited nutrient availability. Therefore, an inhibitor of both TORC1 and TORC2 should effectively block signaling from the PI3K pathway as well as abrogate the cancer cells’ ability to survive in the harsh environment of the tumor thereby providing an effective means of treating cancer. We report here the profile of our small molecule mTOR kinase inhibitor AR-mTOR-26. On enzyme, this compound inhibits mTOR kinase with an IC50 of 1 nM while exhibiting substantial selectivity against PI3Kα as well as a panel of lipid and protein kinases. In cells, AR-mTOR-26 inhibits the TORC1-dependent readouts pS6 (Ser235/6) and p4E-BP1 (Ser37/46) as well as the TORC2 phosphorylation site on Akt, Ser473, with IC50 values of <50 nM. Consistent with its selectivity over PI3Kα, AR-mTOR-26 does not significantly inhibit Thr308 on AKT, a PI3K/PDK1-dependent readout. In addition, we show that AR-mTOR-26 is broadly and potently anti-proliferative across a panel of solid and hematological cancer cell lines, irrespective of their mutational status suggesting the potential for broad therapeutic utility. We then evaluated the in vivo activity of AR-mTOR-26. By oral administration, AR-mTOR-26 exhibits excellent pharmacokinetics in mice with plasma concentrations that are predicted to be efficacious. Doses ranging from 1-10 mg/kg once daily to tumor-bearing mice results in significant anti-tumor activity in several mouse xenograft models, including PC3 prostate [PTEN null] and H460 lung [KRASG12D/PIK3CA]. These effects ranged from tumor growth inhibition to regressions dependent upon the dose and the xenograft model evaluated. In all, these data show that targeting mTOR kinase with AR-mTOR-26 holds promise as a broadly acting therapeutic for oncology. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4484.

Abstract Through alterations in the PTEN and PI3K genes, the PI3K / Akt pathway is constitutively activated in human cancers. mTOR kinase plays an unique role in this pathway as the key component of two independent signaling complexes (mTORC1 (raptor - rapamycin sensitive) and mTORC2 (rictor - rapamycin insensitive)) that are involved at multiple branch points in this signaling cascade. As such, inhibition of mTOR kinase inactivates both mTOR complexes and therefore serves as an attractive means to target this integral pathway for the treatment of human malignancy. We report the biological and pharmaceutical evaluation of our selective mTOR 1/2 kinase inhibitor AR-mTOR-1. AR-mTOR-1 inhibits mTOR kinase with an IC50 of < 10 nM while maintaining selectivity against PI3K as well as a panel of additional lipid kinases, serine/threonine kinases and cytoplasmic and receptor tyrosine kinases. In mechanistic cellular assays, AR-mTOR-1 inhibits pAkt (Ser473), 4E-BP1 (Thr36/46) and pS6 (Ser235/6) with nanomolar potency, thus demonstrating inhibition of signaling from both mTORC1 and mTORC2 complexes. In line with its enzymatic selectivity over PI3K , AR-mTOR-1 does not significantly inhibit pAkt (Thr308) in cells. AR-mTOR-1 is broadly anti-proliferative in both epithelial and hematologic cancer cell lines, irrespective of mutational status, with IC50's ranging from 30 to 550 nM across 20 cell lines, suggesting the potential for broad clinical activity. Once daily dosing of AR-mTOR-1 in several mouse xenograft models, including PC3 prostate, U87 glioblastma, and H460 lung, results in robust anti-tumor activity. Finally, AR-mTOR-1 possesses desired in vitro and in vivo preclinical ADME properties including low clearance, high permeability and good absorption in three preclinical species. In total these data demonstrate that selectively targeting mTORC1 and mTORC2 with AR-mTOR-1 holds promise for broad spectrum clinical utility as a single agent across a wide array of cancer types. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B267.

