Low-dose three-dimensional CT angiography for the evaluation of posterolateral protrusion of the vertebral artery over the posterior arch of the atlas: a quantitative anatomical comparison study of the rotational and neutral positions

AIM

To investigate the changes in relevant anatomical parameters of posterolateral protrusion of the vertebral artery (VA) between head-neck rotational and neutral positions using low-dose three-dimensional computed tomography angiography (3D-CTA).

MATERIALS AND METHODS

Low-dose 3D-CTA images obtained for various craniocervical diseases in 36 non-dominant VA side patients with neutral, left and right head-neck rotational positions were evaluated. The relevant parameters from superior and inferior views, including external diameter (ED), internal diameter (ID), transverse diameter (TD), heights and diameters of posterolateral protrusion of the VA over the posterior arch of the atlas in the neutral and rotational positions, were recorded and compared.

RESULTS

There was no significant differences in the rotational angle (left/right: 31.23 ± 6.60/29.94 ± 6.09°, p>0.05). There were no significant differences in heights and diameters of bilateral VA between rotational and neutral positions (all p>0.05). The contralateral ID, ED, and TD of the rotational positions were significantly shorter than those of the neutral position (all p<0.05), while there were no significant differences in the three ipsilateral diameters (all p>0.05).

CONCLUSIONS

Posterolateral protrusion of the VA is not uncommon in the population, and surgeons should be aware of its presence, especially the increased possibility of injury to the VA caused by head-neck rotation, during the operation; thus, preoperative evaluation by low-dose 3D-CTA should be considered.

Molecular Characteristics of Repotrectinib That Enable Potent Inhibition of TRK Fusion Proteins and Resistant Mutations

NTRK chromosomal rearrangements yield oncogenic TRK fusion proteins that are sensitive to TRK inhibitors (larotrectinib and entrectinib) but often mutate, limiting the durability of response for NTRK ⁺ patients. Next-generation inhibitors with compact macrocyclic structures (repotrectinib and selitrectinib) were designed to avoid resistance mutations. Head-to-head potency comparisons of TRK inhibitors and molecular characterization of binding interactions are incomplete, obscuring a detailed understanding of how molecular characteristics translate to potency. Larotrectinib, entrectinib, selitrectinib, and repotrectinib were characterized using cellular models of wild-type TRKA/B/C fusions and resistance mutant variants with a subset evaluated in xenograft tumor models. Crystal structures were determined for repotrectinib bound to TRKA (wild-type, solvent-front mutant). TKI-naïve and pretreated case studies are presented. Repotrectinib was the most potent inhibitor of wild-type TRKA/B/C fusions and was more potent than selitrectinib against all tested resistance mutations, underscoring the importance of distinct features of the macrocycle structures. Cocrystal structures of repotrectinib with wild-type TRKA and the TRKA^G595R SFM variant elucidated how differences in macrocyclic inhibitor structure, binding orientation, and conformational flexibility affect potency and mutant selectivity. The SFM crystal structure revealed an unexpected intramolecular arginine sidechain interaction. Repotrectinib caused tumor regression in LMNA-NTRK1 xenograft models harboring GKM, SFM, xDFG, and GKM + SFM compound mutations. Durable responses were observed in TKI-naïve and -pretreated patients with NTRK ⁺ cancers treated with repotrectinib (NCT03093116). This comprehensive analysis of first- and second-generation TRK inhibitors informs the clinical utility, structural determinants of inhibitor potency, and design of new generations of macrocyclic inhibitors.

TPX-0131, a Potent CNS-penetrant, Next-generation Inhibitor of Wild-type ALK and ALK-resistant Mutations

Since 2011, with the approval of crizotinib and subsequent approval of four additional targeted therapies, anaplastic lymphoma kinase (ALK) inhibitors have become important treatments for a subset of patients with lung cancer. Each generation of ALK inhibitor showed improvements in terms of central nervous system (CNS) penetration and potency against wild-type (WT) ALK, yet a key continued limitation is their susceptibility to resistance from ALK active-site mutations. The solvent front mutation (G1202R) and gatekeeper mutation (L1196M) are major resistance mechanisms to the first two generations of inhibitors while patients treated with the third-generation ALK inhibitor lorlatinib often experience progressive disease with multiple mutations on the same allele (mutations in cis, compound mutations). TPX-0131 is a compact macrocyclic molecule designed to fit within the ATP-binding boundary to inhibit ALK fusion proteins. In cellular assays, TPX-0131 was more potent than all five approved ALK inhibitors against WT ALK and many types of ALK resistance mutations, e.g., G1202R, L1196M, and compound mutations. In biochemical assays, TPX-0131 potently inhibited (IC50 <10 nmol/L) WT ALK and 26 ALK mutants (single and compound mutations). TPX-0131, but not lorlatinib, caused complete tumor regression in ALK (G1202R) and ALK compound mutation-dependent xenograft models. Following repeat oral administration of TPX-0131 to rats, brain levels of TPX-0131 were approximately 66% of those observed in plasma. Taken together, preclinical studies show that TPX-0131 is a CNS-penetrant, next-generation ALK inhibitor that has potency against WT ALK and a spectrum of acquired resistance mutations, especially the G1202R solvent front mutation and compound mutations, for which there are currently no effective therapies.

Abstract 1469: TPX-0131, a potent inhibitor of wild type ALK and a broad spectrum of both single and compound ALK resistance mutations

Three generations of ALK inhibitors are approved for the treatment of ALK+ NSCLC but their efficacy is often limited by ALK resistance mutations. The solvent front mutation G1202R and gatekeeper mutation L1196M are major resistance mechanisms to the first two generations of inhibitors. Patients treated with second generation inhibitors are reported to progress with multiple mutations on separate alleles (mutations in trans). In contrast, 35 - 48% of patients treated with lorlatinib progress with multiple mutations on the same allele (compound mutations, mutations in cis). TPX-0131 is an ALK inhibitor with a compact macrocyclic structure designed to bind completely within the ATP binding boundary and overcome a spectrum of single and compound ALK resistant mutations. TPX-0131 was profiled against previous generations of ALK inhibitors both in vitro and in vivo. In biochemical assays, TPX-0131 potently inhibits (IC50 &lt;10 nM) wild type (WT) ALK and 26 ALK mutations (single and compound). Cell proliferation assays of WT, single mutations, and compound mutations were used to evaluate TPX-0131 relative to previous generations of ALK inhibitions (crizotinib, alectinib, brigatinib, ceritinib, lorlatinib). TPX-0131 is more potent against WT EML4-ALK (IC50 = 0.4 nM) than previous generations of ALK inhibitors (2-fold, lorlatinib; 10 - 30-fold, second generation inhibitors; &gt;100-fold, crizotinib). TPX-0131 potently inhibits EML4-ALK harboring a G1202R solvent front mutation (IC50 = 0.2 nM) which is &gt;100-fold more potent than previous generations of ALK inhibitors. TPX-0131 potently inhibits ALK harboring a gatekeeper mutation (IC50 = 0.5 nM) and is &gt;10-fold more potent than previous generations of ALK inhibitors. TPX-0131 potently inhibits ALK with a L1198F hinge area mutation (IC50 = 0.2 nM) which is 87 - 3000-fold more potent than previous generations of ALK inhibitors. TPX-0131 is the most potent inhibitor against nine EML4-ALK double and triple compound mutations (6 with IC50 &lt; 1 nM, 3 with IC50 1.6 - 14.9 nM). Evaluation of ALK phosphorylation as a pharmacodynamic marker in tumors showed potent ALK inhibition by TPX-0131 that correlated with TPX-0131 exposure. In Ba/F3 cell-derived xenograft tumor models with EML4-ALK mutations, TPX-0131 (2, 5, 10 mg/kg BID) demonstrated robust anti-tumor activity in the G1202R model (64%, 120%, 200% TGI), G1202R/L1198F model (complete regression, all doses), and G1202R/L1196M model (44%, 83% and 200% TGI). In contrast, lorlatinib (5 mg/kg BID) caused 31% TGI in the G1202R/L1198F model and did not have statistically significant TGI in the G1202R/L1196M model. Taken together, TPX-0131 is a next generation ALK inhibitor that has preclinical potency against WT ALK as well as a broad spectrum of acquired resistance mutations, especially compound mutations, which currently lack any effective ALK inhibitor therapy.

Citation Format: Brion W. Murray, Dayong Zhai, Wei Deng, Evan Rogers, Xin Zhang, Jane Ung, Vivian Nguyen, Han Zhang, Maria Barrera, Ana Parra, Jessica Cowell, Dong Lee, Herve Aloysius. TPX-0131, a potent inhibitor of wild type ALK and a broad spectrum of both single and compound ALK resistance mutations [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 1469.

Abstract 1119: Molecular characteristics of repotrectinib that enable potent inhibition of TRK fusion proteins and broad mutant selectivity

NTRK chromosomal rearrangements yield oncogenic TRK fusion proteins that are sensitive to first-generation TRK inhibitors (larotrectinib, entrectinib) but the emergence of NTRK mutations limits their efficacy. Next-generation TRK inhibitors (repotrectinib, selitrectinib) have compact macrocyclic structures designed to limit the susceptibility to mutations. However, a detailed understanding of mutant potency and precise binding interactions are lacking. TRK inhibitors were evaluated in cellular models expressing TRKA/B/C fusions with wild-type (WT) and resistance mutations: solvent front (SFM), gatekeeper (GKM), activation loop (xDFG), and compound mutations. In cell proliferation assays, differential potencies against wild type TRKA/B/C fusions were observed: larotrectinib (IC50 23.5 - 49.4 nM), entrectinib (IC50 0.3 - 1.3 nM), selitrectinib (IC50 1.8 - 3.9 nM), and repotrectinib (IC50 &lt; 0.2 nM). First generation TRK inhibitors with extended structures had reduced potency against resistance mutations. Larotrectinib had minimal activity (IC50 &gt;600 nM) against all TRK mutations and entrectinib had &gt;400-fold decreased against all mutations except GKM where there was a range of potencies (IC50 &lt; 0.2 - 60.4 nM). Repotrectinib and selitrectinib were less affected by resistance mutations however repotrectinib was approximately 10-fold more potent than selitrectinib against SFM and compound mutations and 100-fold more potent against GKM. For TRKA/B/C xDFG mutations, repotrectinib had moderate potency (IC50 11.8 - 67.6 nM) while selitrectinib was less potent (IC50 124 - 341 nM). Co-crystal structures of repotrectinib with TRKA and TRKA harboring a SFM provide insight into how subtle differences in macrocyclic inhibitor structure and conformational profiles affect potency and mutant selectivity. Analysis of the first protein structure of a kinase harboring a common SFM (TRKA G595R) revealed unexpected intramolecular interactions which provide insight into its prevalence. Repotrectinib, but not selitrectinib, caused tumor regression in LMNA-NTRKA xenograft models harboring GKM, SFM, or GKM+SFM compound mutations. In the clinic, tumor regression was observed with repotrectinib treatment of a larotrectinib-resistant cholangiocarcinoma patient with both LMNA-TRKA GKM and SFM mutations. Repotrectinib has shown responses in patients with TRK driven tumors with or without resistant mutations in the ongoing global registrational TRIDENT-1 study and has been granted 3 fast track designations. Taken together, the current data characterizes TRK inhibitor potency against resistance mutations and highlights structural characteristics of repotrectinib that enable potent inhibition of TRK proteins and evasion of drug resistance mediated by TRK mutations.

