Brain pharmacokinetics and metabolism of the AMP-activated protein kinase selective inhibitor SBI-0206965, an investigational agent for the treatment of glioblastoma

PURPOSE

Emerging evidence suggests that 5' Adenosine Monophosphate-Activated Protein Kinase (AMPK), a key regulator of cellular bioenergetics, is a novel target for the treatment of glioblastoma (GBM), a lethal brain tumor. SBI-0206965, an aminopyrimidine derivative, is a potent AMPK inhibitor being investigated for the treatment of GBM. Here we characterized the systemic and brain pharmacokinetics (PK) and hepatic metabolism of SBI-0206965.

METHODS

We performed intracerebral microdialysis to determine brain partitioning of SBI-0206965 in jugular vein cannulated rats. We assessed systemic PK of SBI-0206965 in rats and C57BL/6 mice following oral administration. Employing human, mouse, and rat liver microsomes we characterized the metabolism of SBI-0206965.

RESULTS

SBI-0206965 is quickly absorbed, achieving plasma and brain extracellular fluid (ECF) peak levels within 0.25 - 0.65 h. Based on the ratio of C_max and AUC in brain ECF to plasma (corrected for protein binding), brain partitioning is ~ 0.6-0.9 in rats. However, the compound has a short elimination half-life (1-2 h) and low relative oral bioavailability (~ 0.15). The estimated in-vitro hepatic intrinsic clearance of SBI-0206965 in mouse, rat and human was 325, 76 and 68 mL/min/kg, respectively. SBI-0206965 metabolites included desmethylated products, and the metabolism was strongly inhibited by ketoconazole, a CYP3A inhibitor.

CONCLUSION

SBI-0206965 has adequate brain permeability but low relative oral bioavailability which may be due to rapid hepatic metabolism, likely catalyzed by CYP3A enzymes. Our observations will facilitate further development of SBI-0206965, and/or other structurally related molecules, for the treatment of GBM and other brain tumors.

Inhibition of perforin enhances T cell and humoral responses after immunization

Cytotoxic lymphocytes such as natural killer (NK) cells release perforin to form pores on plasma membrane of target cells to allow delivery of granzymes that induce apoptosis. We previously showed that NK cells exert a perforin-dependent suppression of follicular helper CD4 T cell and germinal center B cell responses following infection and immunization. Consistent with this activity, genetic ablation of either perforin or NK cells non-additively enhanced the quality and magnitude of humoral immune responses. Therefore, we hypothesize that transient inhibition of perforin represents an innovative means to enhance vaccine efficacy to prevent viral infections such as HIV. Intraperitoneal injection of a selective inhibitor of perforin (35mg/kg) to mice reduced killing activity of NK cells by >50%. A single injection of this inhibitor to mice during alum adjuvanted NP-KLH immunization resulted in a greater than two-fold enhancement of follicular helper CD4 T cell, germinal center B cell, and antigen-specific antibody responses. In summary, transient inhibition of pore-forming protein perforin can block NK-cell immunosuppression to enhance vaccine-elicited T and B cell responses.

National Institute of Heath (NIH) (R01-AI148080)

Inhibition of the RacGEF VAV3 by the small molecule IODVA1 impedes RAC signaling and overcomes resistance to tyrosine kinase inhibition in acute lymphoblastic leukemia

Aberrant RHO guanine nucleotide exchange factor (RhoGEF) activation is chief mechanism driving abnormal activation of their GTPase targets in transformation and tumorigenesis. Consequently, a small-molecule inhibitor of RhoGEF can make an anti-cancer drug. We used cellular, mouse, and humanized models of RAC-dependent BCR-ABL1-driven and Ph-like acute lymphoblastic leukemia to identify VAV3, a tyrosine phosphorylation-dependent RacGEF, as the target of the small molecule IODVA1. We show that through binding to VAV3, IODVA1 inhibits RAC activation and signaling and increases pro-apoptotic activity in BCR-ABL1-transformed cells. Consistent with this mechanism of action, cellular and animal models of BCR-ABL1-induced leukemia in Vav3-null background do not respond to IODVA1. By durably decreasing in vivo RAC signaling, IODVA1 eradicates leukemic propagating activity of TKI-resistant BCR-ABL1(T315I) B-ALL cells after treatment withdrawal. Importantly, IODVA1 suppresses the leukemic burden in the treatment refractory pediatric Ph+ and TKI-resistant Ph+ B-ALL patient-derived xenograft models better than standard-of-care dasatinib or ponatinib and provides a more durable response after treatment withdrawal. Pediatric leukemia samples with diverse genetic lesions show high sensitivity to IODVA1 ex vivo and this sensitivity is VAV3 dependent. IODVA1 thus spearheads a novel class of drugs that inhibits a RacGEF and holds promise as an anti-tumor therapy.

EXTH-52. SYSTEMIC AND BRAIN PHARMACOKINETICS OF THE AMP-ACTIVATED PROTEIN KINASE SELECTIVE INHIBITOR SBI-0206965 AS A POTENTIAL THERAPEUTIC AGENT FOR THE TREATMENT OF GLIOBLASTOMA MULTIFORME

PURPOSE

AMP-activated protein kinase (AMPK) is a molecular hub for cellular metabolic control. Recent evidence suggests that AMPK is a “druggable” novel target for the treatment of Glioblastoma Multiforme (GBM). However, AMPK-inhibitory compounds are largely limited to compound C, which has a poor selectivity profile. SBI-0206965 is a diaminopyrimidine derivative that directly inhibits AMPK with 40-fold greater potency and markedly lower kinase promiscuity than compound C. The current studies provide insights into systemic pharmacokinetics and plasma to brain partitioning of SBI-0206965.