AIM:Profiling the efficacy and pharmacodynamic activity of the kinesin spindle protein (KSP) inhibitor ARRY-520 will aid the identification of responsive tumor types and pharmacodynamic profiles that correlate with activity.MATERIALS AND METHODS:In vivo activity was evaluated in a diverse panel of 16 different tumor xenograft models. Pharmacodynamic activity was evaluated in selected models.RESULTS:ARRY-520 had low nanomolar antiproliferative activity in tumor cell lines. Monopolar spindles were formed at active potencies. Partial or complete responses were observed in 13/16 xenograft models. Hematological tumors were particularly sensitive, with a 100% complete response rate in some models. Maintenance of mitotic block for a sufficient length of time for cells to lose survival signals and progress to apoptosis was a key component of the mechanism of activity. ARRY-520 was also active in several taxane resistant models.CONCLUSION:The data provide a rationale for clinical evaluation of the activity of ARRY-520 in hematological carcinomas and taxane-resistant tumors.

Tumor cells extensively utilize the pentose phosphate pathway for the synthesis of ribose. Transketolase is a key enzyme in this pathway and has been suggested as a target for inhibition in the treatment of cancer. In a pharmacodynamic study, nude mice with xenografted HCT-116 tumors were dosed with 1 ('N3'-pyridyl thiamine'; 3-(6-methyl-2-amino-pyridin-3-ylmethyl)-5-(2-hydroxyethyl)-4-methyl-thiazol-3-ium chloride hydrochloride), an analog of thiamine, the co-factor of transketolase. Transketolase activity was almost completely suppressed in blood, spleen, and tumor cells, but there was little effect on the activity of the other thiamine-utilizing enzymes alpha-ketoglutarate dehydrogenase or glucose-6-phosphate dehydrogenase. Synthesis and SAR of transketolase inhibitors is described. (C) 2007 Elsevier Ltd. All rights reserved.

Transketolase, a key enzyme in the pentose phosphate pathway, has been suggested as a target for inhibition in the treatment of cancer. Compound 5a ('N3'-pyridyl thiamine'; 3-(6-methyl-2-amino-pyridin-3-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium chloride hydrochloride), an analog of the transketolase cofactor thiamine, is a potent transketolase inhibitor but suffers from poor pharmacokinetics due to high clearance and C(max) linked toxicity. An efficient way of improving the pharmacokinetic profile of 5a is to prepare oxidized prodrugs which are slowly reduced in vivo yielding longer, sustained blood levels of the drug. The synthesis of such prodrugs and their evaluation in rodent models is reported.

Kinesins are eukaryotic microtubule-associated motor proteins. There are over 40 known kinesins, approximately 15 of which are closely associated with mitosis. Kinesin Spindle Protein (KSP), also known as Eg5, is a mitotic kinesin that is a required enzyme in mitosis (prophase / prometaphase). This protein plays a key role in the formation of the bipolar spindle, particularly related to its role in centrosome maturation/separation. Because KSP is expressed predominately in proliferating cells and is absent from postmitotic neurons, its inhibition should not produce the peripheral neuropathy associated with traditional microtubule disruption agents (taxanes and vinca alkaloids). We report here the in vitro characterization of a potent KSP inhibitor, ARRY-429520, a member of a series of KSP inhibitors discovered and optimized by structure-based design. ARRY-429520 inhibits human KSP, with an IC50 of 6 nM, by a mechanism which was demonstrated to be uncompetitive with respect to ATP and noncompetitive with respect to tubulin. It was shown to arrest cells in mitosis as measured by FACs analysis as well as the accumulation of phospho- histone H3, with an EC50 of 1.5 nM. Furthermore, this compound was demonstrated to be antiproliferative, with EC50s between 0.3 nM and 6.5 nM against a panel of human tumor cell lines, including various leukemia lines (K-562, KU-812, HL-60, KG-1, MOLT3, MOLT4). In addition, ARRY-429520's potency in MDR-overexpressing cell lines was minimally impacted as compared to paclitaxel. Cellular imaging studies demonstrate that the normal mitotic spindle configuration was disrupted, with the formation of monopolar spindles, a hallmark feature of KSP inhibition, at single digit nanomolar concentrations of ARRY-429520. Markers of mitotic arrest and apoptosis were demonstrated in tumor xenografts from animals treated with ARRY-429520.