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RAS mutations prevalent in high-risk leukemia have been linked to relapse and chemotherapy resistance. Efforts to directly target RAS proteins have been largely unsuccessful. However, since RAS-mediated transformation is dependent on signaling through the RAS-related C3 botulinum toxin substrate (RAC) small GTPase, we hypothesized that targeting RAC may be an effective therapeutic approach in RAS mutated tumors. Here we describe multiple small molecules capable of inhibiting RAC activation in acute lymphoblastic leukemia cell lines. One of these, DW0254, also demonstrates promising anti-leukemic activity in RAS-mutated cells. Using chemical proteomics and biophysical methods, we identified the hydrophobic pocket of phosphodiester 6 subunit delta (PDE6D), a known RAS chaperone, as a target for this compound. Inhibition of RAS localization to the plasma membrane upon DW0254 treatment is associated with RAC inhibition through a phosphatidylinositol-3-kinase/AKT-dependent mechanism. Our findings provide new insights on the importance of PDE6D-mediated transport for RAS-dependent RAC activation and leukemic cell survival.

The activation of RAS signaling has been shown to act as the driver of both de novo and relapsed, chemotherapy resistant acute lymphoblastic leukemia (ALL). Full RAS transformation requires the activity of the small RAS-related C3 botulinum toxin substrate (RAC) protein family, including the hematopoietic-specific RAC2 GTPase and we have previously demonstrated the role of RAC in specific leukemia types. Even though relapsed ALL patients have a 34% overall prevalence of RAS-activating mutations, KRASG12C mutations were not present, suggesting that the only RAS inhibitor currently available (G12C-specific) would not be effective in treating these patients. Phosphodiester 6 subunit delta (PDE6D), initially identified as a subunit of rod-specific photoreceptor phosphodiesterase, is now also known as a transporter of prenylated cargo. In fact, PDE6D has been shown to modulate the activity of RAS family proteins by regulating their subcellular location. When active, RAS proteins migrate to the cell membrane where they interact with a number of effectors triggering pro-survival downstream pathways including the mitogen-activated protein kinase / extracellular signaling-regulated kinase (MAPK/ERK) and the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT). MAPK/ERK and PI3K/AKT pathways in particular are believed to synergize to induce survival and cellular transformation. We carried out a biological screen of small molecular compounds that assessed the inhibition of RAS-mutated ALL cell lines' proliferation through MTT assays, inhibition of RAC activation and the absence of inhibition of normal hematopoietic progenitor growth in colony forming unit (CFU) assays. Lead compounds were further evaluated for their lipophilicity, solubility and potency of biological activity. Here we report the identification of DW0254 which demonstrates arrest of proliferation and induction of apoptosis in RAS-mutant human B- and T-ALL cell lines. We have identified PDE6D as the putative target of this compound through photoaffinity labeling mass spectroscopy (PAL-MS). The cocrystal structure of DW0254 with recombinant PDE6D demonstrated that this small molecule fits inside the hydrophobic pocket and forms hydrogen bond interactions with residues Q88, Y149 and R61. From a molecular perspective, the occupation of the pocket by DW0254 leads to decreased interaction between PDE6D and farnesylated RAS. This impairment of PDE6D's ability to transport RAS leads to the delocalization of both mutant-NRAS and -KRAS4B proteins from the cell membrane to the cytosol, confirmed by real-time fluorescent imaging of recombinant GFP-RAS proteins. Ultimately, RAS delocalization upon DW0254 binding to PDE6D leads to decreased activation of both MAPK/ERK and PI3K/AKT pathways, and potent inhibition of RAC GTPases. CRISPR Cas9 saturating mutagenesis experiments confirmed that mutations in the farnesyl binding pocket leads to compound resistance, giving direct evidence that leukemia growth arrest is caused by molecule binding to PDE6D. Cells that showed increased IC 50 to DW0254 after mutagenesis did not exhibit resistance to Deltarasin, a previously described PDE6D inhibitor. DW0254 anti-leukemic activity was confirmed in an ex vivo murine xenograft model using short-term treated human NRAS-mutated ALL cell line P12-ICHIKAWA. After transplant, DW0254 treated cells showed impaired tumorigenic and engraftment potential when compared to vehicle controls. In conclusion, we have identified DW0254, a PDE6D inhibitor that has anti-leukemic activity in RAS-mutated ALL cell lines. We have successfully co-crystalized this compound with PDE6D showing binding to its farnesyl binding pocket and confirmed that the mechanisms of action of this inhibitor involve the loss of membrane localization of RAS and consequent inhibition of signaling to its downstream effectors. Pocket mutations validate the hypothesis that the effects observed derive from the binding of DW0254 to PDE6D and not from off-target effects. Ex vivo experiments show promising anti-leukemic effects and set the basis for future compound optimization. Disclosures De Vita: Novartis: Current Employment. Anighoro: Relation Therapeutics: Current Employment; Evotec SAS: Ended employment in the past 24 months. Autelitano: Evotec SAS: Current Employment. Beaumont: Evotec SAS: Current Employment. Klingbeil: Evotec SAS: Current Employment. Ermann: Evotec SAS: Ended employment in the past 24 months. Williams: BioMarin: Membership on an entity's Board of Directors or advisory committees, Other: Insertion Site Advisory Board; Geneception: Membership on an entity's Board of Directors or advisory committees, Other: Scientific Advisory Board; Emerging Therapy Solutions: Membership on an entity's Board of Directors or advisory committees, Other: Chief Scientific Chair; Beam Therapeutics: Membership on an entity's Board of Directors or advisory committees, Other: Scientific Advisory Board; Alerion Biosciences: Other: Co-founder (now licensed to Avro Bio, potential for future milestones/royalties); Novartis: Membership on an entity's Board of Directors or advisory committees, Other: Steering Committee, Novartis ETB115E2201 (eltrombopag in aplastic anemia). Advisory fees donated to NAPAAC.; Orchard Therapeutics: Membership on an entity's Board of Directors or advisory committees, Other: Membership on a safety advisory board (SAB): SAB position ended 05/20/2021. Co-founder , Patents & Royalties: Potential for future royalty/milestone income, X-SCID. Provided GMP vector for clinical trial, Research Funding; bluebird bio: Membership on an entity's Board of Directors or advisory committees, Other: Insertion Site Analysis Advisory Board, Patents & Royalties: BCH licensed certain IP relevant to hemoglobinopathies to bluebird bio. The current license includes the potential for future royalty/milestone income. Bluebird has indicated they will not pursue this as a clinical program and BCH is negotiating return of, Research Funding.