Citation Format: Alexander Drilon, Dayong Zhai, Evan Rogers, Wei Deng, Xi Chen, Paul Sprengeler, Siegfried H. Reich, Brion W. Murray. Molecular characteristics of repotrectinib that enable potent inhibition of TRK fusion proteins and broad mutant selectivity [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 1119.

Abstract 1104: Repotrectinib increases effectiveness of MEK inhibitors in KRAS mutant cancer models

KRAS is the most frequently mutated oncogene in cancers, accounting for approximately 25% of non small cell lung cancer (NSCLC), 45% of colorectal cancer (CRC), and 75% of pancreatic cancer. KRAS G12D and G12V mutations account for a large percent of mutant KRAS cancers (36% of NSCLC; 57% of CRC; 71% of pancreatic). MEK1/2 are critical downstream effectors of KRAS signaling and preclinical studies in KRAS mutant models show sensitivity to MEK inhibitors (MEKi). However, clinical studies of single agent MEKi or combinations with docetaxel in mutant KRAS NSCLC patients were associated with low response rates. Preclinical studies show that effectiveness of MEK inhibition can be limited by multiple resistance mechanisms such as compensatory upregulation of PI3K/AKT via SRC/FAK signaling, or activation of the JAK2/STAT3 pathway. Repotrectinib is a next-generation ROS1/TRK inhibitor with SRC/FAK/JAK2 inhibitory potencies which may suppress adaptive resistance to MEK inhibitors. In the current study, repotrectinib combinations with KRAS signaling network inhibitors including MEK (trametinib, selumetinib), MEK/RAF (VS-6766), ERK (LY3214996), SHP2 (TNO155) were explored. Repotrectinib/trametinib and repotrectinib/VS-6766 combinations yielded significant effects on cancer cell viability in NSCLC and pancreatic patient-derived spheroid models harboring KRASG12D and KRASG12V mutations. The repotrectinib/trametinib combination in A427 cells (NSCLC KRASG12D) exhibited increased inhibition of pAKT and pS6 compared to single agent treatments. This coincided with greater upregulation of p27 and elevated PARP cleavage, resulting in enhanced induction of apopotosis. To assess acquired MEKi resistance, several KRAS mutant cancer models were cultured under trametinib selection. Evaluation of trametinib-resistant cancer cells revealed activation of STAT3, FAK, and AKT signaling along with elevated S6 protein phosphorylation, which could be suppressed and resensitized to trametinib by combining with repotrectinib. Repotrectinib/trametinib combination in a syngeneic GEMM KRASG12D lung model had greater tumor growth inhibition than either single agent treatment. A similar combination efficacy benefit was observed in a HCT116 (CRC KRASG13D) xenograft model concomitant with suppression of SRC/FAK/STAT3/ERK activation. Taken together, repotrectinib combinations with MEK inhibitors demonstrated enhanced efficacy in both in vitro and in vivo preclinical models. Repotrectinib was shown to suppress molecular mechanisms of adaptive resistance mechanisms to MEK inhibition in preclinical models. These results suggest that the combination of repotrectinib with MEKi can repress the mutant KRAS signaling network to achieve more potent and durable anti-tumor activity and warrants clinical investigation in patients with KRASG12D and KRASG12V mutant cancers.

Citation Format: Nathan V. Lee, Wei Deng, Dayong Zhai, Laura Rodon, Ana Parra, Jessica Cowell, Afsheen Banisadr, Xin Zhang, Brion W. Murray. Repotrectinib increases effectiveness of MEK inhibitors in KRAS mutant cancer models [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 1104.

[LIM-domain binding protein 2 regulated by m6A modification inhibits lung adenocarcinoma cell proliferation in vitro]

OBJECTIVE

To investigate the role and expression pattern of LIM-domain binding protein 2 (LDB2) in lung adenocarcinoma.

OBJECTIVE

We studied the expression pattern of LDB2 in lung adenocarcinoma based on data from the online databases TCGA, GEO and CPTAC, and the results were verified in lung adenocarcinoma tissues and cells using immunohistochemistry, qRT-PCR and Western blotting. The relationship between LDB2 and the prognosis of patients with lung adenocarcinoma was analyzed using GEPIA and GEO databases. We further analyzed the role of LDB2 in regulating cell behaviors in a H1299 cell model over-expressing LDB2 using cell counting, soft agar colony forming assay and flow cytometry. The m⁶A binding sites on LDB2 were confirmed by bioinformatics analysis and MeRIP-qPCR assays. The effect of YTHDC2 on LDB2 was examined using qRT-PCR and Western blotting, and the binding of YTHDC2 to the transcript of LDB2 was verified with RIP-qPCR assays. Dual luciferase reporter assay was performed to verify YTHDC2 functioning via m⁶A sites.

OBJECTIVE

LDB2 expression was significantly decreased in lung adenocarcinoma in comparison with normal tissues based on data from TCGA, GEPIA and CPTAC, and the same results were obtained from 80 lung adenocarcinoma tissues and 17 adjacent normal tissues. Similarly, LDB2 expression was decreased in lung adenocarcinoma cells as compared with 16HBE cells. The data from Prognoscan and GEPIA suggested that a high LDB2 expression was positively correlated with a more favorable outcome of lung adenocarcinoma patients. LDB2-overexpressing H1299 cells showed a significant inhibition of proliferative activity with cell cycle arrest in S phage. Bioinformatics analysis and MeRIP-qPCR assay confirmed the presence of m⁶A sites on LDB2. The m⁶A reader YTHDC2 was positively related with LDB2 in lung adenocarcinoma based on data from GEPIA (r=0.22). Overexpression YTHDC2 significantly enhanced LDB2 expression in H1299 cells by about 19.35 folds. Dual luciferase reporter assay showed that YTHDC2 enhanced the promoter activity in the wild-type group but not in deletion group.

OBJECTIVE

LDB2 expression can be up-regulated by m⁶A reader YTHDC2 in lung adenocarcinoma to inhibit the proliferation of the tumor cells in vitro.

Abstract 1958: Repotrectinib increases effectiveness of KRAS-G12C inhibitors in KRAS-G12C mutant cancer models via simultaneous SRC/FAK/JAK2 inhibition

KRAS is frequently mutated in multiple cancer types. Therapeutic targeting of KRAS has proven challenging until recent success of KRAS-G12C inhibitor AMG510 that demonstrated tumor regression in lung and colon cancer patients with a KRAS-G12C mutation. However, resistance via feedback reactivation or development of a bypass are expected to limit anti-tumor efficacy of KRAS-G12C inhibitors, favoring a combination approach. Adaptive upregulation of the PI3K/AKT signaling pathway has been recognized as a common resistance mechanism that promotes cancer cell survival and may temper efficacy of KRAS-G12C inhibitors. SRC/FAK signaling promotes tumor cell survival by activation of the PI3K/AKT survival pathway supporting concomitantly targeting SRC/FAK as a promising strategy to potentiate KRAS G12C inhibitors. In addition, oncogenic KRAS induces secretion of various cytokines and growth factors leading to modulation of the tumor microenvironment to promote tumor growth. Targeting the cytokine secretion pathway via JAK2/STAT3 modulation may be important to overcome the resistance to direct KRAS inhibition. Therefore, combinations of KRAS inhibitors with agents that target apoptotic processes and feedback reactivation may represent a promising therapeutic approach. Repotrectinib, a next generation ROS1/TRK/ALK inhibitor, also inhibits SRC/FAK/JAK2 at therapeutically relevant concentrations. Here, we present synergistic effects of repotrectinib in combination with a KRAS-G12C inhibitor in KRAS-G12C mutant cancer models via simultaneous inhibition of SRC/FAK/JAK2. Adding repotrectinib to AMG510 improves AMG510 effectiveness on KRAS-G12C mutant cancer cells with notably increased apoptosis. For example, repotrectinib (1 μM) shifted the antiproliferation IC50 of AMG510 from 213 nM to 3 nM in KRAS-G12C mutant H358 cells. Treatment of H358 cells with AMG510 alone (100 nM) or repotrectinib alone (1 µM) resulted in slight increases in cleaved PARP and caspase-3 proteins, whereas larger increases were observed with the combination. Although high levels of phosphorylated ERK, AKT, STAT3 and FAK were detected in H358 cells, AMG510 (100 nM) was only able to partially modulate phospho-ERK (pERK) with no modulation on pAKT, pSTAT3 and pFAK and repotrectinib (1 μM) suppressed pSTAT3 and pFAK with minimum modulation on pERK and pAKT. The combination in H358 cells results in stronger suppression of pERK and pAKT than either single agent alone, which is consistent with the observed increase in activation of apoptosis. Additional combination data in KRAS-G12C mutant cancer models will be presented. Overall, these studies warrant further clinical investigation on the combination of KRAS-G12C inhibitors with repotrectinib in patients with KRAS-G12C mutation for potential response and duration improvement of current investigational KRAS-G12C inhibitors.