METHODS

We conducted an intracerebral microdialysis study employing jugular vein-cannulated Sprague Dawley rats (males, 6- 8 weeks). Serial brain extracellular fluid (ECF) and venous blood samples were collected up to 10 hrs following intraperitoneal administration of SBI-0206965 (25 mg/kg). These samples were then quantitated for SBI-0206965 levels using a LC/MS method (Thermo Scientific LTQ-FT™, Ionization: Electrospray Ionization; positive ion). PK analysis was performed using the Non–Compartmental Analysis (Phoenix® WinNonlin 8.2 Certara USA, Inc.).

RESULTS

Plasma and ECF peak concentrations (Cmax) were 7.15 µM and 0.68 µM, whereas the time to peak (Tmax) were 0.5 and 1 hr, respectively. The plasma and brain ECF elimination half-lives were 1.5 and 3 hours, respectively. Plasma protein binding of SBI-0206965 was 82%. A comparison of the brain ECF Cmax and area under the curve (AUC) to corresponding plasma values suggested that the brain partitioning of the compound was 10-18%. When corrected for unbound fraction in plasma the AUC ratio was 0.86. Thus, these studies show that SBI-0206965 has adequate brain penetration. Further studies are now in progress to assess selectivity of SBI-0206965 for AMPK expressing cell lines, efficacy against patient-derived GBM and PK in tumor-bearing mice.

CONCLUSION

Results from this study will help to design optimal dosing regimen of SBI-0206965 in our efforts to explore AMPK as a GBM-specific drug target.

Abstract LB198: Inhibition of the RAC Activator VAV3 by the small molecule IODVA1 impedes RAC signaling & overcomes resistance to tyrosine kinase inhibition in lymphoblastic leukemia

Aberrant activation of RHO guanine nucleotide exchange factors (RhoGEFs) is a chief mechanism driving abnormal activation of their RhoGTPase targets in transformation and tumorigenesis. Consequently, a small molecule inhibitor of RhoGEF activities can be used as an anti-cancer drug. Herein, we used cellular, mouse, and humanized models of RAC-dependent BCR-ABL1-driven and Ph-like lymphoblastic leukemia to identify VAV3, a tyrosine phosphorylation-dependent RacGEF, as the target of the small molecule IODVA1. We show that IODVA1 binds tightly to VAV3, inhibits RAC activation and signaling, and increases pro-apoptotic activity in BCR-ABL1-transformed cells only. Consistent with this mechanism of action, both VAV3-deficient leukemic cells and mouse models of BCR-ABL1 leukemia do not respond to IODVA1. IODVA1 eradicates leukemic propagating activity of TKI-resistant BCR-ABL1(T315I) B-ALL cells after treatment withdrawal by decreasing RAC signaling in vivo. Importantly, IODVA1 is superior to standard of care dasatinib and ponatinib at prolonging the survival of PDX models of relapsed pediatric Ph+ and TKI-resistant Ph+ B-ALL with commonly found genetic mutations especially after treatment withdrawal. Cells representing pediatric ALL patients with diverse genetic lesions are highly sensitive to IODVA1 ex vivo and this sensitivity is VAV3-dependent. IODVA1 thus spearheads a novel class of drugs that inhibits a RacGEF and holds promise as an anti-tumor therapeutic agent.

Citation Format: Nicolas N. Nassar, Shailaja Hegde, Kark Wunderlich, Yuan Lin, Reza Ahmadian, William Seibel, Yi Zheng, Benjamin E. Mizukawa, Lisa Privette Vinnedge, Jose A. Cancelas. Inhibition of the RAC Activator VAV3 by the small molecule IODVA1 impedes RAC signaling & overcomes resistance to tyrosine kinase inhibition in lymphoblastic leukemia [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 LB198.

Deep learning to identify and predict cardiotoxicities of anticancer drugs

e15012

Background: Recent advances in cancer treatment have revolutionized patient outcomes. However, toxicities associated with anti-cancer drugs remain a concern with many anti-cancer drugs now implicated in cardiotoxicity. The complete spectrum of cardiotoxicity associated with anti-cancer drugs is only evident post-approval of drugs. Deep Learning methods can identify novel and emerging safety signals in “real-world” clinical settings. Methods: We used AERS Mine, an open-source data mining platform to identify drug toxicity signatures in the FDA’s Adverse Event Reporting System of 16 million patients. We identified 1.3 million patients on traditional and targeted anti-cancer therapy to analyze therapy-specific cardiotoxicity patterns. Cardiotoxicity training dataset contained 1571 molecules characterized with bioassay against hERG potassium channel and included 350 toxic compounds with an IC50 of < 1μM. We implemented a Deep Belief Network to extract a deep hierarchical representation of the training data, and the Extra Tree Classifier to predict the toxicity of drug candidates. Drugs were encoded using 1024-bit Morgan fingerprint representation using SMILES with search radius of 7 atoms. Pharmacovigilance metrics (Relative Risks and safety signals) were used to establish statistical correlation. Results: This analysis identified signatures of arrhythmias and conduction abnormalities associated with common anti-cancer drugs (e.g. atrial fibrillation with ibrutinib, alkylating agents, immunomodulatory drugs; sinus bradycardia with 5FU, paclitaxel, thalidomide; sinus tachycardia with anthracyclines). Our analysis also identified myositis/myocarditis association with newer immune checkpoint inhibitors (e.g., atezolizumab, durvalumab, cemiplimab, avelumab) paralleling earlier signals for pembrolizumab, nivolumab, and ipilimumab. Deep Learning identified signatures of chemical moieties linked to cardiotoxicity, including common motifs in drugs associated with arrhythmias and conduction abnormalities with an accuracy of 89%. Conclusions: Deep Learning provides a comprehensive insight into emerging cardiotoxicity patterns of approved and investigational drugs, allows detection of ‘rogue’ chemical moieties, and shows promise for novel drug discovery and development.