Usp9x was recently shown to be highly expressed in myeloma patients with short progression-free survival and is proposed to enhance stability of the survival protein Mcl-1. In this study, we found that the partially selective Usp9x deubiquitinase inhibitor WP1130 induced apoptosis and reduced Mcl-1 protein levels. However, short hairpin RNA-mediated knockdown (KD) of Usp9x in myeloma cells resulted in transient induction of apoptosis, followed by a sustained reduction in cell growth. A compensatory upregulation of Usp24, a deubiquitinase closely related to Usp9x, in Usp9x KD cells was noted. Direct Usp24 KD resulted in marked induction of myeloma cell death that was associated with a reduction of Mcl-1. Usp24 was found to sustain myeloma cell survival and Mcl-1 regulation in the absence of Usp9x. Both Usp9x and Usp24 were expressed and activated in primary myeloma cells whereas Usp24 protein overexpression was noted in some patients with drug-refractory myeloma and other B-cell malignancies. Furthermore, we improved the drug-like properties of WP1130 and demonstrated that the novel compound EOAI3402143 dose-dependently inhibited Usp9x and Usp24 activity, increased tumor cell apoptosis, and fully blocked or regressed myeloma tumors in mice. We conclude that small-molecule Usp9x/Usp24 inhibitors may have therapeutic activity in myeloma.

A high throughput screening campaign identified aryl 1,4-diazepane compounds as potent and selective cannabinoid receptor 2 agonists as compared to cannabinoid receptor 1. This class of compounds suffered from poor drug-like parameters as well as low microsomal stability and poor solubility. Structure-activity relationships are described with a focus on improving the drug-like parameters resulting in compounds with improved solubility and permeability.

A high-throughput screening campaign has identified 1,4-diazepane compounds which are potent Cannabinoid receptor 2 agonists with excellent selectivity against the Cannabinoid receptor 1. This class of compounds suffered from low metabolic stability. Following various strategies, compounds with a good stability in liver microsomes and rat PK profile have been identified.

A solid-phase synthesis of substituted cyclic urea derivatives as potential heterocyclic library scaffolds is described. 2-Amino-3-nitropyridine is attached to Wang resin via a carbamate linkage. Reduction of the nitro group was achieved with SnCl(2).2H(2)O. Reductive alkylation with a range of substituted benzaldehydes followed by cyclative cleavage afforded a small library of 3-substituted imidazo[4,5-b]pyridine-2-ones in 33-45% yield and 59-88% purity. Subsequently, this methodology was applied to the synthesis of 3-substituted imidazo[4,5-f]quinolin-2-ones.