Citation Format: J. Jean Cui, Dayong Zhai, Wei Deng, Laura Rodon, Nathan Lee, Brion Murray. Repotrectinib increases effectiveness of KRAS-G12C inhibitors in KRAS-G12C mutant cancer models via simultaneous SRC/FAK/JAK2 inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1958.

The next-generation RET inhibitor TPX-0046 is active in drug-resistant and naïve RET-driven cancer models

3616

Background: RET fusions/mutations drive oncogenesis in lung and thyroid cancers, and several other malignancies. Selective RET inhibitors (selpercatinib/pralsetinib) are active in patients with these cancers; unfortunately, resistance often occurs. On-target resistance includes the acquisition of solvent front mutations (SFMs i.e. RET G810 substitutions). TPX-0046 is a structurally differentiated RET inhibitor that is potent against a range of RET fusions and mutations including SFMs. Methods: The rationally-designed, compact, macrocyclic RET/SRC inhibitor TPX-0046 was characterized in RET-driven in vitro and in vivo tumor models. Results: In enzymatic assays, TPX-0046 showed low nanomolar potency against wild-type RET and 18 RET mutations/fusions. It was potent against SRC and spared VEGFR2/KDR. TPX-0046 inhibited RET phosphorylation (IC50 < 10 nM) in tumor cell lines (LC2/ad, CCDC6-RET; TT, RET C634W) and Ba/F3 engineered RET models (WT, G810R). In cell proliferation assays, TPX-0046 inhibited KIF5B-RET Ba/F3, LC2/ad, and TT cells with IC50 values ~1 nM. Ba/F3 RET engineered cells with SFMs (e.g. G810C/R/S) were potently inhibited by TPX-0046 (mean proliferation IC50 1–17 nM). TPX-0046 demonstrated marked in vivo anti-tumor efficacy in RET-driven cell-derived and patient-derived xenograft tumor models. In a Ba/F3 KIF5B-RET xenograft model, a single dose of 5 mg/kg TPX-0046 inhibited > 80% of RET phosphorylation (corresponding mean free plasma concentration: 51 nM). At 5 mg/kg BID, tumor regression was observed in RET-dependent xenograft models, including those that harbor RET SFMs: TT, CTG-0838 PDX (NSCLC, KIF5B-RET), CR1520 PDX (CRC, NCOA4-RET), Ba/F3 KIF5B-RET, and Ba/F3 KIF5B-RET G810R. Conclusions: TPX-0046 is a unique next-generation RET inhibitor that possesses potent in vitro and in vivo activity against a diverse range of RET alterations, including SFM-mediated resistance. A phase 1/2 trial for RET inhibitor-resistant and naïve RET-driven cancers is on-going (NCT04161391).

Abstract 1325: TPX-0022, a polypharmacology inhibitor of MET/CSF1R/SRC inhibits tumor growth by promoting anti-tumor immune responses

In the tumor microenvironment, tumor associated macrophages (TAMs) support tumor growth by suppressing antitumor immune responses and promoting angiogenesis, which is associated with disease progression and poor clinical outcomes. In contrast to the classic phagocytic and cytotoxic pro-inflammatory M1 phenotype of macrophages engulfing and digesting pathogens, TAMs often adopt the anti-inflammatory and immune regulatory M2 phenotype in response to colony stimulating factor 1 (CSF1), which is produced by either tumor cells or stroma cells. Signaling through colony stimulating factor 1 receptor (CSF1R), a receptor tyrosine kinase expressed on the surface of mononuclear phagocytes, is involved in the recruitment of TAMs and has been associated with tumor progression and suppression of the immune response. Thus, CSF1R represents a key therapeutic target. TPX-0022, a type I kinase inhibitor with a novel macrocyclic structure, has been designed and optimized to inhibit MET/CSF1R/SRC with enzymatic kinase inhibition IC50s of 0.14, 0.76 and 0.12 nM, respectively. In a Ba/F3 ETV6-CSF1R cell model, TPX-0022 inhibited both autophosphorylation of CSF1R with an IC50 &lt;3 nM and cell growth with an IC50 of 14 nM. In addition, TPX-0022 effectively inhibited the growth of Ba/F3 ETV6-CSF1R xenograft tumors in vivo. In the CSF1/CSF1R signaling-dependent M-NFS-60 model, TPX-0022 not only exhibited potency with an IC50 of 0.3 nM under baseline condition, but also potently inhibited the growth of M-NFS-60 cells with an IC50 of 11.6 nM in the presence of exogenous CSF1 at 1 ng/mL concentration, a condition mimicking typical in vivo conditions in the presence of advanced tumors. In contrast, in our study, the potency of the type II CSF1R inhibitor PLX-3397 demonstrated a strong dependency on the concentration of mouse CSF1, as the anti-proliferation IC50 shifted from &lt;0.1 nM to 146.4 nM when CSF1 concentration changed from baseline to 1 ng/mL. Finally, in the MC38 syngeneic mouse model, TPX-0022 effectively reduced TAMs, altered the polarity of TAMs toward a more M1 phenotype, increased cytotoxic T cells and inhibited the growth of MC38 tumors. These preclinical results demonstrated a potent CSF1R inhibitory activity of TPX-0022 and the ability of TPX-0022 to inhibit tumor growth and promote a pro-inflammatory anti-tumor microenvironment.

Citation Format: Wei Deng, Dayong Zhai, Evan Rogers, Xin Zhang, Dong Lee, Jane Ung, Han Zhang, Jing Liu, Yuelie Lu, John Huang, Armin Graber, Zach Zimmerman, John Lim, Jeffrey Whitten, J. Jean Cui. TPX-0022, a polypharmacology inhibitor of MET/CSF1R/SRC inhibits tumor growth by promoting anti-tumor immune responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1325.

Abstract 442: Repotrectinib, a next generation TRK inhibitor, overcomes TRK resistance mutations including solvent front, gatekeeper and compound mutations

Oncogenic TRKA/B/C fusions are identified in multiple cancer types in adults and children. TRK inhibitors (TRKis) have demonstrated marked efficacy in patients with these cancers, however, acquired on-target resistance mediated by kinase domain mutations can occur. Next-generation TRKis targeting both wildtype and mutant TRK fusions can address this unmet need. Repotrectinib was designed to potently inhibit wildtype (WT) TRKs and overcome resistance mutations. The anti-proliferative activity of 1st generation (larotrectinib/entrectinib) and next-generation (repotrectinib/LOXO-195) TRKis were compared using engineered Ba/F3 cells expressing WT or mutated TRKs (Table). Repotrectinib was over 10-fold more potent than LOXO-195 against WT TRK fusions and solvent front mutations (SFMs), and more than 100-fold more potent against the gatekeeper mutations TRKA F589L and TRKC F617I. Furthermore, repotrectinib was the only TRKi active against the compound mutation TRKA G595R/F589L in cis in preclinical Ba/F3 cells. In xenograft tumor models, repotrectinib led to significant tumor regression in tumors carrying WT or mutated TRK fusions. In the ongoing TRIDENT-1 phase 1 clinical trial of repotrectinib (NCT03093116), the SFMs TRKA G595R, TRKC G623R and TRKC G623E and the gatekeeper mutation TRKA F589L were detected in plasma cfDNA samples at baseline from three TRKi-resistant patients. Repotrectinib was active against ETV6-TRKC G623E in an entrectinib-resistant patient with a salivary gland tumor (-82%, confirmed partial response, RECIST v1.1). Tumor regression (-33%) was achieved in a larotrectinib-resistant cholangiocarcinoma patient with LMNA-TRKA G595R and F589L mutations in trans. TRIDENT-1 is currently enrolling NTRK fusion-positive patients with advanced solid tumors.

Ba/F3 Cell Proliferation Assay IC50 (nM)LMNA-TRKAETV6-TRKBETV6-TRKCTRK InhibitorWTG595RG667CF589LG595R/F589LWTG639RWTG623RG623EF617IRepotrectinib&lt;0.10.19.2&lt;0.117.4&lt;0.13.2&lt;0.10.40.9&lt;0.2LOXO-1958.613.194.931.6531.11.028.41.724.649.153Larotrectinib15.918981863625.31000013.1300023.2699921625000Entrectinib0.3614186.7&lt;0.220000.220000.41340171261.7

Citation Format: Alexander Drilon, Dayong Zhai, Wei Deng, Xin Zhang, Dong Lee, Evan Rogers, Jeffrey Whitten, Zhongdong Huang, Armin Graber, Juliet Liu, Shanna Stopatschinskaja, J. Jean Cui, Dong-Wan Kim, Byoung Chul Cho, Robert C. Doebele, Sai-Hong Ignatius Ou, Jeeyun Lee, Alice T. Shaw. Repotrectinib, a next generation TRK inhibitor, overcomes TRK resistance mutations including solvent front, gatekeeper and compound mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 442.

Abstract 1321: TPX-0022, a polypharmacology inhibitor of MET/CSF1R/SRC for treatment of cancers with abnormal HGF/MET signaling

Aberrant activation of the HGF/MET pathway has frequently been found in human cancers via MET mutation, gene amplification and translocation, as well as HGF paracrine or autocrine upregulation. The abnormal HGF/MET signaling not only acts as an oncogenic driver but also confers resistance to many cancer therapies, such as EGFR targeted therapy in NSCLC. One key downstream effector for activated MET is SRC, which is also involved in malignancy formation, tumor metastasis and drug resistance. In the tumor microenvironment, CSF1R plays an important role in regulation of tumor associated macrophages, which promote tumor progression and angiogenesis. Therefore, the polypharmacological inhibition of MET/SRC/CSF1R has great potential for more effectively targeting cancers with abnormal HGF/MET signaling via targeting both tumor intrinsic signaling and the tumor microenvironment. TPX-0022, a novel macrocyclic compound, has been designed and optimized to inhibit MET/CSF1R/SRC with enzymatic kinase inhibition IC50s of 0.14, 0.76 and 0.12 nM, respectively. TPX-0022 potently inhibited cell proliferation of the MET-amplified MKN-45 and SNU-5 gastric cancer cells, with IC50s &lt;0.2 nM, which ranked TPX-0022 as one of the most potent MET inhibitors. TPX-0022 caused suppression of MET auto-phosphorylation at an IC50 of approximately 0.3 nM in MKN-45 cell line. TPX-0022 also potently inhibited the phosphorylation of MET downstream signaling effectors, including AKT, ERK, STAT3 and PLCγ2 in a dose-dependent manner. In the cancer cell line- and patient-derived xenograft tumor models from gastric, lung and liver cancers harboring MET amplification or MET exon14 skipping mutations, TPX-0022 caused dramatic tumor regression and tumor growth inhibition, without overt abnormality and body weight loss in treated mice. Furthermore, the tumor inhibitory effect was associated with drastic inhibition of MET activity. Overall, TPX-0022 is a novel and potent MET inhibitor and has demonstrated desirable drug-like properties, a good preclinical safety profiles, that warrants further clinical development and an IND submission is currently planned.