Pharmacological clearance of misfolded rhodopsin for the treatment of RHO-associated retinitis pigmentosa

Rhodopsin mutation and misfolding is a common cause of autosomal dominant retinitis pigmentosa (RP). Using a luciferase reporter assay, we undertook a small-molecule high-throughput screening (HTS) of 68, 979 compounds and identified nine compounds that selectively reduced the misfolded P23H rhodopsin without an effect on the wild type (WT) rhodopsin protein. Further, we found five of these compounds, including methotrexate (MTX), promoted P23H rhodopsin degradation that also cleared out other misfolded rhodopsin mutant proteins. We showed MTX increased P23H rhodopsin degradation via the lysosomal but not the proteasomal pathway. Importantly, one intravitreal injection (IVI) of 25 pmol MTX increased electroretinogram (ERG) response and rhodopsin level in the retinae of Rho^P23H/+ knock-in mice at 1 month of age. Additionally, four weekly IVIs increased the photoreceptor cell number in the retinae of Rho^P23H/+ mice compared to vehicle control. Our study indicates a therapeutic potential of repurposing MTX for the treatment of rhodopsin-associated RP.

Diverse Chemical Scaffolds Enhance Oligodendrocyte Formation by Inhibiting CYP51, TM7SF2, or EBP

Small molecules that promote oligodendrocyte formation have been identified in "drug repurposing" screens to nominate candidate therapeutics for diseases in which myelin is lost, including multiple sclerosis. We recently reported that many such molecules enhance oligodendrocyte formation not by their canonical targets but by inhibiting a narrow range of enzymes in cholesterol biosynthesis. Here we identify enhancers of oligodendrocyte formation obtained by screening a structurally diverse library of 10,000 small molecules. Identification of the cellular targets of these validated hits revealed a majority inhibited the cholesterol biosynthesis enzymes CYP51, TM7SF2, or EBP. In addition, evaluation of analogs led to identification of CW3388, a potent EBP-inhibiting enhancer of oligodendrocyte formation poised for further optimization.

A novel small molecule chaperone of rod opsin and its potential therapy for retinal degeneration

Rhodopsin homeostasis is tightly coupled to rod photoreceptor cell survival and vision. Mutations resulting in the misfolding of rhodopsin can lead to autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration that currently is untreatable. Using a cell-based high-throughput screen (HTS) to identify small molecules that can stabilize the P23H-opsin mutant, which causes most cases of adRP, we identified a novel pharmacological chaperone of rod photoreceptor opsin, YC-001. As a non-retinoid molecule, YC-001 demonstrates micromolar potency and efficacy greater than 9-cis-retinal with lower cytotoxicity. YC-001 binds to bovine rod opsin with an EC50 similar to 9-cis-retinal. The chaperone activity of YC-001 is evidenced by its ability to rescue the transport of multiple rod opsin mutants in mammalian cells. YC-001 is also an inverse agonist that non-competitively antagonizes rod opsin signaling. Significantly, a single dose of YC-001 protects Abca4 -/- Rdh8 -/- mice from bright light-induced retinal degeneration, suggesting its broad therapeutic potential.

Exploiting mitochondrial and metabolic homeostasis as a vulnerability in NF1 deficient cells

Neurofibromatosis type 1 is a disease caused by mutation of neurofibromin 1 (NF1), loss of which results in hyperactive Ras signaling and a concomitant increase in cell proliferation and survival. Patients with neurofibromatosis type 1 frequently develop tumors such as plexiform neurofibromas and malignant peripheral nerve sheath tumors. Mutation of NF1 or loss of the NF1 protein is also observed in glioblastoma, lung adenocarcinoma, and ovarian cancer among other sporadic cancers. A therapy that selectively targets NF1 deficient tumors would substantially advance our ability to treat these malignancies. To address the need for these therapeutics, we developed and conducted a synthetic lethality screen to discover molecules that target yeast lacking the homolog of NF1, IRA2. One of the lead candidates that was observed to be synthetic lethal with ira2Δ yeast is Y100. Here, we describe the mechanisms by which Y100 targets ira2Δ yeast and NF1-deficient tumor cells. Y100 treatment disrupted proteostasis, metabolic homeostasis, and induced the formation of mitochondrial superoxide in NF1-deficient cancer cells. Previous studies also indicate that NF1/Ras-dysregulated tumors may be sensitive to modulators of oxidative and ER stress. We hypothesize that the use of Y100 and molecules with related mechanisms of action represent a feasible therapeutic strategy for targeting NF1 deficient cells.

Compound C/Dorsomorphin: Its Use and Misuse as an AMPK Inhibitor

The evolutionary conserved energy sensor AMPK plays crucial roles in many biological processes-both during normal development and pathology. Loss-of-function genetic studies in mice as well as in lower organisms underscore its importance in embryonic development, stress physiology in the adult, and in key metabolic disorders including cardiovascular disease, diabetes, cancer, and metabolic syndrome. In contrast to several other kinases important in human health and medicine where specific/selective inhibitors are available, no AMPK-specific inhibitors are available. The only reagent called dorsomorphin or compound C that is occasionally used as an AMPK inhibitor unfortunately inhibits several other kinases much more potently than AMPK and is therefore highly non-specific. In this chapter, we discuss the pros and cons of using this reagent to study AMPK functions.

Targeted inhibition of STAT/TET1 axis as a therapeutic strategy for acute myeloid leukemia

Effective therapy of acute myeloid leukemia (AML) remains an unmet need. DNA methylcytosine dioxygenase Ten-eleven translocation 1 (TET1) is a critical oncoprotein in AML. Through a series of data analysis and drug screening, we identified two compounds (i.e., NSC-311068 and NSC-370284) that selectively suppress TET1 transcription and 5-hydroxymethylcytosine (5hmC) modification, and effectively inhibit cell viability in AML with high expression of TET1 (i.e., TET1-high AML), including AML carrying t(11q23)/MLL-rearrangements and t(8;21) AML. NSC-311068 and especially NSC-370284 significantly repressed TET1-high AML progression in vivo. UC-514321, a structural analog of NSC-370284, exhibited a more potent therapeutic effect and prolonged the median survival of TET1-high AML mice over three fold. NSC-370284 and UC-514321 both directly target STAT3/5, transcriptional activators of TET1, and thus repress TET1 expression. They also exhibit strong synergistic effects with standard chemotherapy. Our results highlight the therapeutic potential of targeting the STAT/TET1 axis by selective inhibitors in AML treatment.