Computer-aided drug design scaffold hopping strategies were utilized to identify new classes of CB2 agonists when compounds of an established series with low nanomolar potency were challenging to optimize for good drug-like properties. Use of ligand-based design strategies through BI Builder (a tool for de novo design) and PharmShape (a virtual screening software package) approaches led to the discovery of new chemotypes. Specifically, compounds containing azetidine-, proline-, and piperidine-based cores were found to have low nanomolar and picomolar CB2 agonist activities with drug-like properties considered appropriate for early profiling.

Through a ligand-based pharmacophore model (S)-proline based compounds were identified as potent cannabinoid receptor 2 (CB2) agonists with high selectivity over the cannabinoid receptor 1 (CB1). Structure–activity relationship investigations for this compound class lead to oxo-proline compounds 21 and 22 which combine an impressive CB1 selectivity profile with good pharmacokinetic properties. In a streptozotocin induced diabetic neuropathy model, 22 demonstrated a dose-dependent reversal of mechanical hyperalgesia.

Meeting abstracts Despite significant recent progress, cancer immunotherapy efficacies are still limited, since tumors can down-modulate and escape the immune system by various mechanisms. To overcome these limitations, we aimed to identify low molecular weight molecules that can enhance T cell

An efficient procedure for cross-coupling of 3-bromopyridine and 4-bromoanisole to various mono- and dichloro heteroaryl compounds—giving the corresponding biaryls in 74–96% yield—is described.

An efficient solution phase synthesis of substituted benzimidazol-2-ones is described. Polymer-supported thiophenol is used to remove excess alkylating agents. A library of 24 mono- and di-substituted benzimidazol-2-ones has been prepared in 60–99% yield and 65–99% purity.

An efficient solution phase synthesis of substituted benzimidazol-2-ones is described. Polymer-supported thiophenol is used to remove excess alkylating agents. A library of 24 mono- and di-substituted benzimidazol-2-ones has been prepared in 60–99% yield and 65–99% purity.

Lck, or lymphocyte specific kinase, is a cytoplasmic tyrosine kinase of the Src family expressed in T-cells and NK cells. Genetic evidence from knockout mice and human mutations demonstrates that Lck kinase activity is critical for T-cell receptor-mediated signaling, leading to normal T-cell development and activation. A small molecule inhibitor of Lck is expected to be useful in the treatment of T-cell-mediated autoimmune and inflammatory disorders and/or organ transplant rejection. In this paper, we describe the structure-guided design, synthesis, structure-activity relationships, and pharmacological characterization of 2-amino-6-phenylpyrimido[5',4':5,6]pyrimido[1,2- a]benzimidazol-5(6 H)-ones, a new class of compounds that are potent inhibitors of Lck. The most promising compound of this series, 6-(2,6-dimethylphenyl)-2-((4-(4-methyl-1-piperazinyl)phenyl)amino)pyrimido[5',4':5,6]pyrimido-[1,2- a]benzimidazol-5(6 H)-one ( 25), exhibits potent inhibition of Lck kinase activity. This activity translates into inhibition of in vitro cell-based assays and in vivo models of T-cell activation and arthritis, respectively.

A high-throughput screening campaign resulted in the discovery of a highly potent dual cannabinoid receptor 1 (CB1) and 2 (CB2) agonist. Following a thorough SAR exploration, a series of selective CB2 full agonists were identified.

The lymphocyte-specific kinase (Lck) is a cytoplasmic tyrosine kinase of the Src family expressed in T cells and NK cells. Genetic evidence in both mice and humans demonstrates that Lck kinase activity is critical for signaling mediated by the T cell receptor (TCR), which leads to normal T cell development and activation. A small molecule inhibitor of Lck is expected to be useful in the treatment of T cell-mediated autoimmune and inflammatory disorders and/or organ transplant rejection. In this paper, we describe the synthesis, structure-activity relationships, and pharmacological characterization of 2-aminopyrimidine carbamates, a new class of compounds with potent and selective inhibition of Lck. The most promising compound of this series, 2,6-dimethylphenyl 2-((3,5-bis(methyloxy)-4-((3-(4-methyl-1-piperazinyl)propyl)oxy)phenyl)amino)-4-pyrimidinyl(2,4-bis(methyloxy)phenyl)carbamate (43) exhibits good activity when evaluated in in vitro assays and in an in vivo model of T cell activation.