Citation Format: Dayong Zhai, Evan Rogers, Wei Deng, Xin Zhang, Dong Lee, Jane Ung, Han Zhang, Jing Liu, Yuelie Lu, John Huang, Armin Graber, Zach Zimmerman, John Lim, Jeffrey Whitten, J. Jean Cui. TPX-0022, a polypharmacology inhibitor of MET/CSF1R/SRC for treatment of cancers with abnormal HGF/MET signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1321.

Repotrectinib (TPX-0005) Is a Next-Generation ROS1/TRK/ALK Inhibitor That Potently Inhibits ROS1/TRK/ALK Solvent- Front Mutations

The use of tyrosine kinase inhibitors (TKI) with activity against ALK, ROS1, or TRKA-C can result in significant clinical benefit in patients with diverse tumors harboring ALK, ROS1, or NTRK1-3 rearrangements; however, resistance invariably develops. The emergence of on-target kinase domain mutations represents a major mechanism of acquired resistance. Solvent-front substitutions such as ALK^G1202R, ROS1^G2032R or ROS1^D2033N, TRKA^G595R, and TRKC^G623R are among the most recalcitrant of these mechanisms. Repotrectinib (TPX-0005) is a rationally designed, low-molecular-weight, macrocyclic TKI that is selective and highly potent against ROS1, TRKA-C, and ALK. Importantly, repotrectinib exhibits activity against a variety of solvent-front substitutions in vitro and in vivo As clinical proof of concept, in an ongoing first-in-human phase I/II trial, repotrectinib achieved confirmed responses in patients with ROS1 or NTRK3 fusion-positive cancers who had relapsed on earlier-generation TKIs due to ROS1 or TRKC solvent-front substitution-mediated resistance.Significance: Repotrectinib (TPX-0005), a next-generation ROS1, pan-TRK, and ALK TKI, overcomes resistance due to acquired solvent-front mutations involving ROS1, NTRK1-3, and ALK Repotrectinib may represent an effective therapeutic option for patients with ROS1-, NTRK1-3-, or ALK-rearranged malignancies who have progressed on earlier-generation TKIs. Cancer Discov; 8(10); 1227-36. ©2018 AACR. This article is highlighted in the In This Issue feature, p. 1195.

Abstract 4796: Ropotrectinib is a novel polypharmacology kinase inhibitor against WT and mutant ROS1, TRK and ALK

Tyrosine kinase inhibitors (TKI) have achieved great success for cancer patients with aberrant target genes such as ROS1, NTRKs and ALK. However, the inevitable emergence of drug resistance limits their long-term clinical benefits. Ropotrectinib (TPX-0005), a brain-tumor penetrable ROS1/TRK/ALK kinase inhibitor, was designed not only to target abnormal activity of ROS1, TRK and ALK but also to overcome drug resistance caused by previous ROS1, NTRK and ALK inhibitors. The unique structure design of roporectinib granted it the unique ability to overcome acquired solvent front mutations in the targeted kinase domain caused by other TKIs. Moreover, ropotrectinib displays inhibitory activity for SRC/FAK/JAK2, rendering its potential to overcome drug resistance caused by “by-passing” mechanisms such as EMT.

Ropotrectinib is a superb ROS1 inhibitor. The ALK/ROS1/MET inhibitor crizotinib has been approved by FDA to treat NSCLC patients harboring a rearranged ROS1 fusion gene. Acquired secondary mutations in ROS1 kinase domain is a common drug resistance mechanism in 50-60% patients progressed on crizotinib treatment, with solvent front mutations most frequently observed. Compared to other ROS1 inhibitors, such as lorlatinib, ceritinib, brigatinib and entrectinib, ropotrectinb demonstrated most potent activity against WT and mutant ROS1, especially solvent front mutations such as G2032R in cellular assays and potently inhibited xenograft tumors.

Ropotrectinib is the most potent TRK inhibitors in clinic, with IC50s &lt; 1nM in cellular assays. Preclinic in vitro and in vivo studies further demonstrated that ropotrectinib overcomes clinical resistance mutations which occur in patients progressed on TRK inhibitors, such as entrectinib and larotrectinib. In a phosphorylation assay using engineered NIH3T3 cells expressing a TRKAG595R fusion gene, ropotrectinib (IC50 &lt; 0.1nM) exhibited activities at least ten folds more potent than the recently reported activity of LOXO-195 (IC50 = 7nM), a second generation of TRK inhibitor in clinic.

Ropotrectinib is also a ALK inhibitor with CNS activity, inhibiting growth and viability of ALK+ cells, inducing tumor regression in a ALK+ PDX tumor model and significantly improving overall survival of mice bearing CNS ALK+ H2228 tumors. In particular, compared to previous generations of ALK inhibitors (e.g. crizontinib, ceritinib, alectinib, and brigatinib), it exhibited superb activity in those acquired mutations, especially the G1202R solvent front mutation and double mutations containing L1198F. Roporectinib dose-dependently down-regulated EGFR, CD44 and vimentin expression levels via SRC/FAK inhibition, suggesting a potential to prevent EMT.

In summary, ropotrectinib exerts unique pharmacological properties for clinical applications in patients harboring aberrant ROS1/TRK/ALK. A Phase 1/2 clinical trial of TPX-0005 is actively pursued (NCT03093116).

Citation Format: Wei Deng, Dayong Zhai, John Huang, Evan Rogers, Jeffrey Whitten, John Lim, Yishan Li, Jean Cui. Ropotrectinib is a novel polypharmacology kinase inhibitor against WT and mutant ROS1, TRK and ALK [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 4796.

Quantum Wires and Waveguides Formed in Graphene by Strain

Confinement of electrons in graphene to make devices has proven to be a challenging task. Electrostatic methods fail because of Klein tunneling, while etching into nanoribbons requires extreme control of edge terminations, and bottom-up approaches are limited in size to a few nanometers. Fortunately, its mechanical flexibility raises the possibility of using strain to alter graphene's properties and create novel straintronic devices. Here, we report transport studies of nanowires created by linearly-shaped strained regions resulting from individual folds formed by layer transfer onto hexagonal boron nitride. Conductance measurements across the folds reveal Coulomb blockade signatures, indicating confined charges within these structures, which act as quantum dots. Along folds, we observe sharp features in traverse resistivity measurements, attributed to an amplification of the dot conductance modulations by a resistance bridge incorporating the device. Our data indicates ballistic transport up to ∼1 μm along the folds. Calculations using the Dirac model including strain are consistent with measured bound state energies and predict the existence of valley-polarized currents. Our results show that graphene folds can act as straintronic quantum wires.

Abstract B186: TPX-0005, a polypharmacology inhibitor, overcomes ALK treatment resistance from acquired mutations, bypass signaling, and EMT

ALK kinase inhibitors have achieved tremendous success in the treatment of lung cancer patients with abnormal ALK gene. However, the emergence of drug resistance limits their long-term clinical applications. The mechanisms of resistance often include gene amplification, acquired mutations, bypass signaling, and epithelial-mesenchymal transition (EMT). More than 10 different mutations have been identified in clinic, and recently the compound mutations represent new challenges after multiple ALK inhibitor treatments. The bypass and EMT-based resistance mechanisms constitute a large portion of the resistant patient population. None of the current ALK inhibitors can overcome bypass or EMT-based resistance when applied as a single-agent therapy. Therefore, a different strategy needs to be deployed for the design of new-generation ALK inhibitors to overcome multi-resistance mechanisms simultaneously. TPX-0005, a novel three-dimensional macrocycle with a much smaller size than current ALK inhibitors in the clinic, was designed to overcome clinical resistance mutations systematically. TPX-0005 potently inhibited both wild type and mutant ALK fusion proteins including gatekeeper, solvent front, and compound mutations as shown in the table. In addition to its primary targets, TPX-0005 is also a potent SRC/FAK inhibitor with IC50s of 70-80 nM in H2228 cells. H2228 lung cancer cell line, endogenously expressing EML4-ALKv3 protein, is refractory to crizotinib and ceritinib. The upregulation of multiple RTKs including EGFR and IGFR, as well as cancer stem cell marker CD44 and mesenchymal marker vimentin, is believed to induce the primary resistance to selective ALK inhibitors. Inhibition of SRC/FAK kinases will modulate bypass RTK expression, cancer stem-like properties, and EMT to restore the sensitivity to ALK inhibition. TPX-0005 dose-dependently downregulated EGFR, CD44, and vimentin expression levels via SRC/FAK inhibition. TPX-0005 effectively inhibited cancer cell migration in wound healing assays, and induced dramatic tumor regression in human PDX NSCLC tumor model. In addition, TPX-0005 significantly extended survival time in mouse H2228 orthotopic brain tumor model. Overall, TPX-0005 exerts unprecedented polypharmacology profile for combating multiple resistance mechanisms. A phase 1/2 clinical trial of TPX-0005 is actively being pursued (NCT03093116). EML4-ALK Ba/F3 Cell Proliferation Assay IC50 (nM)InhibitorWTG1202RL1196ML1198F/C1156YL1198F/G1202RL1198F/L1196MTPX-000517.820.5501.10.234.8Crizotinib74.8359.47132243.7350.7Ceritinib2.138861123476.81794Alectinib18.950713115813691249Brigatinib11.8399131181187341Lorlatinib0.7ND1889131.61169

ND: not determined

Citation Format: Dayong Zhai, Wei Deng, Evan Rogers, Zhongdong Huang, Jeffrey Whitten, John Lim, Yishan Li, J. Jean Cui. TPX-0005, a polypharmacology inhibitor, overcomes ALK treatment resistance from acquired mutations, bypass signaling, and EMT [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B186.

