First-in-Human Study of the Reversible BTK Inhibitor Nemtabrutinib in Patients with Relapsed/Refractory Chronic Lymphocytic Leukemia and B-Cell Non-Hodgkin Lymphoma

Nemtabrutinib is an orally bioavailable, reversible inhibitor of Bruton tyrosine kinase (BTK) and C481S mutant BTK. We evaluated the safety, pharmacology, and antitumor activity of nemtabrutinib in relapsed/refractory hematologic malignancies. Forty-eight patients with chronic lymphocytic leukemia (CLL), B-cell non-Hodgkin lymphoma (NHL), or Waldenström macroglobulinemia (WM), relapsed/refractory after ≥2 prior therapies were enrolled in the open-label, single-arm, phase I MK-1026-001 study (NCT03162536) to receive nemtabrutinib 5 to 75 mg once daily in 28-day cycles. Dose finding progressed using a 3 + 3 dose escalation design. Primary endpoints were safety and the recommended phase II dose (RP2D). Among 47 treated patients, 29 had CLL, 17 had NHL, and 1 had WM. Grade ≥3 treatment-emergent adverse events occurred in 37 (89%), most commonly neutropenia (11; 23.4%), febrile neutropenia (7; 14.9%), and pneumonia (7; 14.9%). The RP2D was 65 mg daily. An overall response rate of 75% was observed in patients with CLL at 65 mg daily.

SIGNIFICANCE

This first-in-human phase I study demonstrates the safety and preliminary efficacy of nemtabrutinib in patients with relapsed/refractory B-cell malignancies. These data support further exploration of nemtabrutinib in larger clinical studies. This article is featured in Selected Articles from This Issue, p. 5.

Abstract 3396: Discovery of BDTX-1535, a novel 4th generation, irreversible, potent, wild type sparing EGFR MasterKey inhibitor that targets oncogenic kinase domain mutations as well as extracellular domain alterations for the treatment of NSCLC and GBM

Acquired resistance to 3rd generation EGFR inhibitors used in the treatment of NSCLC is common. While the EGFR C797S substitution is a frequently reported post-osimertinib resistance mutation, real world evidence indicates the emergence of additional EGFR alterations that can drive drug resistance: kinase domain mutations (e.g., S768I), extracellular domain alterations (e.g., EGFRvIII, A289X), and EGFR amplification. Moreover, while osimertinib targets the classical EGFR mutations, primary NSCLC tumors are also driven by other oncogenic kinase domain mutations including G719X, S768I, and L861Q, which confer de novo (intrinsic) resistance to 3rd generation EGFR TKIs. A family of extracellular domain alterations occurs in nearly 50% of GBM patients, and these alterations are clinically resistant to all current generation inhibitors. Real world data in GBM demonstrate these EGFR alterations often co-occur and persist throughout treatment with current standard of care therapy. Of critical importance is the observation that the oncogenic isoform of EGFR in GBM is a covalent homo-dimer which can be formed and paradoxically activated by the binding of reversible 1st generation EGFR inhibitors. There is a significant clinical need to develop a potent CNS penetrant EGFR inhibitor that would target both acquired and intrinsic resistance mutations expressed in NSCLC and co-occurring EGFR alterations in GBM. An effective inhibitor should meet four design principles; 1) potent and selective against a broad family of intracellular, extracellular EGFR oncogenic alterations and amplification, 2) wild type EGFR sparing, 3) irreversible to avoid paradoxical activation, and 4) CNS penetrant. BDTX-1535 is a 4th generation irreversible CNS penetrant EGFR MasterKey inhibitor targeting a family of oncogenic EGFR extracellular domain alterations and amplification in GBM patients and EGFR resistance mutations in NSCLC. BDTX-1535 meets all four criteria for a highly effective EGFR inhibitor and was designed using the MAP Discovery Engine to target the activated conformations used by oncogenic EGFR to drive tumorigenesis. BDTX-1535 achieves potent anti-tumor activity against EGFR alterations and amplification across models including NSCLC and GBM PDX and intracranial tumors. BDTX-1535 is currently in a phase I clinical study in patients with NSCLC and GBM harboring sensitive EGFR alterations (NCT05256290).

Citation Format: Matthew O'Connor, Matthew Lucas, Sherri Smith, Anthony Trombino, Sudharshan Eathiraj, Elizabeth Buck. Discovery of BDTX-1535, a novel 4th generation, irreversible, potent, wild type sparing EGFR MasterKey inhibitor that targets oncogenic kinase domain mutations as well as extracellular domain alterations for the treatment of NSCLC and GBM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3396.

Preclinical evaluation of combination nemtabrutinib and venetoclax in chronic lymphocytic leukemia

Inhibitors of B cell receptor (BCR) signaling such as the Bruton's tyrosine kinase (BTK) inhibitors are effective therapeutics for chronic lymphocytic leukemia (CLL). The first-in-class covalent BTK inhibitor, ibrutinib, produces durable responses in most CLL patients; however, complete responses are only observed in a minority of patients. B cell lymphoma 2 (BCL2), an anti-apoptotic protein that contributes to CLL cell survival, has also been investigated as a therapeutic target. The BCL2 inhibitor venetoclax is effective in patients with CLL and can produce undetectable minimal residual disease, allowing discontinuation of therapy. In combination, ibrutinib and venetoclax have shown preclinical synergy and clinical efficacy. Nemtabrutinib is a next generation, reversible inhibitor of BTK that potently inhibits BCR signaling in treatment-naïve and ibrutinib-refractory CLL cells ex vivo. The clinical efficacy of combining BTK inhibitors with BCL2 inhibitors motivated us to evaluate the novel combination of nemtabrutinib and venetoclax. In vitro studies show that nemtabrutinib and venetoclax are not antagonistic to each other. In an adoptive transfer CLL mouse model, mice treated with nemtabrutinib and venetoclax had prolonged survival compared to mice treated with ibrutinib and venetoclax. Our preclinical studies further validate the combination of BTK inhibitors with venetoclax and justify further investigation of combining nemtabrutinib with venetoclax in CLL.

Abstract P02-04: BDTX-1535, a CNS penetrant MasterKey inhibitor of common, uncommon and resistant EGFR mutations, demonstrates in vivo efficacy and has potential to treat osimertinib-resistant NSCLC with or without brain metastases

NSCLC accounts for approximately 85% of lung cancer cases worldwide. NSCLC harboring EGFR mutations constitutes 10-20% of all lung cancer cases in Europe and North America, and up to 50% of those in Asia. The majority (80-90%) of these mutations are either Exon19del or L858R. Uncommon EGFR mutations, of which G719X, S768I and L861Q are amongst the most frequent, account for 10-20% of EGFR mutations in NSCLC. Additionally, secondary EGFR mutations such as C797S that emerge during treatment with osimertinib occur in ~10% of patients. Current generation EGFR inhibitors with efficacy against common, uncommon and/or resistance mutations are either poorly brain penetrant or do not have broad spectrum activity against multiple mutations. BDTX-1535 is an irreversible, spectrum selective MasterKey inhibitor of common, uncommon and resistance EGFR mutations such as G719X and C797S that occur in NSCLC (IC50<10nM). BDTX-1535 is differentiated from many EGFR inhibitors by its CNS-penetrating properties. BDTX-1535 has a Kpuu, defined as the ratio of the unbound brain tissue concentration over the unbound plasma concentration, of 0.8 in rat. In studies of EGFR Exon19del+C797S, BDTX-1535 achieved pEGFR suppression exceeding 24 hours in vitro and following a single dose in vivo. BDTX-1535 has demonstrated robust tumor growth inhibition and regressions in multiple pre-clinical models, including PDX intracranial models. Thus, BDTX-1535 has potential to treat patients with NSCLC harboring a broad range of mutations, both common and uncommon, as well as those associated with resistance to the current standard of care TKIs. The CNS penetrating properties may help to treat CNS metastases or to prevent them from occurring. BDTX-1535 is currently being evaluated in IND-enabling studies.