Ten-eleven translocation 1 (TET1) is a critical oncoprotein in AML. Here, the authors identify 2 compounds that target the binding of STAT3/5 specifically to the TET1 promoter, inhibiting its expression and AML cell viability.

Identification of Novel Bisbenzimidazole Derivatives as Anticancer Vacuolar (H⁺)-ATPase Inhibitors

The vacuolar (H⁺)-ATPases (V-ATPases) are a family of ATP-driven proton pumps and they have been associated with cancer invasion, metastasis, and drug resistance. Despite the clear involvement of V-ATPases in cancer, the therapeutic use of V-ATPase-targeting small molecules has not reached human clinical trials to date. Thus, V-ATPases are emerging as important targets for the identification of potential novel therapeutic agents. We identified a bisbenzimidazole derivative (V) as an initial hit from a similarity search using four known V-ATPase inhibitors (I–IV). Based on the initial hit (V), we designed and synthesized a focused set of novel bisbenzimidazole analogs (2a–e). All newly prepared compounds have been screened for selected human breast cancer (MDA-MB-468, MDA-MB-231, and MCF7) and ovarian cancer (A2780, Cis-A2780, and PA-1) cell lines, along with the normal breast epithelial cell line, MCF10A. The bisbenzimidazole derivative (2e) is active against all cell lines tested. Remarkably, it demonstrated high cytotoxicity against the triple-negative breast cancer (TNBC) cell line, MDA-MB-468 (IC₅₀ = 0.04 ± 0.02 μM). Additionally, it has been shown to inhibit the V-ATPase pump that is mainly responsible for acidification. To the best of our knowledge the bisbenzimidazole pharmacophore has been identified as the first V-ATPase inhibitor in its class. These results strongly suggest that the compound 2e could be further developed as a potential anticancer V-ATPase inhibitor for breast cancer treatment.

A High-Throughput Drug Screening Strategy for Detecting Rhodopsin P23H Mutant Rescue and Degradation

PURPOSE

Inherent instability of the P23H mutant opsin accounts for approximately 10% of autosomal dominant retinitis pigmentosa cases. Our purpose was to develop an overall set of reliable screening strategies to assess if either stabilization or enhanced degradation of mutant rhodopsin could rescue rod photoreceptors expressing this mutant protein. These strategies promise to reveal active compounds and clarify molecular mechanisms of biologically important processes, such as inhibition of target degradation or enhanced target folding.

METHODS

Cell-based bioluminescence reporter assays were developed and validated for high-throughput screening (HTS) of compounds that promote either stabilization or degradation of P23H mutant opsin. Such assays were further complemented by immunoblotting and image-based analyses.

RESULTS

Two stabilization assays of P23H mutant opsin were developed and validated, one based on β-galactosidase complementarity and a second assay involving bioluminescence resonance energy transfer (BRET) technology. Moreover, two additional assays evaluating mutant protein degradation also were employed, one based on the disappearance of luminescence and another employing the ALPHA immunoassay. Imaging of cells revealed the cellular localization of mutant rhodopsin, whereas immunoblots identified changes in the aggregation and glycosylation of P23H mutant opsin.

CONCLUSIONS

Our findings indicate that these initial HTS and following assays can identify active therapeutic compounds, even for difficult targets such as mutant rhodopsin. The assays are readily scalable and their function has been proven with model compounds. High-throughput screening, supported by automated imaging and classic immunoassays, can further characterize multiple steps and pathways in the biosynthesis and degradation of this essential visual system protein.

Expansion of first-in-class drug candidates that sequester toxic all-trans-retinal and prevent light-induced retinal degeneration

All-trans-retinal, a retinoid metabolite naturally produced upon photoreceptor light activation, is cytotoxic when present at elevated levels in the retina. To lower its toxicity, two experimentally validated methods have been developed involving inhibition of the retinoid cycle and sequestration of excess of all-trans-retinal by drugs containing a primary amine group. We identified the first-in-class drug candidates that transiently sequester this metabolite or slow down its production by inhibiting regeneration of the visual chromophore, 11-cis-retinal. Two enzymes are critical for retinoid recycling in the eye. Lecithin:retinol acyltransferase (LRAT) is the enzyme that traps vitamin A (all-trans-retinol) from the circulation and photoreceptor cells to produce the esterified substrate for retinoid isomerase (RPE65), which converts all-trans-retinyl ester into 11-cis-retinol. Here we investigated retinylamine and its derivatives to assess their inhibitor/substrate specificities for RPE65 and LRAT, mechanisms of action, potency, retention in the eye, and protection against acute light-induced retinal degeneration in mice. We correlated levels of visual cycle inhibition with retinal protective effects and outlined chemical boundaries for LRAT substrates and RPE65 inhibitors to obtain critical insights into therapeutic properties needed for retinal preservation.