Abstract B185: TPX-0005, a supreme ROS1 inhibitor, overcomes crizotinib-resistant ROS1 mutations including solvent front mutation G2032R and gatekeeper mutation L2026M

The fusion kinases of ROS1 and ALK have been identified as oncogene drivers in small portions of many malignancies, especially in non-small cell lung cancer (NSCLC). ALK/ROS1/MET inhibitor crizotinib has been approved by the US Food and Drug Administration for the treatment of ALK or ROS1-positive non-small cell lung cancer in 2011 and 2016, respectively. The emergence of drug resistance presents a major issue for targeted therapy. Although ceritinib, alectinib, and brigatinib have been approved for crizotinib-refractory ALK+ patients with NSCLC, treatment options for patients with ROS1+ NSCLC are limited, especially for crizotinib-refractory patients. Ceritinib and entectinib demonstrated clinical efficacy only in crizotinib-naïve ROS1+ patients. The most common resistance mechanisms to crizotinib treatment in ROS1+ NSCLC is the solvent front mutation ROS1 G2032R and gatekeeper mutation ROS1 L2026M. TPX-0005, a novel three-dimensional macrocycle with a much smaller size than current ROS1 inhibitors in the clinic, was designed to overcome clinical resistance mutations systematically. TPX-0005 potently inhibited both wild type and mutant ROS1s including solvent front mutations and gatekeeper mutations. TPX-0005 showed pico-molar activity against ROS1 kinase (IC50 0.076 nM) in Reaction Biology kinase assay. The comparison of TPX-0005 with other ROS1 inhibitors in Ba/F3 cell proliferation assays is presented in the table. In the xenograft tumor model studies, TPX-0005 dramatically caused tumor regression in the tumors carrying WT or solvent-front mutated ROS1 fusion gene. Overall, TPX-0005 demonstrated desired drug-like properties, good safety profile, and is a supreme ROS1 inhibitor against WT and various mutated ROS1s. A phase 1/2 clinical trial of TPX-0005 is actively being pursued (NCT03093116). CD74-ROS1 Ba/F3 Cell Proliferation Assay IC50 (nM)InhibitorWTG2032RD2033NL2026MS1986FS1986YTPX-0005&lt;0.28.40.210&lt;0.2&lt;0.2Crizotinib9.71402139606.420.919Lorlatinib0.5262.42.4ND0.30.3Entrectinib25.42404ND2026NDNDCeritinib131.92000NDND14.226.9Brigatinib28.61385167.1211527.724.6Cabozantinib1.060.70.129.1NDND

ND: not determined.

Citation Format: J. Jean Cui, Dayong Zhai, Wei Deng, Evan Rogers, Zhongdong Huang, Jeffrey Whitten, John Lim, Yishan Li. TPX-0005, a supreme ROS1 inhibitor, overcomes crizotinib-resistant ROS1 mutations including solvent front mutation G2032R and gatekeeper mutation L2026M [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B185.

Abstract B184: TPX-0005, a highly potent TRK inhibitor, effectively overcomes clinical-resistance TRK mutations including solvent front mutants TRKA G595R, TRKB G639R, and TRKC G623R

The tropomyosin receptor kinases (TRKs), including TRKA/B/C encoded by NTRK1/2/3 genes, are high-affinity receptors for neurotrophins. Oncogenic rearrangement of NTRK1, NTRK2, and NTRK3 have been identified in many solid malignancies. The use of TRK inhibitors entrectinib and larotrectinib has led to clinical benefit in patients with solid malignancies harboring oncogenic NTRK fusions. Similar to ALK and ROS1 inhibitor treatment, the solvent front mutations TRKA G595R and TRKC G623R (both analog to ALK G1202R) were reported in clinic from treatment-resistant patients. A new generation of TRK inhibitors targeting both wild type and mutated TRKs is highly needed for effectively treating patients harboring fusion TRKs. TPX-0005, a novel three-dimensional macrocycle with a much smaller size than current TRK inhibitors in the clinic, was designed to overcome clinical resistance mutations systematically. TPX-0005 potently inhibited both wild type and mutant TRKs including solvent front mutations. TPX-0005 showed pico-molar activity against TRK kinases (IC50s 0.83 nM, 0.05 nM, and 0.10 nM for TRKA/B/C, respectively) in Reaction Biology kinase assay. TPX-0005 is the most potent TRK inhibitor in clinic and effectively overcomes clinical resistance TRK mutations as shown in the table in cell proliferation assays. It was recently reported that LOXO-195 inhibited the phosphorylation of TRKA and ERK kinases in NIH3T3 cell line expressing ΔTRKA G595R or ETV6-TRKC G623R with IC50s of 7 nM and 45.5 nM, respectively. TPX-0005 is more than 10-fold more potent than LOXO-195. In the xenograft tumor model studies including human PDX model, TPX-0005 dramatically caused tumor regression in the tumors carrying WT or solvent-front mutated TRK fusion gene. Overall, TPX-0005 demonstrated desired drug-like properties, good safety profile, and is a supreme TRK inhibitor against WT and mutated TRKs. A phase 1/2 clinical trial of TPX-0005 is actively being pursued (NCT03093116). KM-12 IC50 (nM)Ba/F3 Cell Proliferation Assay IC50 (nM)InhibitorTPM3-TRKAWTLMNA-TRKA WTLMNA-TRKA G595RETV6-TRKB WTETV6-TRKB G639RETV6-TRKC WTETV6-TRKC G623RTPX-0005&lt;0.2&lt;0.20.4&lt;0.20.6&lt;0.23Entrectinib9.20.3705&lt;0.513840.61000Larotrectinib12.33.5102410.9300010.21500

Citation Format: J. Jean Cui, Dayong Zhai, Wei Deng, Evan Rogers, Zhongdong Huang, Jeffrey Whitten, John lim, Yishan Li. TPX-0005, a highly potent TRK inhibitor, effectively overcomes clinical-resistance TRK mutations including solvent front mutants TRKA G595R, TRKB G639R, and TRKC G623R [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B184.

Abstract 3161: TPX-0005, an ALK/ROS1/TRK inhibitor, overcomes multiple resistance mechanisms by targeting SRC/FAK signaling

ALK, ROS1, and TRK inhibitors have achieved marked efficacy in treating cancer patients expressing abnormal ALK, ROS1 or NTRK genes. However, the initial success of these therapies is rapidly overshadowed with the development of acquired resistance. In addition, approximately 30-40% of ALK + or ROS1+ NSCLC patients fail to respond to initial crizotinib treatment, representing intrinsic resistance. Target gene amplification, acquired resistance mutations, bypass signaling, epithelial-mesenchymal transition (EMT) and metastasis are the common resistance mechanisms. None of the current ALK, ROS1 or TRK inhibitors can overcome bypass or EMT-based resistance when applied as a single agent therapy. TPX-0005 is a potent kinase inhibitor against WT and mutated ALK, ROS1 and TRK family kinases, especially the clinically significant solvent front mutations. At clinically relevant concentrations, TPX-0005 also inhibits JAK2, SRC and FAK that are important targets in modulating multiple resistance mechanisms. H2228 lung cancer cell line endogenously expresses EML4-ALK v3 and was reported to be resistant to ALK inhibitor TAE684. Upregulation of the bypass signaling kinase EGFR, EMT marker vimentin, and cancer stem-like marker CD44 was reported in H2228 cells, likely leading to intrinsic resistance to ALK inhibitors. In the anti-proliferation assay, both crizotinib and ceritinib were resistant in H2228 cells with IC50 values around 1000 nM, however, TPX-0005 was able to overcome the intrinsic resistance with an IC50 of 100 nM. In H2228 cells, TPX-0005 suppressed the phosphorylation of SRC, FAK and paxillin with IC50 values in a range of 80-100 nM, and downregulated the expression of EGFR, CD44, and vimentin with IC50 values around 100 nM. In addition, TPX-0005 inhibited the phosphorylation of the oncogenic transcription/translation factor YB-1 with an IC50 value around 100 nM in H2228 cells. YB-1 is involved in many aspects of gene expression control that lead to tumor cell growth and drug resistance, including modulation of EGFR upregulation, EMT, and cancer stemness. Therefore, it was postulated that inhibition of SRC/FAK by TPX-0005 suppressed the phosphorylation of YB-1, leading to the downregulation of EGFR, CD44 and vimentin, and eventually to anti-proliferation effect on H2228 cells. TPX-0005 demonstrated an in vitro anti-metastatic activity by inhibiting cell migration in both H2228 cells and HT1080 human fibrosarcoma cells. Taken together, the potent kinase inhibitory activities against SRC/FAK signaling provide a unique polypharmacology profile to TPX-0005 for combatting multiple resistance mechanisms simultaneously, including a broad spectrum of acquired mutations, bypass signaling, EMT, cancer stemness, and metastasis.

Citation Format: Dayong Zhai, Wei Deng, John Huang, Evan Rogers, J. Jean Cui. TPX-0005, an ALK/ROS1/TRK inhibitor, overcomes multiple resistance mechanisms by targeting SRC/FAK signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3161. doi:10.1158/1538-7445.AM2017-3161

[Genotyping of ABO Blood Group in Partial Population of Yunnan Province by SNaPshot Technology]

OBJECTIVES

To detect the genotype of ABO blood group by SNaPshot technology.

METHODS

DNA were extracted from the peripheral blood samples with known blood groups （obtained by serology） of 107 unrelated individuals in Yunnan. Six SNP loci of the 261th, 297th, 681th, 703th, 802th, and 803th nucleotide positions were detected by SNaPshot Multiplex kit, and relevant genetics parameters were calculated.