Citation Format: Matthew C. Lucas, Melinda S. Merchant, Matthew O'Connor, Carl Cook, Sherri Smith, Anthony Trombino, Wu-Yan Zhang, Irache Visiers, Kate Tith, Reza Foroughi, Nigel Waters, Iwona Wrona, Michael Pickard, Sudharshan Eathiraj, Karsten Witt, Christopher Roberts, Rachel Humphrey, Elizabeth Buck. BDTX-1535, a CNS penetrant MasterKey inhibitor of common, uncommon and resistant EGFR mutations, demonstrates in vivo efficacy and has potential to treat osimertinib-resistant NSCLC with or without brain metastases [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P02-04.

Inhibition of the BTK-IDO-mTOR axis promotes differentiation of monocyte-lineage dendritic cells and enhances anti-tumor T cell immunity

Monocytic-lineage inflammatory Ly6c+CD103+ dendritic cells (DCs) promote antitumor immunity, but these DCs are infrequent in tumors, even upon chemotherapy. Here, we examined how targeting pathways that inhibit the differentiation of inflammatory myeloid cells affect antitumor immunity. Pharmacologic inhibition of Bruton's tyrosine kinase (BTK) and the tryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO) or deletion of Btk or Ido1 allowed robust differentiation of inflammatory Ly6c+CD103+ DCs during chemotherapy, promoting antitumor T cell responses and inhibiting tumor growth. Immature Ly6c+c-kit+ precursor cells had epigenetic profiles similar to conventional DC precursors; deletion of Btk or Ido1 promoted differentiation of these cells. Mechanistically, a BTK-IDO axis inhibited a tryptophan-sensitive differentiation pathway driven by GATOR2 and mTORC1, and disruption of the GATOR2 in monocyte-lineage precursors prevented differentiation into inflammatory DCs in vivo. IDO-expressing DCs and monocytic cells were present across a range of human tumors. Thus, a BTK-IDO axis represses differentiation of inflammatory DCs during chemotherapy, with implications for targeted therapies.

The new small tyrosine kinase inhibitor ARQ531 targets acute myeloid leukemia cells by disrupting multiple tumor-addicted programs

Tyrosine kinases have been implicated in promoting tumorigenesis of several human cancers. Exploiting these vulnerabilities has been shown to be an effective anti-tumor strategy as demonstrated for example by the Bruton's tyrosine kinase (BTK) inhibitor, ibrutinib, for treatment of various blood cancers. Here, we characterize a new multiple kinase inhibitor, ARQ531, and evaluate its mechanism of action in preclinical models of acute myeloid leukemia. Treatment with ARQ531, by producing global signaling pathway deregulation, resulted in impaired cell cycle progression and survival in a large panel of leukemia cell lines and patient-derived tumor cells, regardless of the specific genetic background and/or the presence of bone marrow stromal cells. RNA-seq analysis revealed that ARQ531 constrained tumor cell proliferation and survival through Bruton's tyrosine kinase and transcriptional program dysregulation, with proteasome-mediated MYB degradation and depletion of short-lived proteins that are crucial for tumor growth and survival, including ERK, MYC and MCL1. Finally, ARQ531 treatment was effective in a patient-derived leukemia mouse model with significant impairment of tumor progression and survival, at tolerated doses. These data justify the clinical development of ARQ531 as a promising targeted agent for the treatment of patients with acute myeloid leukemia.

Preclinical efficacy for a novel tyrosine kinase inhibitor, ArQule 531 against acute myeloid leukemia

BACKGROUND

Acute myeloid leukemia (AML) is the most common type of adult leukemia. Several studies have demonstrated that oncogenesis in AML is enhanced by kinase signaling pathways such as Src family kinases (SFK) including Src and Lyn, spleen tyrosine kinase (SYK), and bruton's tyrosine kinase (BTK). Recently, the multi-kinase inhibitor ArQule 531 (ARQ 531) has demonstrated potent inhibition of SFK and BTK that translated to improved pre-clinical in vivo activity as compared with the irreversible BTK inhibitor ibrutinib in chronic lymphocytic leukemia (CLL) models. Given the superior activity of ARQ 531 in CLL, and recognition that this molecule has a broad kinase inhibition profile, we pursued its application in pre-clinical models of AML.

METHODS

The potency of ARQ 531 was examined in vitro using FLT3 wild type and mutated (ITD) AML cell lines and primary samples. The modulation of pro-survival kinases following ARQ 531 treatment was determined using AML cell lines. The effect of SYK expression on ARQ 531 potency was evaluated using a SYK overexpressing cell line (Ba/F3 murine cells) constitutively expressing FLT3-ITD. Finally, the in vivo activity of ARQ 531 was evaluated using MOLM-13 disseminated xenograft model.

RESULTS

Our data demonstrate that ARQ 531 treatment has anti-proliferative activity in vitro and impairs colony formation in AML cell lines and primary AML cells independent of the presence of a FLT3 ITD mutation. We demonstrate decreased phosphorylation of oncogenic kinases targeted by ARQ 531, including SFK (Tyr416), BTK, and fms-related tyrosine kinase 3 (FLT3), ultimately leading to changes in down-stream targets including SYK, STAT5a, and ERK1/2. Based upon in vitro drug synergy data, we examined ARQ 531 in the MOLM-13 AML xenograft model alone and in combination with venetoclax. Despite ARQ 531 having a less favorable pharmacokinetics profile in rodents, we demonstrate modest single agent in vivo activity and synergy with venetoclax.

CONCLUSIONS

Our data support consideration of the application of ARQ 531 in combination trials for AML targeting higher drug concentrations in vivo.