Abstract LB-10: Rational design of small molecules targeting the Ras GEF, SOS1

Ras GTPases regulate multiple intracellular signaling processes involved in gene expression, cell proliferation, and cell survival. Driver mutations of Ras signaling components including K,N,H-Ras, EGFR, PDGFR, Raf, PI3K, and Akt have been found in many types of human cancers. The activation of Ras is catalyzed by guanine-nucleotide exchange factors (GEFs), which stimulate the exchange of GDP for GTP. SOS1 is a major RasGEF that transduces receptor tyrosine kinase signals to Ras and associated ERK/Akt pathways. SOS1 gain-of-function mutations have been found in Noonan syndrome patients. In addition, SOS1 has been shown to be differentially expressed in prostate and breast cancer cells, and is involved in malignancies dependent upon aberrant Ras signaling. In the current studies, we undertake a structure-based virtual screening approach, coupled with biochemical and cell biological validations, to identify lead chemical inhibitors targeting the Ras catalytic domain of SOS1. From a 118,500 compound subset of the NCI/DTP Open Chemical Repository, 135 showed optimal docking energy to a grid of the SOS1 catalytic site from which 36 were selected for experimental screening by a guanine nucleotide exchange assay, i.e. FL-GDP dissociation of Ras under the catalysis of SOS1. Two compounds were confirmed as true hits (NSC-674954 and NSC-658497), of which NSC-658497 displayed micromolar IC50s in both inhibiting FL-GDP dissociation (IC50 - 22.2 µM) from Ras and TR-GTP loading (IC50 - 40.8 µM) of Ras catalyzed by Sos1. In addition, NSC-658497 displayed a target binding Kd of ∼7.0 µM as assayed by microscale thermophoresis, along with dose-dependently disrupting the SOS1 interaction with Ras as assayed by a GST-Ras pull-down analysis. Mutagenesis studies mapped NSC-658497 action site to the catalytic site in SOS1, involving specifically residues I825, T828, T829, and Y912. SAR analysis revealed that NSC-658497 elicits its inhibitory effect on SOS1 through a benzopyran and nitrophenyl moiety. In fibroblast cells, NSC-658497 showed dose-dependent efficacy in inhibiting EGF-stimulated Ras and ERK/AKT activities. Furthermore, NSC-658497 dose-dependently inhibited NIH/3T3, MEF, and MIA-PaCa-2 pancreatic cancer cell proliferation in conjunction with their respective downstream Ras-dependent ERK/AKT activities. Thus, we have identified a class of lead chemical inhibitors targeting SOS1 that can serve as useful tools for studying SOS1 mediated oncogenesis and as hits for further development of future cancer therapeutics.

Citation Format: Chris Evelyn, Xin Duan, Jacek Biesiada, William Seibel, Jaroslaw Meller, Yi Zheng. Rational design of small molecules targeting the Ras GEF, SOS1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-10. doi:10.1158/1538-7445.AM2014-LB-10

Identification and characterization of novel inhibitors of Mammalian aspartyl aminopeptidase

Aspartyl aminopeptidase (DNPEP) has been implicated in the control of angiotensin signaling and endosome trafficking, but its precise biologic roles remain incompletely defined. We performed a high-throughput screen of ∼25,000 small molecules to identify inhibitors of DNPEP for use as tools to study its biologic functions. Twenty-three confirmed hits inhibited DNPEP-catalyzed hydrolysis of angiotensin II with micromolar potency. A counter screen against glutamyl aminopeptidase (ENPEP), an enzyme with substrate specificity similar to that of DNPEP, identified eight DNPEP-selective inhibitors. Structure-activity relationships and modeling studies revealed structural features common to the identified inhibitors, including a metal-chelating group and a charged or polar moiety that could interact with portions of the enzyme active site. The compounds identified in this study should be valuable tools for elucidating DNPEP physiology.

Discovery of a novel class of potent HCV NS4B inhibitors: SAR studies on piperazinone derivatives

HTS screening identified compound 2a (piperazinone derivative) as a low micromolar HCV genotype 1 (GT-1) inhibitor. Resistance mapping studies suggested that this piperazinone chemotype targets the HCV nonstructural protein NS4B. Extensive SAR studies were performed around 2a and the amide function and the C-3/C-6 cis stereochemistry of the piperazinone core were essential for HCV activity. A 10-fold increase in GT-1 potency was observed when the chiral phenylcyclopropyl amide side chain of 2a was replaced with p-fluorophenylisoxazole-carbonyl moiety (67). Replacing the C-6 nonpolar hydrophobic moiety of 67 with a phenyl moiety (95) did not diminish the GT-1 potency. A heterocyclic thiophene moiety (103) and an isoxazole moiety (108) were incorporated as isosteric replacements for the C-6 phenyl moiety (95), resulting in significant improvement in GT-1b and 1a potency. However, the piperazonone class of compounds lacks GT-2 activity and, consequently, were not pursued further into development.

Targeting the hydrophobic pocket of autotaxin with virtual screening of inhibitors identifies a common aromatic sulfonamide structural motif

Modulation of autotaxin (ATX), the lysophospholipase D enzyme that produces lysophosphatidic acid, with small-molecule inhibitors is a promising strategy for blocking the ATX-lysophosphatidic acid signaling axis. Although discovery campaigns have been successful in identifying ATX inhibitors, many of the reported inhibitors target the catalytic cleft of ATX. A recent study provided evidence for an additional inhibitory surface in the hydrophobic binding pocket of ATX, confirming prior studies that relied on enzyme kinetics and differential inhibition of substrates varying in size. Multiple hits from previous high-throughput screening for ATX inhibitors were obtained with aromatic sulfonamide derivatives interacting with the hydrophobic pocket. Here, we describe the development of a ligand-based strategy and its application in virtual screening, which yielded novel high-potency inhibitors that target the hydrophobic pocket of ATX. Characterization of the structure-activity relationship of these new inhibitors forms the foundation of a new pharmacophore model of the hydrophobic pocket of ATX.

Inhibition of the growth factor MDK/midkine by a novel small molecule compound to treat non-small cell lung cancer

Midkine (MDK) is a heparin-binding growth factor that is highly expressed in many malignant tumors, including lung cancers. MDK activates the PI3K pathway and induces anti-apoptotic activity, in turn enhancing the survival of tumors. Therefore, the inhibition of MDK is considered a potential strategy for cancer therapy. In the present study, we demonstrate a novel small molecule compound (iMDK) that targets MDK. iMDK inhibited the cell growth of MDK-positive H441 lung adenocarcinoma cells that harbor an oncogenic KRAS mutation and H520 squamous cell lung cancer cells, both of which are types of untreatable lung cancer. However, iMDK did not reduce the cell viability of MDK-negative A549 lung adenocarcinoma cells or normal human lung fibroblast (NHLF) cells indicating its specificity. iMDK suppressed the endogenous expression of MDK but not that of other growth factors such as PTN or VEGF. iMDK suppressed the growth of H441 cells by inhibiting the PI3K pathway and inducing apoptosis. Systemic administration of iMDK significantly inhibited tumor growth in a xenograft mouse model in vivo. Inhibition of MDK with iMDK provides a potential therapeutic approach for the treatment of lung cancers that are driven by MDK.