RESULTS

In 107 blood samples, the allele frequencies of types A, B, O^A, and O^G were 0.355 1, 0.168 2, 0.230 0 and 0.247 6, respectively, while that of types A^G and cis AB were not detected. The genotyping results of ABO blood group were consistent with that of serologic testing.

CONCLUSIONS

SNaPshot technology can be adapted for genotyping of ABO blood group.

Ultra-High-Throughput Screening of Natural Product Extracts to Identify Proapoptotic Inhibitors of Bcl-2 Family Proteins

Antiapoptotic Bcl-2 family proteins are validated cancer targets composed of six related proteins. From a drug discovery perspective, these are challenging targets that exert their cellular functions through protein-protein interactions (PPIs). Although several isoform-selective inhibitors have been developed using structure-based design or high-throughput screening (HTS) of synthetic chemical libraries, no large-scale screen of natural product collections has been reported. A competitive displacement fluorescence polarization (FP) screen of nearly 150,000 natural product extracts was conducted against all six antiapoptotic Bcl-2 family proteins using fluorochrome-conjugated peptide ligands that mimic functionally relevant PPIs. The screens were conducted in 1536-well format and displayed satisfactory overall HTS statistics, with Z'-factor values ranging from 0.72 to 0.83 and a hit confirmation rate between 16% and 64%. Confirmed active extracts were orthogonally tested in a luminescent assay for caspase-3/7 activation in tumor cells. Active extracts were resupplied, and effort toward the isolation of pure active components was initiated through iterative bioassay-guided fractionation. Several previously described altertoxins were isolated from a microbial source, and the pure compounds demonstrate activity in both Bcl-2 FP and caspase cellular assays. The studies demonstrate the feasibility of ultra-high-throughput screening using natural product sources and highlight some of the challenges associated with this approach.

Three-dimensional structure of Bax-mediated pores in membrane bilayers

B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax) is a member of the Bcl-2 protein family having a pivotal role in triggering cell commitment to apoptosis. Bax is latent and monomeric in the cytosol but transforms into its lethal, mitochondria-embedded oligomeric form in response to cell stress, leading to the release of apoptogenic factors such as cytochrome C. Here, we dissected the structural correlates of Bax membrane insertion while oligomerization is halted. This strategy was enabled through the use of nanometer-scale phospholipid bilayer islands (nanodiscs) the size of which restricts the reconstituted system to single Bax-molecule activity. Using this minimal reconstituted system, we captured structural correlates that precede Bax homo-oligomerization elucidating previously inaccessible steps of the core molecular mechanism by which Bcl-2 family proteins regulate membrane permeabilization. We observe that, in the presence of BH3 interacting domain death agonist (Bid) BH3 peptide, Bax monomers induce the formation of ~3.5-nm diameter pores and significantly distort the phospholipid bilayer. These pores are compatible with promoting release of ions as well as proteinaceous components, suggesting that membrane-integrated Bax monomers in the presence of Bid BH3 peptides are key functional units for the activation of the cell demolition machinery.

Abstract 4540: Development of a biochemical High Throughput Screening (HTS) assay for chemical inhibitors of MALT1, a target for lymphoma therapeutics

MALT1 plays critical role in antigen receptor-mediated lymphocyte activation and lymphomagenesis. MALT1 acts both as a scaffold protein to recruit upstream signal transducers and as an intracellular cysteine protease with proteolytic activity that cleaves substrate proteins involved in NF-kB induction. Dysregulation of MALT1 activity occurs in lymphoma as a result of chromosomal translocations that fuse the catalytic domain of MALT1 with portions of BirC3 (c-IAP2). Previous studies have shown that MALT1’s proteolytic activity is required for its participation in NF-kB induction and for promoting cell viability of certain types of lymphomas, particularly the activated B-cell (ABC) type of diffuse large B-cell lymphoma.

To lay a foundation for discovery of drug-like chemical inhibitors of MALT1, we developed a fluorescence-based, biochemical assay for measuring protease activity of MALT1 in vitro in 384 and 1,536 well formats. The assay components included recombinant purified full-length MALT1 protein, the MALT1-binding protein, Bcl-10, and the fluorigenic substrate Ac-LRSR-AMC (Ac-Leu-Arg-Ser-Arg-7-amino-4-methylcoumarin). Experiments showed that addition of Bcl-10 increases MALT1‘s protease activity up to 20-40 fold. The high throughput screening (HTS) assay was validated with excellent Z’ factors (&gt;0.7) in both 384 and 1,536 well formats, with performance remaining robust for more than 6 hours, and thus suitable for screening of large chemical libraries. The HTS assay was validated by performing pilot screens with two small collections of compounds enriched in bioactive molecules (n = 1280 for LopacTM and 2000 for SpectrumTM library), yielding confirmed hit rates of 0.2 % and 0.7%, respectively. Counter-screening assays were also generated using other types of intracellular cysteine proteases, specifically Caspase-3 and Autophagin-1 (ATG4B), for eliminating non-specific inhibitors. Various supporting cell-based assays have also been generated to support hit characterization. In conclusion, we have generated a robust biochemical HTS assays for detection of chemical inhibitors of the MALT1 protease. We plan to utilize the HTS assay for screening large compound libraries as a starting point for discovery of novel therapeutics for treatment of lymphoma, autoimmunity, and allograft rejection.

Citation Format: Dayong Zhai, Chih-Wen Shu, Paul Diaz, John C. Reed. Development of a biochemical High Throughput Screening (HTS) assay for chemical inhibitors of MALT1, a target for lymphoma therapeutics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4540. doi:10.1158/1538-7445.AM2013-4540

A Pan-BCL2 inhibitor renders bone-marrow-resident human leukemia stem cells sensitive to tyrosine kinase inhibition

Leukemia stem cells (LSCs) play a pivotal role in the resistance of chronic myeloid leukemia (CML) to tyrosine kinase inhibitors (TKIs) and its progression to blast crisis (BC), in part, through the alternative splicing of self-renewal and survival genes. To elucidate splice-isoform regulators of human BC LSC maintenance, we performed whole-transcriptome RNA sequencing, splice-isoform-specific quantitative RT-PCR (qRT-PCR), nanoproteomics, stromal coculture, and BC LSC xenotransplantation analyses. Cumulatively, these studies show that the alternative splicing of multiple prosurvival BCL2 family genes promotes malignant transformation of myeloid progenitors into BC LSCS that are quiescent in the marrow niche and that contribute to therapeutic resistance. Notably, sabutoclax, a pan-BCL2 inhibitor, renders marrow-niche-resident BC LSCs sensitive to TKIs at doses that spare normal progenitors. These findings underscore the importance of alternative BCL2 family splice-isoform expression in BC LSC maintenance and suggest that the combinatorial inhibition of prosurvival BCL2 family proteins and BCR-ABL may eliminate dormant LSCs and obviate resistance.

SU-E-T-585: Application of IMAT in Non-Small-Cell Lung Cancer with Simultaneously Integrated Boost Radiation Therapy

PURPOSE

To compare and analyze the characteristics of intensity-modulated arc therapy(IMAT) versus fixed-gantry intensity-modulated radiotherapy(IMRT) in treatment of non-small-cell lung cancer.

METHODS

Twelve patients treated in our radiotherapy center were selected for this study. The patient subsequently underwent 4D-CT simulation.Margins of 5 mm and 10mm were added to the ITV to generate the CTV and PTV respectively. Three treatment plans (IMRT,one single arc (RA1),double arcs (RA2))were generated with Eclipse ver.8.6 planning systems. Using a dose level of75Gy in 15fractions to the ITV,60Gy in 15fractions to the CTV and 45Gy in 15fractions to the PTV respectively. The target and normol tissue volumes were compared, as were the dosimetry parameters.

RESULTS

There were no significant differences in CI of ITV,PTV, HI of ITV,CTV and PTV, V5,V10,V15,V20,V25,V30,V45,V50 of total-lung and mean lung dose (all p>0.05). However, the differences were significant in terms of CI of CTV, V5 of B-P (all p<0.05). On the MU, IMRT=1540MU,RA1=1006 MU and RA2=1096 MU. (F=12.00,P=0.000).On the treatment time, IMRT= 13.5min,RA1= 1.5min, and RA2=2.5 min (F= 30.11,P=0.000).

CONCLUSIONS

IMAT is equal to IMRT in dosimetril evaluation. Due to much less Mu and delivery time,IMAT is an ideal technique in treating patients by reduceing the uncomfortable influnce which could effect the treatment.

High-throughput fluorescence polarization assay for chemical library screening against anti-apoptotic Bcl-2 family member Bfl-1

Overexpression of the anti-apoptotic Bcl-2 family proteins occurs commonly in human cancers. Bfl-1 is highly expressed in some types of malignant cells, contributing significantly to tumor cell survival and chemoresistance. Therefore, it would be desirable to have chemical antagonists of Bfl-1. To this end, we devised a fluorescence polarization assay (FPA) using Bfl-1 protein and fluorescein-conjugated Bid BH3 peptide, which was employed for high-throughput screening of chemical libraries. Approximately 66 000 compounds were screened for the ability to inhibit BH3 peptide binding to Bfl-1, yielding 14 reproducible hits with ≥50% displacement. After dose-response analysis and confirmation using a secondary assay based on time-resolved fluorescence resonance energy transfer (TR-FRET), two groups of Bfl-1-specific inhibitors were identified, including chloromaleimide and sulfonylpyrimidine series compounds. FPAs generated for each of the six anti-apoptotic Bcl-2 proteins demonstrated selective binding of both classes of compounds to Bfl-1. Analogs of the sulfonylpyrimidine series were synthesized and compared with the original hit for Bfl-1 binding by both FPAs and TR-FRET assays. The resulting structure-activity relation analysis led to the chemical probe compound CID-2980973 (ML042). Collectively, these findings demonstrate the feasibility of using the HTS assay for discovery of selective chemical inhibitors of Bfl-1.