The BTK Inhibitor ARQ 531 Targets Ibrutinib-Resistant CLL and Richter Transformation

Targeted inhibition of Bruton tyrosine kinase (BTK) with the irreversible inhibitor ibrutinib has improved outcomes for patients with hematologic malignancies, including chronic lymphocytic leukemia (CLL). Here, we describe preclinical investigations of ARQ 531, a potent, reversible inhibitor of BTK with additional activity against Src family kinases and kinases related to ERK signaling. We hypothesized that targeting additional kinases would improve global inhibition of signaling pathways, producing more robust responses. In vitro treatment of patient CLL cells with ARQ 531 decreases BTK-mediated functions including B-cell receptor (BCR) signaling, viability, migration, CD40 and CD86 expression, and NF-κB gene transcription. In vivo, ARQ 531 was found to increase survival over ibrutinib in a murine Eμ-TCL1 engraftment model of CLL and a murine Eμ-MYC/TCL1 engraftment model resembling Richter transformation. Additionally, ARQ 531 inhibits CLL cell survival and suppresses BCR-mediated activation of C481S BTK and PLCγ2 mutants, which facilitate clinical resistance to ibrutinib.Significance: This study characterizes a rationally designed kinase inhibitor with efficacy in models recapitulating the most common mechanisms of acquired resistance to ibrutinib. Reversible BTK inhibition is a promising strategy to combat progressive CLL, and multikinase inhibition demonstrates superior efficacy to targeted ibrutinib therapy in the setting of Richter transformation. Cancer Discov; 8(10); 1300-15. ©2018 AACR. This article is highlighted in the In This Issue feature, p. 1195.

Abstract LB-018: ARQ 531, a novel and reversible inhibitor of Bruton's tyrosine kinase, displays favorable oral bioavailability and exposure in patients with B-cell malignancies

Background: ARQ 531 is a novel, ATP competitive reversible inhibitor Bruton's tyrosine kinase (BTK). BTK is a key regulator of the B cell receptor (BCR) signaling pathway that mediates signaling from the cell surface to the cytoplasm and into the nucleus. ARQ 531 is not metabolized by any of the major drug metabolizing CYP450 enzymes. Here we report pharmacokinetic profile of ARQ 531 in a phase I study evaluating safety, pharmacokinetics and pharmacodynamics activity and clinical activity of ARQ 531 in selected subjects with relapsed/refractory B-cell malignancies. Preclinical studies in rats, dogs and monkeys are also described.

Methods: Oral and intravenous single dose pharmacokinetic studies of ARQ 531 were conducted in rats, dogs, and monkeys to determine oral bioavailability and drug exposure. In a standard ‘3+3' dose-escalation study design, ARQ 531 was given orally once per day beginning at 5 mg/dose and escalating for 4 weeks [NCT03162536]. Plasma samples were collected to determine ARQ 531 concentrations and whole blood / PBMCx to quantify pBTK inhibition. Plasma samples from each species were analyzed by liquid chromatography-mass spectrometry/ mass spectrometry (LC-MS/MS).

Results: Consistent with preclinical studies, patients enrolled in the phase I study showed favorable exposures, the steady state peak to trough ratio was generally 3:1 or lower. ARQ 531 had an elimination half-life at steady state of ~24 hr and Cmax occurred 2 to 3 hours after dosing. Pharmacodynamic changes included suppression of BTK phosphorylation. No drug related AEs or DLTs have been observed thus far in the study.

Conclusions: ARQ 531 demonstrates a favorable PK profile in humans supporting once daily dosing. Sufficient plasma levels are attained and high levels of pBTK inhibition in peripheral blood can be achieved following oral dosing. Additional dose and schedule evaluations continue, and updated clinical and biomarker results will be presented.

Citation Format: Terence Hall, Yi Yu, Sudharshan Eathiraj, Deborah Stephens, Ian Flinn, Jennifer Woyach, Brian Schwartz, Ronald E. Savage. ARQ 531, a novel and reversible inhibitor of Bruton's tyrosine kinase, displays favorable oral bioavailability and exposure in patients with B-cell malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-018.

Abstract 2943: In vivo combination of miransertib (ARQ 092) with anti-PD-1 antibody, trametinib, lapatinib, trastuzumab and paclitaxel

Dysregulation of the PI3K-AKT signaling pathway has been implicated as a key driver in cancer initiation and progression. AKT is a serine/threonine kinase and a critical component mediating the PI3K-AKT signaling axis. Although AKT inhibitors have been extensively studied, clinical outcome has not been impressive. Interestingly, it has been shown that PI3K/AKT pathway has been involved in resistance to conventional chemotherapy, and inhibition of AKT enhances targeted therapy and sensitizes radiation therapy. Miransertib is a potent and selective pan-AKT inhibitor and currently in early clinical studies. In this study, we assessed combined effect of Miransertib with immune checkpoint inhibitor, anti-MEK and anti-HER2 agents, and a chemotherapeutic agent in vivo. Miransertib at doses of range from 20mg/kg to 120mg/kg was tested in combination with anti-PD-1 antibody, trametinib, lapatinib, trastuzumab, or paclitaxel. Anti-tumor efficacy was assessed in syngeneic mouse CT-26 colon and 4T1 breast tumor models and xenografts models with endometrial (AN3CA) and breast (HCC1954, KPL-4, ZR-75-1) tumors, two patient-derived (PDX) models of endometrial cancer (with PIK3CAH1047R and R93W+D350G mutations) and in one vemurafenib-resistant melanoma PDX (with BRAFV600E and PIK3CA H1047R mutations). Combinability and efficacy of Miransertib and anti-PD-1 antibody was assessed in syngeneic mouse CT-26 colon tumor model. Miransertib at 60 mg/kg and anti-PD-1 antibody at 10mg/kg were combinable. Combined dosing of Miransertib with Anti-PD-1 antibody exerted superior anti-tumor activity in comparison to the single agents (TGI: 65% for combination, 50% for Miransertib and 55% for anti-PD-1 antibody after dosing for 9 days and more significant difference after 12 day dosing). In 4T1 breast tumor model, combination of Miransertib and anti-PD-1 antibody showed a very modest anti-tumor activity whereas there is no effect as single agents. In one of the endometrial PDX models, the combination of Miransertib with trametinib enhanced anti-tumor activity of each drug alone, reducing tumor growth by 67% compared to single-agent tumor reductions by 43% for either Miransertib or trametinib. In a vemurafenib-resistant melanoma PDX model, tumor growth was reduced by 73% when Miransertib was combined with trametinib, while trametinib alone only reduced tumor growth by 26% for trametinib and by 16% by Miransertib. Miransertib enhanced efficacy of in combination with trastuzumab, lapatinib, or paclitaxel, by reducing tumor growth as much as 92%, 73% and 85% respectively, while single agent comparators reduced tumors by less than 50%. Miransertib is combinable with anti-PD-1 antibody, trametinib, lapatinib, trastuzumab, and paclitaxel and exhibits enhanced anti-tumor activity. These results provide us rationale for the combination study of Miransertib in a clinical setting.

Citation Format: Yi Yu, Terence Hall, Sudharshan Eathiraj, Ron E. Savage, Brian Schwartz. In vivo combination of miransertib (ARQ 092) with anti-PD-1 antibody, trametinib, lapatinib, trastuzumab and paclitaxel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2943.