Hits of a high-throughput screen identify the hydrophobic pocket of autotaxin/lysophospholipase D as an inhibitory surface

Autotaxin (ATX), a lysophospholipase D, plays an important role in cancer invasion, metastasis, tumor progression, tumorigenesis, neuropathic pain, fibrotic diseases, cholestatic pruritus, lymphocyte homing, and thrombotic diseases by producing the lipid mediator lysophosphatidic acid (LPA). A high-throughput screen of ATX inhibition using the lysophosphatidylcholine-like substrate fluorogenic substrate 3 (FS-3) and ∼10,000 compounds from the University of Cincinnati Drug Discovery Center identified several small-molecule inhibitors with IC₅₀ vales ranging from nanomolar to low micromolar. The pharmacology of the three most potent compounds: 918013 (1; 2,4-dichloro-N-(3-fluorophenyl)-5-(4-morpholinylsulfonyl) benzamide), 931126 (2; 4-oxo-4-{2-[(5-phenoxy-1H-indol-2-yl)carbonyl]hydrazino}-N-(4-phenylbutan-2-yl)butanamide), and 966791 (3; N-(2,6-dimethylphenyl)-2-[N-(2-furylmethyl)(4-(1,2,3,4-tetraazolyl)phenyl)carbonylamino]-2-(4-hydroxy-3-methoxyphenyl) acetamide), were further characterized in enzyme, cellular, and whole animal models. Compounds 1 and 2 were competitive inhibitors of ATX-mediated hydrolysis of the lysophospholipase substrate FS-3. In contrast, compound 3 was a competitive inhibitor of both FS-3 and the phosphodiesterase substrate p-nitrophenyl thymidine 5'-monophosphate. Computational docking and mutagenesis suggested that compounds 1 and 2 target the hydrophobic pocket, thereby blocking access to the active site of ATX. The potencies of compounds 1-3 were comparable to each other in each of the assays. All of these compounds significantly reduced invasion of A2058 human melanoma cells in vitro and the colonization of lung metastases by B16-F10 murine melanoma cells in C57BL/6 mice. The compounds had no agonist or antagonist effects on select LPA or sphingosine 1-phosphate receptors, nor did they inhibit nucleotide pyrophosphatase/phosphodiesterase (NPP) enzymes NPP6 and NPP7. These results identify the molecular surface of the hydrophobic pocket of ATX as a target-binding site for inhibitors of enzymatic activity.

High-throughput screening for small-molecule inhibitors of Staphylococcus epidermidis RP62a biofilms

High-throughput screening (HTS) of 42 865 compounds was performed to identify compounds that inhibit formation of or kill Staphylococcus epidermidis RP62a biofilms. Three biological processes were assayed, including (1) growth of planktonic/biofilm bacteria, (2) assessment of metabolically active biofilm bacteria using a resazurin assay, and (3) assessment of biofilm biomass by crystal violet staining. After completing the three tiers (primary screening, hit confirmation, and dose-response curves), 352 compounds (representing ~0.8%) were selected as confirmed hit compounds from the HTS assay. The compounds were divided into groups based on their effectiveness on S. epidermidis biofilm properties. The majority of these affected both inhibition and killing of bacterial biofilm cultures. Only 16 of the confirmed hit compounds that have either an AC50 lower than 10 µM and/or Sconst ≥70 from those processed were selected for further study by confocal laser scanning microscopy (CLSM). The CLSM was used to evaluate the confirmed hit compounds on (1) inhibition of biofilm formation and (2) killing of preexisting S. epidermidis biofilms. Taken together, with further testing (e.g., disease-related conditions), such compounds may have applications as broad antimicrobial/antibiofilm use for prophylactic or therapeutic intervention to combat infections in surgical and intensive care clinics and battlefield settings.

Rational design of small molecule inhibitors targeting the Rac GTPase-p67(phox) signaling axis in inflammation

The NADPH oxidase enzyme complex, NOX2, is responsible for reactive oxygen species production in neutrophils and has been recognized as a key mediator of inflammation. Here, we have performed rational design and in silico screen to identify a small molecule inhibitor, Phox-I1, targeting the interactive site of p67(phox) with Rac GTPase, which is a necessary step of the signaling leading to NOX2 activation. Phox-I1 binds to p67(phox) with a submicromolar affinity and abrogates Rac1 binding and is effective in inhibiting NOX2-mediated superoxide production dose-dependently in human and murine neutrophils without detectable toxicity. Medicinal chemistry characterizations have yielded promising analogs and initial information of the structure-activity relationship of Phox-I1. Our studies suggest the potential utility of Phox-I class inhibitors in NOX2 oxidase inhibition and present an application of rational targeting of a small GTPase-effector interface.

Discovery of a small molecule targeting IRA2 deletion in budding yeast and neurofibromin loss in malignant peripheral nerve sheath tumor cells

Malignant peripheral nerve sheath tumor (MPNST) is a life-threatening complication of neurofibromatosis type 1 (NF1). NF1 is caused by mutation in the gene encoding neurofibromin, a negative regulator of Ras signaling. There are no effective pharmacologic therapies for MPNST. To identify new therapeutic approaches targeting this dangerous malignancy, we developed assays in NF1(+/+) and NF1(-/-) MPNST cell lines and in budding yeast lacking the NF1 homologue IRA2 (ira2Δ). Here, we describe UC1, a small molecule that targets NF1(-/-) cell lines and ira2Δ budding yeast. By using yeast genetics, we identified NAB3 as a high-copy suppressor of UC1 sensitivity. NAB3 encodes an RNA binding protein that associates with the C-terminal domain of RNA Pol II and plays a role in the termination of nonpolyadenylated RNA transcripts. Strains with deletion of IRA2 are sensitive to genetic inactivation of NAB3, suggesting an interaction between Ras signaling and Nab3-dependent transcript termination. This work identifies a lead compound and a possible target pathway for NF1-associated MPNST, and shows a novel model system approach to identify and validate target pathways for cancer cells in which NF1 loss drives tumor formation.