Discovery and characterization of 2-aminobenzimidazole derivatives as selective NOD1 inhibitors

NLR family proteins play important roles in innate immune response. NOD1 (NLRC1) activates various signaling pathways including NF-κB in response to bacterial ligands. Hereditary polymorphisms in the NOD1 gene are associated with asthma, inflammatory bowel disease, and other disorders. Using a high throughput screening (HTS) assay measuring NOD1-induced NF-κB reporter gene activity, followed by multiple downstream counter screens that eliminated compounds impacting other NF-κB effectors, 2-aminobenzimidazole compounds were identified that selectively inhibit NOD1. Mechanistic studies of a prototypical compound, Nodinitib-1 (ML130; CID-1088438), suggest that these small molecules cause conformational changes of NOD1 in vitro and alter NOD1 subcellular targeting in cells. Altogether, this inaugural class of inhibitors provides chemical probes for interrogating mechanisms regulating NOD1 activity and tools for exploring the roles of NOD1 in various infectious and inflammatory diseases.

A new approach with less damage: intranasal delivery of tetracycline-inducible replication-defective herpes simplex virus type-1 vector to brain

Gene therapy holds great potential for treating neurological disorders. However, delivering gene vectors to the brain has been either invasive or inefficacious in most studies to date. The aim of this study was to develop a safe and efficacious strategy for delivering gene vectors to the brain. A tetracycline-inducible replication-defective herpes simplex virus type-1 vector, QR9TO-LacZ, was administered to rats intranasally. QR9TO-LacZ could infect primary cortical neurons and express the reporter gene without detectable replication. QR9TO-LacZ was observed in the olfactory bulb, hippocampus, striatum, cortex, medulla, cerebellum, ventricles, and nasal septum after intranasal administration. Expression of the reporter gene could be controlled effectively by tetracycline. In vitro, introduction of QR9TO-LacZ did not change the structure of transfected neurons. In vivo, QR9TO-LacZ did not increase apoptosis in neurons and did not alter levels of interleukin 6 and tumor necrosis factor α in the brain after intranasal delivery. Our data suggest that intranasally applied QR9TO-LacZ has a wide distribution and expresses the reporter gene in the brain under the control of tetracycline with less cytotoxicity than intravenous or stereotactic delivery methods.

Expression, purification, and characterization of recombinant NOD1 (NLRC1): A NLR family member

NOD1 (NLRC1) is a member of the NLR family of innate immunity proteins, which are important cellular sensors of various pathogens. Deregulated NOD1 signaling is involved in various autoimmune, inflammatory, and allergic diseases, making it a potential target for drug discovery. However, to date, the successful high-yield purification NOD1 protein has not been reported. Here we describe the large-scale expression of recombinant NOD1 protein in non-adherent mammalian cells. One-step immunoaffinity purification was carried out, yielding highly pure protein with excellent yields. Gel-sieve chromatography studies showed that the purified NOD1 protein eluted almost exclusively as a monomer. Addition of the NOD1 ligand (γ-Tri-DAP) stimulated NOD1 protein oligomerization. Using purified NOD1 protein for nucleotide binding studies by the Fluorescence Polarization Assay (FPA) method, we determined that NOD1 binds preferentially to ATP over ADP and AMP or dATP. We also documented that purified NOD1 protein binds directly to purified pro-apoptotic protein Bid, thus extending recent data that have identified Bid as an enhancer of NOD1 signaling. This expression and purification strategy will enable a wide variety of biochemical studies of mechanisms of NOD1 regulation, as well as laying a foundation for future attempts at drug discovery.

An optically pure apogossypolone derivative as potent pan-active inhibitor of anti-apoptotic bcl-2 family proteins

Our focus in the past several years has been on the identification of novel and effective pan-Bcl-2 antagonists. We have recently reported a series of Apogossypolone (ApoG2) derivatives, resulting in the chiral compound (±) BI97D6. We report here the synthesis and evaluation on its optically pure (-) and (+) atropisomers. Compound (-) BI97D6 potently inhibits the binding of BH3 peptides to Bcl-X(L), Bcl-2, Mcl-1, and Bfl-1 with IC(50) values of 76 ± 5, 31 ± 2, 25 ± 8, and 122 ± 28 nM, respectively. In a cellular assay, compound (-) BI97D6 effectively inhibits cell growth in the PC-3 human prostate cancer and H23 human lung cancer cell lines with EC(50) values of 0.22 ± 0.08 and 0.14 ± 0.02 μM, respectively. Similarly, compound (-) BI97D6 effectively induces apoptosis in the BP3 human lymphoma cell line in a dose-dependent manner. The compound also shows little cytotoxicity against bax(-/-)/bak(-/-) cells, suggesting that it kills cancers cells predominantly via a Bcl-2 pathway. Moreover, compound (-) BI97D6 displays in vivo efficacy in both a Bcl-2-transgenic mouse model and in a prostate cancer xenograft model in mice. Therefore, compound (-) BI97D6 represents a promising drug lead for the development of novel apoptosis-based therapies for cancer.

Structural determinants of caspase-9 inhibition by the vaccinia virus protein, F1L

In multicellular organisms, apoptosis is a powerful method of host defense against viral infection. Apoptosis is mediated by a cascade of caspase-family proteases that commit infected cells to a form of programmed cell death. Therefore, to replicate within host cells, viruses have developed various strategies to inhibit caspase activation. In the mitochondrial cell-death pathway, release of cytochrome c from mitochondria into the cytosol triggers assembly of the oligomeric apoptosome, resulting in dimerization and activation of the apical caspase-9 (C9), and in turn its downstream effector caspases, leading to apoptosis. We previously showed that the vaccinia virus-encoded Bcl-2-like protein, F1L, which suppresses cytochrome c release by binding Bcl-2 family proteins, is also a C9 inhibitor. Here, we identify a novel motif within the flexible N-terminal region of F1L that is necessary and sufficient for interaction with and inhibition of C9. Based on functional studies and mutagenesis, we developed an atomic model of the complex in which F1L inhibits C9 by engaging the active site in the reverse orientation with respect to substrate peptides, in a manner analogous to that of XIAP-mediated inhibition of caspases-3 and -7. These studies offer new insights into the mechanism of apoptosome inhibition by F1L as well as novel probes to understand the molecular bases of apoptosome regulation and turnover. They also suggest how the two distinct functionalities of F1L (inhibition of C9 and suppression of pro-apoptotic Bcl-2 family proteins) may operate in a cellular setting.

High-throughput screen for the chemical inhibitors of antiapoptotic bcl-2 family proteins by multiplex flow cytometry

The human Bcl-2 family includes six antiapoptotic members (Bcl-2, Bcl-B, Bcl-W, Bcl-X(L), Bfl-1, and Mcl-1) and many proapoptotic members, wherein a balance between the two determines cell life or death in many physiological and disease contexts. Elevated expression of various antiapoptotic Bcl-2 members is commonly observed in cancers, and chemical inhibitors of these proteins have been shown to promote apoptosis of malignant cells in culture, in animal models, and in human clinical trials. All six antiapoptotic members bind a helix from the proapoptotic family member Bim, thus quenching Bim's apoptotic signal. Here, we describe the use of a multiplex, high-throughput flow cytometry assay for the discovery of small molecule modulators that disrupt the interaction between the antiapoptotic members of the Bcl-2 family and Bim. The six antiapoptotic Bcl-2 family members were expressed as glutathione-S-transferase fusion proteins and bound individually to six glutathione bead sets, with each set having a different intensity of red fluorescence. A fluorescein-conjugated Bcl-2 homology region 3 (BH3) peptide from Bim was employed as a universal ligand. Flow cytometry measured the amount of green peptide bound to each bead set in a given well, with inhibitory compounds resulting in a decrease of green fluorescence on one or more bead set(s). Hits and cheminformatically selected analogs were retested in a dose-response series, resulting in three "active" compounds for Bcl-B. These three compounds were validated by fluorescence polarization and isothermal titration calorimetry. We discuss some of the lessons learned about screening a chemical library provided by the National Institutes of Health Small Molecule Repository (∼195,000 compounds) using high-throughput flow cytometry.

High-Throughput Fluorescence Assay for Small-Molecule Inhibitors of Autophagins/Atg4

Autophagy is an evolutionarily conserved process for catabolizing damaged proteins and organelles in a lysosome-dependent manner. Dysregulation of autophagy may cause various diseases, such as cancer and neurodegeneration. However, the relevance of autophagy to diseases remains controversial because of the limited availability of chemical modulators. Herein, the authors developed a fluorescence-based assay for measuring activity of the autophagy protease, autophagin-1(Atg4B). The assay employs a novel reporter substrate of Atg4B composed of a natural substrate (LC3B) fused to an assayable enzyme (PLA2) that becomes active upon cleavage by this cysteine protease. A high-throughput screening (HTS) assay was validated with excellent Z′ factor (>0.7), remaining robust for more than 5 h and suitable for screening of large chemical libraries. The HTS assay was validated by performing pilot screens with 2 small collections of compounds enriched in bioactive molecules ( n = 1280 for Lopac™ and 2000 for Spectrum™ library), yielding confirmed hit rates of 0.23% and 0.70%, respectively. As counterscreens, PLA2 and caspase-3 assays were employed to eliminate nonspecific inhibitors. In conclusion, the LC3B-PLA2 reporter assay provides a platform for compound library screening for identification and characterization of Atg4B-specific inhibitors that may be useful as tools for interrogating the role of autophagy in disease models.

Inhibition of Bfl-1 with N-aryl maleimides

High-throughput screening of 66,000 compounds using competitive binding of peptides comprising the BH3 domain to anti-apoptotic Bfl-1 led to the identification of 14 validated 'hits' as inhibitors of Bfl-1. N-Aryl maleimide 1 was among the validated 'hits'. A chemical library encompassing over 280 analogs of 1 was prepared following a two-step synthesis. Structure-activity studies for inhibition of Bfl-1 by analogs of N-aryl maleimide 1 revealed a preference for electron-withdrawing substituents in the N-aryl ring and hydrophilic amines appended to the maleimide core. Inhibitors of Bfl-1 are potential development candidates for anti-cancer therapeutics.