Abstract 1882: Preclinical evaluation of the tyrosine kinase inhibitor ARQ 531 in AML

Acute Myeloid Leukemia (AML) is a rapidly progressing hematopoietic malignancy arising from bone marrow myeloid progenitor cells. Treatment with cytotoxic chemotherapy has not changed for over four decades resulting in poor survival. The dismal prognosis could be attributed to the heterogeneity of this disease, where multiple genetically aberrant clones exist within the same patient. Mutations in the FMS-like tyrosine kinase (FLT3) occurs in 30% of AML patients, typically as an internal tandem duplication (ITD) resulting in a constitutively active FLT3 survival pathway. This has prompted the generation of selective FLT3 inhibitors such as Quizartinib and Gilteritinib which are currently being pursued in clinical trials. Still, acquired resistance to these selective FLT3 inhibitors due to the acquisition of tyrosine kinase domain mutations (TKD) can occur. This suggests that the use of an agent with a broader kinome inhibition profile (such as the recently granted FDA approved Midostaurin) could achieve more durable clinical benefit.

ARQ 531 is a novel potent BTK inhibitor currently being investigated in a Phase 1 trial in patients with relapsed/refractory hematological malignancies (ClinicalTrials.gov Identifier: NCT03162536). We have found that ARQ 531 also has inhibitory activity against members of the Src family of kinases (SFK; including downstream target SYK) as well as FLT3. SYK directly binds to and trans-activates FLT3 which is essential for FLT3-ITD tumorigenicity, suggesting that ARQ 531 has therapeutic potential in AML. Therefore we have investigated the in vitro and in vivo efficacy of ARQ 531 in AML.

Our preliminary studies demonstrate cytotoxicity for ARQ 531 in patient-derived primary AML cells harboring FLT3 wild type and FLT3-ITD, as well as multiple AML cell lines. Importantly, ARQ 531 is effective in a MOLM-13 tyrosine kinase inhibitor (TKI) resistant cell line harboring a FLT3-ITD-TKD-D835Y mutation. Furthermore, we show that ARQ 531 can reduce the level of phosphorylated FLT3, but unlike selective FLT3 inhibitors, it can also inhibit Src family phosphorylation and SYK phosphorylation. Additionally, ARQ 531 exhibited an anti-clonogenic effect on primary patient blasts using Methocult colony forming unit assay. Finally, to investigate the in vivo effect of ARQ 531, we used an aggressive AML MOLM-13 disseminated xenograft mouse model. NSG mice were randomized one-week post engraftment to either vehicle or daily oral gavage of 50 mg/kg ARQ 531. The estimated median survival for the ARQ 531 group was 23 days compared to 21 days for the vehicle group (p = 0.002) suggesting in vivo efficacy for ARQ 531 in AML.

Collectively, we provide for the first time promising preclinical efficacy for ARQ 531 in AML supporting further mechanistic investigation of this agent, and potentially, expansion of the ongoing clinical studies to include AML patients.

E. H. and J.C. B. contributed equally as co-senior authors to this work

Citation Format: Ola A. Elgamal, Bridget Carmichael, Amy Lehman, Shelley J. Orwick, Minh Tran, Virginia M. Goettl, Shaneice Mitchell, Rosa Lapalombella, Jae Yoon Jeon, Sharyn D. Baker, Sudharshan Eathiraj, Brian Schwartz, Erin Hertlein, John C. Byrd. Preclinical evaluation of the tyrosine kinase inhibitor ARQ 531 in AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1882.

Abstract 1963: ARQ 531, a potent reversible BTK inhibitor, exhibits potent antitumor activity in ibrutinib-resistant diffuse large B-cell lymphoma

Background: B-cell receptor (BCR)-mediated signaling plays an important role in the pathogenesis of a subset of diffuse large B-cell lymphoma (DLBCL). Despite major advances in the treatment, ~40% of the relapsed/refractory DLBCL patients still experience early treatment failure after initial response to chemotherapy. ARQ 531, a reversible inhibitor of BTK and BTK-C481S mutant, also potently suppresses BCR signaling. Here we demonstrate that ARQ 531 targets additional kinases and suppresses multiple oncogenic pathways, this inhibitory potency is coupled to broad anti-tumor activity in DLBCL subtypes including tumors resistant to BCR targeted therapy.

Methods: Biochemical inhibition and broad kinase profiling were assessed using recombinant proteins. Binding kinetics and the residence time with BTK and BTK-C481S were measured by Surface Plasmon Resonance (SPR) assay. Binding mode of ARQ 531 with BTK was determined by protein crystallography. Pathway inhibition assessments, in vivo efficacy and in vivo target inhibition were performed in DLBCL tumor models derived from TMD8, SUDHL-4 and DOHH-2 cell lines.

Results: ARQ 531 potently inhibited BTK (IC50 = 0.85 nM), the binding potency was accompanied by long residence time (51 min). Crystal structure of BTK/ARQ 531 complex showed that ARQ 531 occupies the ATP-binding pocket. Kinase selectivity profile suggested that ARQ 531 inhibits sub-families of Tec, Src, Trk kinases. Significant anti-proliferative activity (GI50 = < 1µM) was observed in hematological malignant cell lines characterized by addiction to BTK signaling and primarily resistant to ibrutinib. Pathway inhibition analysis suggested that ARQ 531 targets multiple oncogenic signaling pathways in both ABC- and GCB-DLBCL cell lines. Unlike ibrutinib, ARQ 531 suppressed both the upstream activating signals (via inhibition of a select member of Src kinase family) and the downstream signaling pathways (via pAKT and pERK kinases). In GCB-DLBCL cell lines (SUDHL-4 and DOHH-2), ARQ 531 potently suppressed expression of anti-apoptotic c-Myc and BCL6 oncoproteins in a dose dependent fashion, and concomitantly induced apoptotic cleavage of PARP protein. In the ibrutinib-resistant SUDHL-4 mouse xenograft model, ARQ 531 potently suppressed tumor growth (>80% inhibition) compared to the control group when dosed orally at 75 mg/kg. Additionally, preliminary data suggest that ARQ 531 crosses the blood, brain-barrier.

Conclusion: ARQ 531 is a potent reversible inhibitor of BTK, its distinct kinase selectivity profile offers significant advantage for simultaneous inhibition of multiple therapeutically relevant targets. ARQ 531 attenuated the expression of key oncogenic drivers via inhibition of downstream BCR activating kinases. These results highlight the therapeutic potential of inhibition of BCR signaling inhibition by ARQ 531 in the treatment of DLBCL.

Citation Format: Sudharshan Eathiraj, Yi Yu, Ron Savage, Jennifer A. Woyach, Sean D. Reiff, Amy J. Johnson, Brian Schwartz. ARQ 531, a potent reversible BTK inhibitor, exhibits potent antitumor activity in ibrutinib-resistant diffuse large B-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1963.