Identifying novel molecular structures for advanced melanoma by ligand-based virtual screening

We recently discovered a new class of thiazole analogs that are highly potent against melanoma cells. To expand the structure-activity relationship study and to explore potential new molecular scaffolds, we performed extensive ligand-based virtual screening against a compound library containing 342,910 small molecules. Two different approaches of virtual screening were carried out using the structure of our lead molecule: (1) connectivity-based search using Scitegic Pipeline Pilot from Accelerys and (2) molecular shape similarity search using Schrodinger software. Using a testing compound library, both approaches can rank similar compounds very high and rank dissimilar compounds very low, thus validating our screening methods. Structures identified from these searches were analyzed, and selected compounds were tested in vitro to assess their activity against melanoma cancer cell lines. Several molecules showed good anticancer activity. While none of the identified compounds showed better activity than our lead compound, they provided important insight into structural modifications for our lead compound and also provided novel platforms on which we can optimize new classes of anticancer compounds. One of the newly synthesized analogs based on this virtual screening has improved potency and selectivity against melanoma.

Theoretical and practical considerations in virtual screening: a beaten field?

In this review, several aspects of virtual screening are presented. Although, docking and scoring have been the most widely employed techniques, ligand-based virtual screening has also gained momentum in recent years. We have classified the docking programs into four categories, based on their underline theories, and accordingly describe the most up-to-date algorithms and newest versions. Similarly, three categories of scoring functions are presented, while their weighting schemes on particular binding terms are discussed. The latter is important, since knowledge of the function can be used to select the ones that could be more appropriate for targets of similar nature. Challenging aspects, such as protein flexibility and practices to select the most appropriate docking/scoring schemes, are also discussed. Finally, a real-life example is presented where a pharmacophore-driven approach combined with a docking exercise were undertaken in an iterative manner to successfully enhance the virtual screening hit rates. In the end, we present our own perspective for best practices in the field based on our experiences.

[The influence of consumer and direction on the quality of agricultural products and nutrition]

The modern consumer is very much interested in healthy food. The reason is that a special group of consumers is focusing more and more attention on health and nutrition problems. Further, there is increased emphasis on education in food science at universities as well as polytechnics. For some years worldwide dietary goals are published with the intention to reduce nutrition-based sickness. For the first time in our nutrition report 1988, clear proposals for optimal nutrition were formulated.

Anatomical study of the position of the mesial roots of mandibular molars

In order to determine the position of the anatomical apex of the mesial roots of the first and second molars, the horizontal distance from the outer surface of the buccal cortical plate to the apex and the vertical distance from the superior border of the neurovascular bundle to the apex were examined in 33 human cadaver mandible halves. The vertical distances were compared with measurements taken from periapical radiographs between the apex of each mesial root and the superior border of the mandibular canal prior to sectioning. The means of the horizontal buccal distances of the second molar were found to be significantly greater than those of the first molar. The means of the vertical distances of the second molar were found to be significantly less than those of the first molar. A high correlation was found between the vertical anatomic and radiographic measurements. In the majority of the sections, the neurovascular bundle was found in the lingual half of the mandible.

Cutaneous papillomatous hyperplasia in cyclosporine-A treated beagles

All twelve Beagle dogs undergoing long-term therapy (26 weeks) with the immunosuppressive drug cyclosporine-A (30 mg/kg), developed cutaneous papillomatous hyperplasia. By week 7 all dogs developed generalized lesions distributed over the entire body. These occurred as irregular, oval, sessile, unpigmented, firm masses. The incidence and severity of the skin lesions varied among dogs and anatomic site, with no correlation to the blood level of cyclosporine. Microscopic analysis revealed that the epidermis formed short papillary folds on broad fibrovascular stalks and was hyperkeratotic and acanthotic. Mild hyperplasia of hair follicles and sebaceous glands was also evident. A mild diffuse infiltrate of lymphocytes and plasma cells was present in the papillary dermis. No histopathologic changes typical of papillomavirus infection were identified, nor were papillomavirus group-specific antigens or viral DNA detected. Other cutaneous side effects included hyperkeratosis of footpads, increased growth of hair and nails, and hyperkeratinization of the haired skin of the prepuce. All cutaneous lesions regressed spontaneously within 8 weeks following termination of cyclosporine administration. The hyperplastic lesions may have resulted from the action of cyclosporine via the T-lymphocyte system. Conversely a direct action of this drug on epithelial cells may have stimulated proliferation and keratinization.

Cyclosporine-induced gingival overgrowth in beagle dogs

Development of gingival overgrowth during daily long-term cyclosporine A treatment was studied in 2-yr-old beagles. Gingival enlargement developed in five of 12 dogs (42%), primarily in the mandibular anterior area. The earliest gingival changes occurred by 3 wk as an increase in the size of the interdental papillae. The lesions progressively became more severe, in some cases obscuring portions of teeth by wk 6. The redundant tissue exhibited an increase in connective tissue components and an inflammatory infiltrate primarily of plasma cells. Severity of the overgrowth varied in responding animals; both incidence and severity were related to the CSA concentration in blood. The mean CSA blood levels of responders were significantly greater than nonresponders at wk 3, 6 and 10. Since beagles develop gingival overgrowth similar to humans, they provide an excellent model to investigate the roles of local and systemic factors in the induction of gingival overgrowth.