Synthesis and biological evaluation of Apogossypolone derivatives as pan-active inhibitors of antiapoptotic B-cell lymphoma/leukemia-2 (Bcl-2) family proteins

Overexpression of antiapoptotic Bcl-2 family proteins is commonly related with tumor maintenance, progression, and chemoresistance. Inhibition of these antiapoptotic proteins is an attractive approach for cancer therapy. Guided by nuclear magnetic resonance (NMR) binding assays, a series of 5,5' substituted compound 6a (Apogossypolone) derivatives was synthesized and identified pan-active antagonists of antiapoptotic Bcl-2 family proteins, with binding potency in the low micromolar to nanomolar range. Compound 6f inhibits the binding of BH3 peptides to Bcl-X(L), Bcl-2, and Mcl-1 with IC(50) values of 3.10, 3.12, and 2.05 μM, respectively. In a cellular assay, 6f potently inhibits cell growth in several human cancer cell lines in a dose-dependent manner. Compound 6f further displays in vivo efficacy in transgenic mice and demonstrated superior single-agent antitumor efficacy in a PPC-1 mouse xenograft model. Together with its negligible toxicity, compound 6f represents a promising drug lead for the development of novel apoptosis-based therapies for cancer.

Synthetic substrates for measuring activity of autophagy proteases: autophagins (Atg4)

Atg4 cysteine proteases (autophagins) play crucial roles in autophagy by proteolytic activation of Atg8 paralogs for targeting to autophagic vesicles by lipid conjugation, as well as in subsequent deconjugation reactions. However, the means to measure the activity of autophagins is limited. Herein, we describe two novel substrates for autophagins suitable for a diversity of in vitro assays, including (i) fluorogenic tetrapeptide acetyl-Gly-L-Thr-L-Phe-Gly-AFC (Ac-GTFG-AFC) and (ii) a fusion protein comprised of the natural substrate LC3B appended to the N-terminus of phospholipase A(2) (LC3B-PLA(2)), which upon cleavage releases active PLA(2) for fluorogenic assay. To generate the synthetic tetrapeptide substrate, the preferred tetrapeptide sequence recognized by autophagin-1/Atg4B was determined using a positional scanning combinatorial fluorogenic tetrapeptide library. With the LC3B-PLA(2) substrate, we show that mutation of the glycine proximal to the scissile bond in LC3B abolishes activity. Both substrates showed high specificity for recombinant purified autophagin-1/Atg4B compared to closely related proteases and the LC3B-PLA(2) substrate afforded substantially higher catalytic rates (k(cat)/K(m) 5.26 x 10(5) M(-1)/sec(-1)) than Ac-GTFG-AFC peptide (0.92 M(-1)/sec(-1)), consistent with substrate-induced activation. Studies of autophagin-1 mutants were also performed, including the protease lacking a predicted autoinhibitory domain at residues 1 to 24 and lacking a regulatory loop at residues 259 to 262. The peptide and fusion protein substrates were also employed for measuring autophagin activity in cell lysates, showing a decrease in cells treated with autophagin-1/Atg4B siRNA or transfected with a plasmid encoding Atg4B (Cys74Ala) dominantnegative. Therefore, the synthetic substrates for autophagins reported here provide new research tools for studying autophagy.

BI-97C1, an optically pure Apogossypol derivative as pan-active inhibitor of antiapoptotic B-cell lymphoma/leukemia-2 (Bcl-2) family proteins

In our continued attempts to identify novel and effective pan-Bcl-2 antagonists, we have recently reported a series of compound 2 (Apogossypol) derivatives, resulting in the chiral compound 4 (8r). We report here the synthesis and evaluation on its optically pure individual isomers. Compound 11 (BI-97C1), the most potent diastereoisomer of compound 4, inhibits the binding of BH3 peptides to Bcl-X(L), Bcl-2, Mcl-1, and Bfl-1 with IC(50) values of 0.31, 0.32, 0.20, and 0.62 microM, respectively. The compound also potently inhibits cell growth of human prostate cancer, lung cancer, and lymphoma cell lines with EC(50) values of 0.13, 0.56, and 0.049 microM, respectively, and shows little cytotoxicity against bax(-/-)bak(-/-) cells. Compound 11 displays in vivo efficacy in transgenic mice models and also demonstrated superior single-agent antitumor efficacy in a prostate cancer mouse xenograft model. Therefore, compound 11 represents a potential drug lead for the development of novel apoptosis-based therapies against cancer.

Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention

The 14 kDa homodimeric N1L protein is a potent vaccinia and variola (smallpox) virulence factor. It is not essential for viral replication, but it causes a strong attenuation of viral production in culture when deleted. The N1L protein is predicted to contain the BH3-like binding domain characteristic of Bcl-2 family proteins, and it is able to bind the BH3 peptides. Its overexpression has been reported to prevent infected cells from committing apoptosis. Therefore, interfering with the N1L apoptotic blockade may be a legitimate therapeutic strategy affecting the viral growth. By using in silico ligand docking and an array of in vitro assays, we have identified submicromolar (600 nM) N1L antagonists belonging to the family of polyphenols. Their affinity is comparable to that of the BH3 peptides (70-1000 nM). We have also identified the natural polyphenol resveratrol as a moderate N1L inhibitor. Finally, we show that our ligands efficiently inhibit growth of vaccinia virus.

A survey of the anti-apoptotic Bcl-2 subfamily expression in cancer types provides a platform to predict the efficacy of Bcl-2 antagonists in cancer therapy

We investigated the mRNA expression levels of all six antiapoptotic Bcl-2 subfamily members in 68 human cancer cell lines using qPCR techniques and measured the ability of known Bcl-2 inhibitors to induce cell death in 36 of the studied tumor cell lines. Our study reveals that Mcl-1 represents the anti-apoptotic Bcl-2 subfamily member with the highest mRNA levels in the lung, prostate, breast, ovarian, renal, and glioma cancer cell lines. In leukemia/lymphoma and melanoma cancer cell lines, Bcl-2 and Bfl-1 had the highest levels of mRNA, respectively. The observed correlation between the cell killing properties of known Bcl-2 inhibitors and the relative mRNA expression levels of anti-apoptotic Bcl-2 proteins provide critical insights into apoptosis-based anticancer strategies that target Bcl-2 proteins. Our data may explain current challenges of selective Bcl-2 inhibitors in the clinic, given that severe expression of Bcl-2 seems to be limited to leukemia cell lines. Furthermore, our data suggest that in most cancer types a strategy targeted to Mcl-1 inhibition, or combination of Bfl-1 and Mcl-1 inhibition for melanoma, may prove to be more successful than therapies targeting only Bcl-2.

Vaccinia virus protein F1L is a caspase-9 inhibitor

Apoptosis plays important roles in host defense, including the elimination of virus-infected cells. The executioners of apoptosis are caspase family proteases. We report that vaccinia virus-encoded F1L protein, previously recognized as anti-apoptotic viral Bcl-2 family protein, is a caspase-9 inhibitor. F1L binds to and specifically inhibits caspase-9, the apical protease in the mitochondrial cell death pathway while failing to inhibit other caspases. In cells, F1L inhibits apoptosis and proteolytic processing of caspases induced by overexpression of caspase-9 but not caspase-8. An N-terminal region of F1L preceding the Bcl-2-like fold accounts for caspase-9 inhibition and significantly contributes to the anti-apoptotic activity of F1L. Viral F1L thus provides the first example of caspase inhibition by a Bcl-2 family member; it functions both as a suppressor of proapoptotic Bcl-2 family proteins and as an inhibitor of caspase-9, thereby neutralizing two sequential steps in the mitochondrial cell death pathway.

Apogossypol derivatives as pan-active inhibitors of antiapoptotic B-cell lymphoma/leukemia-2 (Bcl-2) family proteins

Guided by nuclear magnetic resonance (NMR) binding assays and computational docking studies, a series of 5,5' substituted apogossypol derivatives was synthesized that resulted in potent pan-active inhibitors of antiapoptotic Bcl-2 family proteins. Compound 8r inhibits the binding of BH3 peptides to Bcl-X(L), Bcl-2, Mcl-1, and Bfl-1 with IC(50) values of 0.76, 0.32, 0.28, and 0.73 microM, respectively. The compound also potently inhibits cell growth of human lung cancer and BP3 human B-cell lymphoma cell lines with EC(50) values of 0.33 and 0.66 microM, respectively. Compound 8r shows little cytotoxicity against bax(-/-)bak(-/-) cells, indicating that it kills cancers cells via the intended mechanism. The compound also displays in vivo efficacy in transgenic mice in which Bcl-2 is overexpressed in splenic B-cells. Together with its improved chemical, plasma, and microsomal stability relative to compound 2 (apogossypol), compound 8r represents a promising drug lead for the development of novel apoptosis-based therapies for cancer.

Apogossypol derivatives as antagonists of antiapoptotic Bcl-2 family proteins

Guided by a combination of nuclear magnetic resonance binding assays and computational docking studies, we synthesized a library of 5,5' substituted Apogossypol derivatives as potent Bcl-XL antagonists. Each compound was subsequently tested for its ability to inhibit Bcl-XL in an in vitro fluorescence polarization competition assay and exert single-agent proapoptotic activity in human cancer cell lines. The most potent compound BI79D10 binds to Bcl-XL, Bcl-2, and Mcl-1 with IC50 values of 190, 360, and 520 nmol/L, respectively, and potently inhibits cell growth in the H460 human lung cancer cell line with an EC50 value of 680 nmol/L, expressing high levels of Bcl-2. BI79D10 also effectively induces apoptosis of the RS11846 human lymphoma cell line in a dose-dependent manner and shows little cytotoxicity against bax-/-bak-/- mouse embryonic fibroblast cells, in which antiapoptotic Bcl-2 family proteins lack a cytoprotective phenotype, implying that BI79D10 has little off-target effects. BI79D10 displays in vivo efficacy in transgenic mice, in which Bcl-2 is overexpressed in splenic B cells. Together with its improved plasma and microsomal stability relative to Apogossypol, BI79D10 represents a lead compound for the development of novel apoptosis-based therapies for cancer.