In-vitro and in-vivo combined effect of ARQ 092, an AKT inhibitor, with ARQ 087, a FGFR inhibitor

The PI3K/AKT pathway plays an important role in the initiation and progression of cancer, and the drug development efforts targeting this pathway with therapeutic interventions have been advanced by academic and industrial groups. However, the clinical outcome is moderate. Combination of inhibition of PI3K/AKT and other targeted agents became a feasible approach. In this study we assessed the combined effect of ARQ 092, a pan-AKT inhibitor, and ARQ 087, a pan-FGFR inhibitor, in vitro and in vivo. In a panel of 45 cancer cell lines, on 24% (11 out of 45) the compounds showed synergistic effect, on 62% (28 out of 45) additive, and on 13% (6 out of 45) antagonistic. The highest percentage of synergism was found on endometrial and ovarian cancer cell lines. Mutational analysis revealed that PIK3CA/PIK3R1 mutations and aberrant activation of FGFR2 predicted synergism, whereas Ras mutations showed a reverse correlation. Pathway analysis revealed that a combination of ARQ 092 and ARQ 087 enhanced the inhibition of both the AKT and FGFR pathways in cell lines in which synergistic effects were found (AN3CA and IGROV-1). Cell cycle arrest and apoptotic response occurred only in AN3CA cell, and was not seen in IGROV-1 cells. Furthermore, enhanced antitumor activity was observed in mouse models with endometrial cancer cell line and patient-derived tumors when ARQ 092 and ARQ 087 were combined. These results from in-vitro and in-vivo studies provide a strong rationale in treating endometrial and other cancers with the activated PI3K/AKT and FGFR pathways.

Preclinical Activity of ARQ 087, a Novel Inhibitor Targeting FGFR Dysregulation

Dysregulation of Fibroblast Growth Factor Receptor (FGFR) signaling through amplifications, mutations, and gene fusions has been implicated in a broad array of cancers (e.g. liver, gastric, ovarian, endometrial, and bladder). ARQ 087 is a novel, ATP competitive, small molecule, multi-kinase inhibitor with potent in vitro and in vivo activity against FGFR addicted cell lines and tumors. Biochemically, ARQ 087 exhibited IC50 values of 1.8 nM for FGFR2, and 4.5 nM for FGFR1 and 3. In cells, inhibition of FGFR2 auto-phosphorylation and other proteins downstream in the FGFR pathway (FRS2α, AKT, ERK) was evident by the response to ARQ 087 treatment. Cell proliferation studies demonstrated ARQ 087 has anti-proliferative activity in cell lines driven by FGFR dysregulation, including amplifications, fusions, and mutations. Cell cycle studies in cell lines with high levels of FGFR2 protein showed a positive relationship between ARQ 087 induced G1 cell cycle arrest and subsequent induction of apoptosis. In addition, ARQ 087 was effective at inhibiting tumor growth in vivo in FGFR2 altered, SNU-16 and NCI-H716, xenograft tumor models with gene amplifications and fusions. ARQ 087 is currently being studied in a phase 1/2 clinical trial that includes a sub cohort for intrahepatic cholangiocarcinoma patients with confirmed FGFR2 gene fusions (NCT01752920).

Abstract 374: In vitro and in vivo anti-tumor activity of ARQ 751, a potent and selective AKT inhibitor

Dysregulation of the PI3K-AKT signaling pathway is associated with a number of cancers. AKT can be activated through activated receptor tyrosine kinases, gain-of-function mutations of PIK3CA, PTEN deficiency, and AKT amplification or activating mutations such as AKT1-E17K. We present here the preclinical characterization of ARQ 751, which has distinct physico-chemical properties compared to our first generation inhibitor, ARQ 092.

ARQ 751 has IC50 values of 0.55 nM, 0.81 nM and 1.31 nM for AKT1, 2 and 3, respectively, and does not inhibit any other kinase (out of the 245 tested) by greater than 50% at 5 μM, nor does it inhibit AKT lacking the PH domain. ARQ 751 strongly binds to wild-type AKT1 and mutant AKT1-E17K with Kd of 1.2 nM and 8.6 nM, respectively, and suppresses pAKT(S473) in 293T cells transiently transfected with AKT1-E17K. Additionally, membrane translocation of both wild-type and AKT1-E17K is inhibited in NIH 3T3 cells transiently transfected with wild-type AKT1 or mutant AKT1-E17K. Tests on 240 cancer cell lines (Oncopanel) showed the best antiproliferative effects on esophageal (100%, 3/3), breast (87.5%, 14/16), and head and neck cancer cells (67%, 4/6), with GI50 values GI50 < 1 μM. Cancer cell lines with PIK3CA/PIK3R1 mutations (73%; 33/45) are more sensitive to ARQ 751 (GI50<1μM) compared to wild-type (42%, 74/175). Interestingly, among PIK3CA/PIK3R1 wild type cell lines, the PTEN mutant (55%, 11/20) exhibited a similar sensitivity to PTEN wild-type cell lines (48%, 95/197). Of 17 tested breast cancer cell lines, all 8 with PIK3CA mutations are sensitive to ARQ 751. An in vivo efficacy study in AN3CA endometrial cancer xenograft model shows that ARQ 751 inhibits tumor growth (by up to 92% at the well tolerated continuous daily dose of 120 mg/kg) in a dose-dependent manner. Additionally, ARQ 751 exerted dose-dependent anti-tumor activity (by up to 98% at the 5 days on, 2 days off dose of 75mg/kg) in an AKT1-E17K mutant endometrial patient-derived xenograft (PDX) model. ARQ 751 causes significant pathway inhibition in vitro (at the concentrations of 3 nM on pAKT[S473] and 70 nM on pPRAS40 [T246]) and in vivo (on both pAKT[S473] and pPRAS40[T246] after 6 hours of dosing as low as 10 mg/kg) using AN3CA models. Pharmacokinetic data from repeat doses of ARQ 751 show a plasma half-life of 4 to 5 hours and no tissue accumulation.

In conclusion, ARQ 751 is a potent and selective allosteric AKT inhibitor. PIK3CA/PIK3R1 and AKT mutations but not PTEN may predict ARQ 751 sensitivity. Our analysis suggests that endometrial, breast, esophageal, and head and neck cancers may represent viable indications for ARQ 751. Both PIK3CA/PIK3R1 and AKT1 mutations could be predictive biomarkers for patient selection, regardless of tumor type.

Citation Format: Yi Yu, Ronald E. Savage, Sudharshan Eathiraj, Terence Hall, Brian Schwartz, Giovanni Abbadessa. In vitro and in vivo anti-tumor activity of ARQ 751, a potent and selective AKT inhibitor. [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 374.

Discovery of 3-(3-(4-(1-Aminocyclobutyl)phenyl)-5-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin-2-amine (ARQ 092): An Orally Bioavailable, Selective, and Potent Allosteric AKT Inhibitor

The work in this paper describes the optimization of the 3-(3-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin-2-amine chemical series as potent, selective allosteric inhibitors of AKT kinases, leading to the discovery of ARQ 092 (21a). The cocrystal structure of compound 21a bound to full-length AKT1 confirmed the allosteric mode of inhibition of this chemical class and the role of the cyclobutylamine moiety. Compound 21a demonstrated high enzymatic potency against AKT1, AKT2, and AKT3, as well as potent cellular inhibition of AKT activation and the phosphorylation of the downstream target PRAS40. Compound 21a also served as a potent inhibitor of the AKT1-E17K mutant protein and inhibited tumor growth in a human xenograft mouse model of endometrial adenocarcinoma.