[Protein quality of flatbread and extruded dry flatbread made from full-grain rye groats]

The effect of various processing methods used for the production of dry flatbread from ground whole rye on the nutritional protein quality were investigated by means of the nitrogen balance method in growing rats. The following products were tested: untreated ground whole rye, baked crisp bread, extruded flatbread without and with the addition of 2.5% and 5.0% of saccharose. The apparent protein digestibility (PD) of the 5 samples varied between 69% and 72% and was neither affected by the method of processing nor by the difference in sugar content. Compared to the untreated raw material (NPU = 41%; BV = 59%) net protein utilization and biological value in crisp bread baked by the traditional method (NPU = 35%; BV = 48%) and in extruded flat bread with 5% sugar (NPU = 35%; BV = 51%) were significantly reduced (P less than 0.05). In extruded flatbread without and with 2.5% sugar, NPU and BV of the raw material were essentially maintained. The results indicate that in comparison with the baking process the extrusion of flatbread is more suitable to protect the protein quality. The addition of more than 2.5% sugar caused protein damage in extruded flatbread, presumably as a result of Maillard reactions.

[Effect of various extrusion conditions on the protein quality of soybean and whole rye meal]

Using a Creusot-Loire twin-screw extruder (Type BC 45), ground soy bean and whole rye meal were extruded under various processing conditions (12% and 18% water content in the raw material, 129 degrees C and 165 degrees C product temperature in the case of soy bean, 12% and 18% water content, 165 degrees C product temperature in the case of rye, screw speed of 150 R/min, for all samples). The nutritional protein quality (apparent protein digestibility PV, net protein utilization NPU, and biological value BW) of the extrudates was determined by the nitrogen balance technique in growing rats. Compared to the untreated raw material no decrease in PV or NPU was noted for extrudates made from soy bean or rye. Extrusion of ground soy bean at 165 degrees C and 18% water content caused a significant decrease of BW from 68% to 64%. The lower water content (12%) induced a slight improvement of PV in soy extrudates and of NPU and BW in rye extrudates. The results indicate that the extrusion at low water content and moderate temperature can safely be used to process ground soy bean and whole rye meal without and damage to the nutritional protein quality.

[Bacteriological findings in conjunctival smears]

Between February and December 1981 a total of 2,053 conjunctival smears were taken on chocolate agar plates. Of these specimens, 1,720 were taken from clear, noninflamed eyes on the day preceding intraocular surgery; 202 (11.7%) of the smears were positive. The most common pathogens were gram-positive cocci (119 X) and Staphylococcus aureus (47 X). In 333 cases the smears were taken from the anterior segments of eyes with manifest infection and inflammatory signs. In this group pathogens grew on 95 smears (26%), the most common being gram-positive cocci (92 X) and Staphylococcus aureus (32 X). As more than one pathogen grew in 80 of the 95 smear cultures, a total of 174 pathogens were found in this group.

Growth pattern and citrate production in organ cultures of adult rat ventral prostate

Prostate rudiments from Wistar rats were cultured in MEM supplemented with 15% FBS and insulin (2 microgram/ml). In situ prostate acinar epithelium consists of tall columnar and low basal cells. Ultrastructure of the columnar cells is that of typical secretory cells; however, the basal cells are poor in cell organelle. During the first week of culture many secretory cells degenerated and were replaced by cuboidal or low columnar cells. In the presence of testosterone (2 microgram/ml) the secretory cells remained viable for 8-10 days before undergoing necrosis. At the termination of the experiment the acinar epithelium consisted of low cuboidal cells. The cultures showed a pattern of citrate production which reached a maximum at 5 days and remained-relatively constant thereafter. Ultrastructure of 1-week cultures exhibited Golgi complexes with dilated cisternae. Although a paucity of cell organelle was found in 7-day cultures, older cultures (19 days) exhibited morphologic characteristics of normal secretory cells.

The effects of nicotine on mouse first molar tooth germs in organ culture

Mandibular first molars, extirpated from 18-day mouse fetuses were cultured in BGJb medium (Fitton-Jackson modification) in a Trowell type culture system. Two-day cultures were treated with 78, 117, 156, and 312 microgram/ml nicotine sulfate. Untreated control tooth germs demonstrated normal growth in vitro. The peripheral cell layer of mesenchymal papilla and the inner enamel epithelium differentiated into odontoblasts and ameloblasts respectively with subsequent elaboration of extracellular matrix. Tooth germs treated with 78 microgram/ml nicotine were only slightly affected where as higher doses of the drug produced extensive cell damage. Dental papilla appeared more sensitive than the enamel organ. Large necrotic foci were present in the pulp mesenchyme involving in some cases the odontogenic layer and severely limiting production of predentin. The basement membrane in these areas was partially disrupted and stained poorly for PAS. The inner enamel epithelium was not affected by 78 microgram/ml dose of nicotine, however, higher doses produced extensive cell necrosis in this layer. Although enamel matrix was abundantly present in untreated controls, the tooth germs exposed to 117, 156, and 312 microgram/ml nicotine sulfate failed to elaborate this extracellular matrix. Tooth germs exposed to nicotine for 24 hours followed by culturing in control medium demonstrated complete recovery. Treated cultures maintained in vitro for 7-9 days in control media had replaced the necrotic cells in the ameloblastic and odontoblastic layers and demonstrated abundant dentin and enamel matrices.

Ultrastructural localization of adenosine triphosphatase in the stellate reticulum, stratum intermedium and ameloblasts of the mouse molar

ATPase activity in the developing first mandibular molar of the mouse was demonstrated at the electron microscopic level with the method of Wachstein & Meisel (1957). It was localized along the cell surfaces of the ameloblast and stratum intermedium interface, the stratum intermedium and the stellate reticulum. The ATPase final reaction product was also present at the cell membranes of the proximal region of adjacent ameloblasts and extended to the level of the nuclei. The demonstration of ATPase mainly on the plasma membranes was similar to the observations by other investigators of various non-odontogenic cell types involved in the exchange of materials across plasma membranes.