Abstract B183: Targeting PI3K pathway dependent endometrial tumors with allosteric AKT inhibitors, ARQ 092 and ARQ 751

Background: In endometrial cancer more frequently than in other tumors, abnormal activation of the AKT pathway drives tumorigenesis and can be induced by both PI3K and AKT alterations, being associated with aggressive disease and poor prognosis. ARQ 092 is a highly selective, allosteric, potent AKT inhibitor currently under clinical investigation, and ARQ 751 is the next generation AKT inhibitor, with different physical-chemical properties.

Methods: ARQ 092 and ARQ 751 were profiled using a Cell-TiterGlo® viability assay and the inhibition of AKT and downstream targets were measured by Western and immunohistochemistry analyses in an AN3CA endometrial cell line with activated PI3K (via PIK3R1 mutation). The efficacy and pharmacodynamics effect of ARQ 092 and ARQ 751 on phospho-AKT and phospho-pRAS40 were determined in AN3CA xenografts after repeated daily oral dosing. ARQ 092 was also tested against 23 endometrial patient-derived tumor models (PDX). Lastly, endometrial cancer patients are being enrolled in the expanded cohort of ARQ 092-101, a phase 1 study, at 2 schedules: intermittent (200mg once a day, 1 week on, 1 week off) or weekly (300mg twice daily, 1 day on, 6 days off).

Results: In AN3CA cell lines, ARQ 092, and more potently ARQ 751, inhibited AKT signaling including inhibition of phosphorylation of downstream targets in a dose dependent manner. Both inhibitors exhibited strong anti-proliferative activity. However, while ARQ 092 inhibited 6 out of 9 cell lines with GI50 below 1 μM, ARQ 751 inhibited all 5 cell lines with GI50 below the 150 nM range. Of the 22 tested PDX models, 12 responded (>50% tumor control compared to placebo). Both ARQ 092 and ARQ 751 exhibited over 90% AKT inhibition after 6 hrs exposure to a 40 mg/kg dose in an AN3CA mouse xenograft. In this model, at the maximum tolerated dose of 120mg/Kg, ARQ 092 and ARQ 751 resulted in 79% and 92% tumor growth reduction, respectively. Additionally, for ARQ 092, plasma Cmax in mouse models at the 100 mg/kg dose was compared to the Phase I human results. Plasma Cmax in mice was 2.1 μM whereas in patients enrolled at the intermittent and weekly schedules Cmax were 1.3 and 1.5 μM, respectively. Of the 19 enrolled patients with endometrial cancer, only one was treated at full dose, had a PIK3CA mutation (H1047R), and obtained a durable partial response after 2 months on therapy.

Conclusions: Both ARQ 092 and ARQ 751 demonstrated potent inhibition of p-AKT and downstream pathway signaling. In addition, both compounds exhibited potent antitumor activity in human endometrial cancer cells in vitro and in vivo. Such preclinical observations were recapitulated in the clinic by the rapid objective response observed in the first endometrial patient with PIK3CA mutation enrolled at full dose in the expanded cohort of the ongoing ARQ 092-101 Phase I clinical trial. Overall, these data provide a strong mechanistic rationale for further evaluation of ARQ 092, and possibly ARQ 751, in patients with PI3K-driven endometrial malignancies.

Citation Format: Sudharshan Eathiraj, Brian Schwartz, Yi Yu, Michael J. Wick, Terence Hall, Feng Chai, Jasgit Sachdev, Giovanni Abbadessa. Targeting PI3K pathway dependent endometrial tumors with allosteric AKT inhibitors, ARQ 092 and ARQ 751. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B183.

Targeting AKT1-E17K and the PI3K/AKT Pathway with an Allosteric AKT Inhibitor, ARQ 092

As a critical component in the PI3K/AKT/mTOR pathway, AKT has become an attractive target for therapeutic intervention. ARQ 092 and a next generation AKT inhibitor, ARQ 751 are selective, allosteric, pan-AKT and AKT1-E17K mutant inhibitors that potently inhibit phosphorylation of AKT. Biochemical and cellular analysis showed that ARQ 092 and ARQ 751 inhibited AKT activation not only by dephosphorylating the membrane-associated active form, but also by preventing the inactive form from localizing into plasma membrane. In endometrial PDX models harboring mutant AKT1-E17K and other tumor models with an activated AKT pathway, both compounds exhibited strong anti-tumor activity. Combination studies conducted in in vivo breast tumor models demonstrated that ARQ 092 enhanced tumor inhibition of a common chemotherapeutic agent (paclitaxel). In a large panel of diverse cancer cell lines, ARQ 092 and ARQ 751 inhibited proliferation across multiple tumor types but were most potent in leukemia, breast, endometrial, and colorectal cancer cell lines. Moreover, inhibition by ARQ 092 and ARQ 751 was more prevalent in cancer cell lines containing PIK3CA/PIK3R1 mutations compared to those with wt-PIK3CA/PIK3R1 or PTEN mutations. For both ARQ 092 and ARQ 751, PIK3CA/PIK3R1 and AKT1-E17K mutations can potentially be used as predictive biomarkers for patient selection in clinical studies.

Discovery and optimization of a series of 3-(3-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin-2-amines: orally bioavailable, selective, and potent ATP-independent Akt inhibitors

This paper describes the implementation of a biochemical and biophysical screening strategy to identify and optimize small molecule Akt1 inhibitors that act through a mechanism distinct from that observed for kinase domain ATP-competitive inhibitors. With the aid of an unphosphorylated Akt1 cocrystal structure of 12j solved at 2.25 Å, it was possible to confirm that as a consequence of binding these novel inhibitors, the ATP binding cleft contained a number of hydrophobic residues that occlude ATP binding as expected. These Akt inhibitors potently inhibit intracellular Akt activation and its downstream target (PRAS40) in vitro. In vivo pharmacodynamic and pharmacokinetic studies with two examples, 12e and 12j, showed the series to be similarly effective at inhibiting the activation of Akt and an additional downstream effector (p70S6) following oral dosing in mice.

Abstract LB-1: Discovery and optimization of orally bioavailable, selective and potent ATP-independent Akt inhibitors

Herein we describe the implementation of a biochemical and biophysical screening strategy to discover small molecules that inhibit Akt through a mechanism distinct from ATP-competitive inhibitors. A series of novel derivatives of the core scaffold 3H-imidazo[4,5-b]pyridine were identified and optimized. These Akt inhibitors demonstrated potent inhibition of intracellular Akt and downstream targets including PRAS40 activation in vitro. Pharmacodynamic and pharmacokinetic studies in vivo demonstrated the effectiveness of the series at inhibiting the activation of Akt and an additional downstream effector (p70S6) following oral dosing in mice. Co-crystallization studies with un-phosphorylated Akt1 revealed that as a consequence of binding these novel, potent and selective, ATP-independent inhibitors the ATP binding cleft is occupied by non-polar residues which are associated as tight clusters. The cleft is closed with a ‘hydrophobic lock’ which may function to sterically exclude the binding of both ATP and ATP-competitive inhibitors.

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 LB-1. doi:1538-7445.AM2012-LB-1

Abstract 3905: Synthesis and structure activity relationship of substituted N,6-diphenyl-5,6-dihydrobenzo[h]quinazolin-2-amine as inhibitors of fibroblast growth factor receptors (FGFR)

Utilization of hydrophobic motifs present in auto-inhibited protein kinases has resulted in the identification of a series of 5,6-dihydrobenzo [h]quinazolin-2-amines with activity as fibroblast growth factor receptor (FGFR) tyrosine kinase inhibitors. Herein we describe the combination of a proprietary in silico design process, a new screening paradigm using an array of biochemical and biophysical technologies in conjunction with an established parallel chemistry process for the identification and optimization of a series of novel FGFR inhibitors. These potent FGFR inhibitors exhibit a preference for the inactive form of the kinase, are non-ATP competitive, and exhibit robust cellular pharmacodynamic inhibition as well as in vitro anti-proliferative effects in cells dependent on FGFR and significant anti-tumor activity in appropriate xenograft models in vivo. The design strategy, synthesis, structure activity relationships and in vitro and in vivo biology of selected inhibitors will be presented.

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 3905. doi:1538-7445.AM2012-3905

Abstract 2914: Creation of a novel biochemical and biophysical assay suite to enable the identification of inhibitors targeting inactive kinases

We have recently reported the implementation of a structural biology-based drug design platform for the identification of protein kinase inhibitors which utilize hydrophobic clusters to stabilize the inactive state of a kinase. These clusters are not formed in active kinases and result in the conversion of the ATP binding cleft into a non-polar environment which is sterically and electrostatically incompatible with ATP binding. We have industrialized this approach, designated the ArQule Kinase Inhibitor Platform (AKIPTM), and synthesized a library of more than 15,000 small molecules through the application of an in silico guided process. This has allowed us to rapidly generate leads to a variety of kinases, including receptor tyrosine kinases, non-receptor tyrosine kinases, and serine-threonine kinases. By virtue of their unique binding modes, many of these inhibitors would not be identified in standard assays using highly activated kinases. We have therefore deliberately re-engineered standard biochemical kinase assays using unphosphorylated inactive kinases to aid in the optimization of these inhibitors. In addition to these biochemical assays, we have also implemented a variety of well-established technologies not commonly used early in the hit generation process, including a thermal shift assay (TSA), affinity mass spectrometry, endogenous tryptophan fluorescence detection, an ATP-exclusion assay using a non-hydrolyzable ATP analogue, classical kinetic analysis to assess ATP-dependence and mechanism-of-inhibition, X-ray crystallography, and finally, cross-competition experiments with known inhibitors. Using the cumulative knowledge gained from these technologies throughout the hit generation, hit-to-lead, and lead optimization stages has enabled us to make informed decisions and resulted in identification of many potent ATP-independent inhibitors. The AKIP technology to date has produced at least one clinical candidate, ARQ 092, which potently inhibits AKT with a high degree of selectivity amongst the human kinome. Further examples of the application of these various technologies will be provided for a diverse range of kinases, including c-Met, FGFR, Ack, and TNIK.

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 2914. doi:1538-7445.AM2012-2914

Discovery of a novel mode of protein kinase inhibition characterized by the mechanism of inhibition of human mesenchymal-epithelial transition factor (c-Met) protein autophosphorylation by ARQ 197

A number of human malignancies exhibit sustained stimulation, mutation, or gene amplification of the receptor tyrosine kinase human mesenchymal-epithelial transition factor (c-Met). ARQ 197 is a clinically advanced, selective, orally bioavailable, and well tolerated c-Met inhibitor, currently in Phase 3 clinical testing in non-small cell lung cancer patients. Herein, we describe the molecular and structural basis by which ARQ 197 selectively targets c-Met. Through our analysis we reveal a previously undisclosed, novel inhibitory mechanism that utilizes distinct regulatory elements of the c-Met kinase. The structure of ARQ 197 in complex with the c-Met kinase domain shows that the inhibitor binds a conformation that is distinct from published kinase structures. ARQ 197 inhibits c-Met autophosphorylation and is highly selective for the inactive or unphosphorylated form of c-Met. Through our analysis of the interplay between the regulatory and catalytic residues of c-Met, and by comparison between the autoinhibited canonical conformation of c-Met bound by ARQ 197 to previously described kinase domains of type III receptor tyrosine kinases, we believe this to be the basis of a powerful new in silico approach for the design of similar inhibitors for other protein kinases of therapeutic interest.

A novel mode of protein kinase inhibition exploiting hydrophobic motifs of autoinhibited kinases: discovery of ATP-independent inhibitors of fibroblast growth factor receptor

Protein kinase inhibitors with enhanced selectivity can be designed by optimizing binding interactions with less conserved inactive conformations because such inhibitors will be less likely to compete with ATP for binding and therefore may be less impacted by high intracellular concentrations of ATP. Analysis of the ATP-binding cleft in a number of inactive protein kinases, particularly in the autoinhibited conformation, led to the identification of a previously undisclosed non-polar region in this cleft. This ATP-incompatible hydrophobic region is distinct from the previously characterized hydrophobic allosteric back pocket, as well as the main pocket. Generalized hypothetical models of inactive kinases were constructed and, for the work described here, we selected the fibroblast growth factor receptor (FGFR) tyrosine kinase family as a case study. Initial optimization of a FGFR2 inhibitor identified from a library of commercial compounds was guided using structural information from the model. We describe the inhibitory characteristics of this compound in biophysical, biochemical, and cell-based assays, and have characterized the binding mode using x-ray crystallographic studies. The results demonstrate, as expected, that these inhibitors prevent activation of the autoinhibited conformation, retain full inhibitory potency in the presence of physiological concentrations of ATP, and have favorable inhibitory activity in cancer cells. Given the widespread regulation of kinases by autoinhibitory mechanisms, the approach described herein provides a new paradigm for the discovery of inhibitors by targeting inactive conformations of protein kinases.

Abstract A139: Discovery and biological profiling of potent fibroblast growth factor receptor (FGFR) kinase inhibitors derived from in silico design with in vivo antitumor activity against FGFR2-dependent human tumors

Dysregulation of members of the FGFR tyrosine kinase family has been increasingly implicated in a number of human cancers, including gastric, breast, endometrial, and bladder carcinomas. A proprietary structure-based design paradigm was employed to identify inhibitors which favor a mode of binding that is distinct from the commonly described ATP competitive inhibitors. A molecular template was identified (ARQ 523) which, upon further modification, provided molecules that were shown to inhibit FGFR kinases in the low micromolar range, to bind to FGFR2 in an enantiomeric-specific fashion, to bind to unphosphorylated FGFR2 with a KD of 5 µM; and, after pre-incubation with inactive FGFR2, to prevent a fluorescent analogue of ATP from binding to the enzyme. We have designated this novel type of kinase inhibitor as “ATP-exclusionary” or “Type IV” to differentiate these inhibitors from extant molecules. Following a lead optimization campaign, biochemical potencies of 1 nM or less against FGFR kinases with corresponding increases in binding affinities to FGFR2 in biophysical assays were documented in several compounds in two distinct series. These compounds showed sub-micromolar activity in both FGFR2-dependent pharmacodynamic and cytotoxicity assays, and demonstrated a moderately high degree of selectivity across the human kinome. A representative compound showed marked FGFR2 pharmacodynamic suppression and corresponding growth inhibition in KATO III and SNU-16 human gastric carcinoma cells. In addition, growth of SNU-16 tumor xenografts in athymic mice was markedly suppressed (58% regression as compared to vehicle-treated controls) after daily intraperitoneal administration for 9 days. A paired Ba/F3 xenograft model was also employed, using both Ba/F3 cells transfected with either FGFR2 or the unrelated insulin receptor. Significant tumor growth inhibition (77% inhibition as compared to vehicle-treated controls) was observed in treated mice bearing FGFR2-transfected Ba/F3 tumors but not in the insulin receptor transfectants. In summary, we have achieved proof-of-principle of a structure-based kinase inhibitor design paradigm for the identification of a series of FGFR kinase inhibitors that exhibits a preference for the inactive form of the kinase and excludes ATP upon binding. One advanced lead molecule demonstrated the ability to exert profound anti-tumor effects against cancer cell lines in which FGFR2 is the dominant oncogenic driver. The opportunity now exists to significantly expand the number of new chemotypes available for drug discovery against disease-relevant kinases in oncology and in other therapeutic areas, since it is predicted that approximately half of the human kinome is amenable to this novel mode of inhibition.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A139.

Structural basis for Rab11-mediated recruitment of FIP3 to recycling endosomes

The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognize the active form of Rab11. Normal completion of cytokinesis requires a complex between Rab11 and FIP3. Here, we report the crystal structure and mutational analysis of a heterotetrameric complex between constitutively active Rab11 and a FIP3 construct that includes the RBD. Two Rab11 molecules bind to dyad symmetric sites at the C terminus of FIP3, which forms a non-canonical coiled-coiled dimer with a flared C terminus and hook region. The RBD overlaps with the coiled coil and extends through the C-terminal hook. Although FIP3 engages the switch and interswitch regions of Rab11, the mode of interaction differs significantly from that of other Rab-effector complexes. In particular, the switch II region undergoes a large structural rearrangement from an ordered but non-complementary active conformation to a remodeled conformation that facilitates the interaction with FIP3. Finally, we provide evidence that FIP3 can form homo-oligomers in cells, and that a critical determinant of Rab11 binding in vitro is necessary for FIP3 recruitment to recycling endosomes during cytokinesis.

TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism

Rab GTPases regulate membrane trafficking by cycling between inactive (GDP-bound) and active (GTP-bound) conformations. The duration of the active state is limited by GTPase-activating proteins (GAPs), which accelerate the slow intrinsic rate of GTP hydrolysis. Proteins containing TBC (Tre-2, Bub2 and Cdc16) domains are broadly conserved in eukaryotic organisms and function as GAPs for Rab GTPases as well as GTPases that control cytokinesis. An exposed arginine residue is a critical determinant of GAP activity in vitro and in vivo. It has been expected that the catalytic mechanism of TBC domains would parallel that of Ras and Rho family GAPs. Here we report crystallographic, mutational and functional analyses of complexes between Rab GTPases and the TBC domain of Gyp1p. In the crystal structure of a TBC-domain-Rab-GTPase-aluminium fluoride complex, which approximates the transition-state intermediate for GTP hydrolysis, the TBC domain supplies two catalytic residues in trans, an arginine finger analogous to Ras/Rho family GAPs and a glutamine finger that substitutes for the glutamine in the DxxGQ motif of the GTPase. The glutamine from the Rab GTPase does not stabilize the transition state as expected but instead interacts with the TBC domain. Strong conservation of both catalytic fingers indicates that most TBC-domain GAPs may accelerate GTP hydrolysis by a similar dual-finger mechanism.

ESCRT complexes assembled and GLUEd

The ESCRT-I, -II, and -III complexes act sequentially to sort monoubiquitinated transmembrane proteins into multivesicular bodies for targeted degradation in the lysosome. Two papers published in a recent issue of Cell provide insights into the structural organization and functional interactions of the ESCRT-I complex and ESCRT-II GLUE domain.

Structural basis of family-wide Rab GTPase recognition by rabenosyn-5

Rab GTPases regulate all stages of membrane trafficking, including vesicle budding, cargo sorting, transport, tethering and fusion. In the inactive (GDP-bound) conformation, accessory factors facilitate the targeting of Rab GTPases to intracellular compartments. After nucleotide exchange to the active (GTP-bound) conformation, Rab GTPases interact with functionally diverse effectors including lipid kinases, motor proteins and tethering complexes. How effectors distinguish between homologous Rab GTPases represents an unresolved problem with respect to the specificity of vesicular trafficking. Using a structural proteomic approach, we have determined the specificity and structural basis underlying the interaction of the multivalent effector rabenosyn-5 with the Rab family. The results demonstrate that even the structurally similar effector domains in rabenosyn-5 can achieve highly selective recognition of distinct subsets of Rab GTPases exclusively through interactions with the switch and interswitch regions. The observed specificity is determined at a family-wide level by structural diversity in the active conformation, which governs the spatial disposition of critical conserved recognition determinants, and by a small number of both positive and negative sequence determinants that allow further discrimination between Rab GTPases with similar switch conformations.

Determinants of Rab5 interaction with the N terminus of early endosome antigen 1

The Rab5 effector early endosome antigen 1 (EEA1) is a parallel coiled coil homodimer with an N-terminal C(2)H(2) Zn(2+) finger and a C-terminal FYVE domain. Rab5 binds to independent sites at the N and C terminus of EEA1. To gain further insight into the structural determinants for endosome tethering and fusion, we have characterized the interaction of Rab5C with truncation and site-specific mutants of EEA1 using quantitative binding measurements. The results demonstrate that the C(2)H(2) Zn(2+) finger is both essential and sufficient for the N-terminal interaction with Rab5. Although the heptad repeat C-terminal to the C(2)H(2) Zn(2+) finger provides the driving force for stable homodimerization, it does not influence either the affinity or stoichiometry of Rab5 binding. Hydrophobic residues predicted to cluster on a common face of the C(2)H(2) Zn(2+) finger play a critical role in the interaction with Rab5. Although the homologous C(2)H(2) Zn(2+) finger of the Rab5 effector Rabenosyn binds to Rab5 with comparable affinity, the analogous C(2)H(2) Zn(2+) finger of the yeast homologue Vac1 shows no detectable interaction with Rab5, reflecting non-conservative substitutions of critical residues. Large changes in the intrinsic tryptophan fluorescence of Rab5 accompany binding to the C(2)H(2) Zn(2+) finger of EEA1. These observations can be explained by a mode of interaction in which a partially exposed tryptophan residue located at the interface between the switch I and II regions of Rab5 lies within a hydrophobic interface with a cluster of non-polar residues in the C(2)H(2) Zn(2+) finger of EEA1.