G protein-coupled receptor (GPCR) signaling is regulated by four ubiquitously expressed GPCR kinase isoforms (GRKs), namely GRK2, GRK3, GRK5, and GRK6. Overexpression of individual GRKs occurs in diseases like cancer and heart failure, prompting a search for potent GRK inhibitors. While various in silico and in vitro approaches exist, few methods assess inhibitor efficacy in cellular systems. To address this, we used HEK293 cell lines co-expressing the β2 adrenergic receptor (β2) and one GRK isoform on a quadruple GRK2/3/5/6 knockout background (ΔQ-GRK). We evaluated the inhibition of isoproterenol (ISO)-induced T360/S364-β2 phosphorylation using the 7TM phosphorylation assay. This combination allowed comprehensive evaluation of commercially available GRK inhibitors. We conclude that compound 8h (GRK2/3 inhibitor) and compound 18 (GRK5/6 inhibitor) are highly recommendable tools for the study of GPCR phosphorylation and function in cellular systems. Together, these cell-based GRK inhibitor assays can facilitate medium- to high-throughput screening of future GRK-targeted drug candidates. A GRK-isoform immunoassay was used to quantify GPCR phosphorylation and evaluate the potency of GRK inhibitors in a controlled cellular system.

Restoring the tumor suppressive activity of the Hippo signaling pathway lost through dysregulation of the NUAK1/2 and MARK2/3 kinase axis and downstream transcriptional effectors YAP/TAZ has emerged as a new modality for the treatment of several human cancers. Small molecule inhibition of NUAK1/2 and MARK2/3 constitutes a rational approach to block YAP/TAZ nuclear translocation and prevent a pro-oncogenic gene expression program. Modest structural changes to lead compound OICR14489, discovered through computational studies using a NUAK2 homology model, afforded the potent and selective dual NUAK1/2 and MARK2/3 inhibitor OICR16422. Further optimization led to inhibitor OICR19451, which produced an increase in YAP phosphorylation and enhanced cytoplasmic YAP/TAZ localization. In vitro growth inhibition of several cancer cell lines, coupled with the robust in vivo pharmacokinetic properties of OICR19451 marked it as an advanced tool compound suitable for in vivo evaluation. Accordingly, in an orthotopic model of highly metastatic breast cancer, MDA-MB-231 tumor-bearing mice treated with OICR19451 showed reduced metastases, tumor encapsulation and an overall increase in survival indicative of favorable Hippo pathway modulation.

Abstract Diffuse Intrinsic Pontine Glioma (DIPG) is a rare and aggressive pediatric cancer located in the pons region of the brainstem, classified as part of a broader class of H3 K27M mutant Diffuse Midline Gliomas (DMG). Focal radiation remains the standard of care; however the median survival is only 9-12 months, with no effective chemotherapeutic options available. Somatic missense mutations in the bone morphogenetic protein (BMP) type I receptor ACVR1 gene, which encodes activin receptor-like kinase-2 (ALK2), are present in approximately 25% of DMG tumours. Using an Open Science approach to promote transparency and collaboration, we previously reported ALK2 inhibitors with high potency (ALK2 IC50 < 10 nM, nanoBRET ALK2 IC50 < 20 nM), selectivity (>100-fold over ALK5) and brain penetration (Cbrain,4h/Cplasma,4h > 0.5, 10 mg/kg, NOD-SCID male mice). These inhibitors are highly orally bioavailable and demonstrate high in vivo exposure and dose linearity. In vitro, compounds have been screened in a panel of patient-derived DMG models including ACVR1 mutant and wild-type, with GI50s ranging from 0.3–14 µM, and selectivity for mutant over wild-type. In vivo, compounds showed an extension of survival in both an orthotopic PDX model (HSJD-DIPG-007, H3.3_K27M, ACVR1_R206H), and in an allograft of RCAS-ACVR1_R206H/H3.1_K27M in an immune competent background. From this series, we describe the selection process for a clinical development candidate. This work highlights the potential of ALK2 inhibitors as a therapeutic strategy for ACVR1 mutant gliomas and the value of Open Science in accelerating drug discovery for rare diseases.

Large-scale genome sequencing data from The Cancer Genome Atlas Program (TCGA) and the International Cancer Genome Consortium (ICGC) provided rich and comprehensive catalogues of many cancer types/subtypes for a large number of donors across many different cancer types. Manually curated knowledge from databases such as Reactome (https://reactome.org), OncoKB (https://www.oncokb.org), and many others, provided complementary information on pathways, clinical relevance, and therapeutic targets that are invaluable for mining biomarkers and druggable targets. One of the challenges is to harmonize all of the data so they can be uniformly processed to identify and rank potential targets. We obtained and preprocessed data (mRNA, mutations, CNVs, protein abundance, etc.) for all 32 cancer types. We also developed an internal data portal with a web interface using the Overture portal UI (https://www.overture.bio/) that allows users to efficiently interact with our preprocessed data. We are also implementing machine learning models to classify and rank potential targets for each of the available cancer types. Our machine learning models will include predictors such as differential expression between tumor and normal, tissue specificity, co-expressions with known oncogenes/tumor suppressors, copy number variations and mutation rates. Potential predictors will be evaluated and the most relevant will be included in the final models. Using known positive and negative test cases from literature, we will evaluate, optimize, and determine the best and most relevant predictors and machine learning models to use. The selected models will then be used to prioritize and rank targets by their biomarker potential. We will manually curate our results and select candidates for validation. This project provides a harmonized data structure and ML models for searching and ranking potential biomarkers and targets in an efficient and automated way. In addition, our data portal and preprocessed data allow more efficient sharing of data and improved data accessibility and reproducibility. The use of machine learning models using the preprocessed data, combined with the data portal, additional data and literature, can result in the generation of new knowledge and advances in drug discovery. Samantha Majoros, Mitchell Shiell, Joe Wang, Justin Richardsson, Quang M. Trinh, Richard Marcellus, David Uehling, Rima Al-awar, Shraddha Pai, Melanie Courtot, Lincoln Stein. Data Curation and Knowledge Integration Pipeline for Biomarker Discovery [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Artificial Intelligence and Machine Learning; 2025 Jul 10-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(13_Suppl):Abstract nr A006.

Diffuse Large B-Cell Lymphoma (DLBCL) is one of the most aggressive forms of lymphoid malignancies. About 40 % of patients eventually relapse and succumb to the disease within 5 years after diagnosis, underscoring the need for new treatment modalities. B-Cell Lymphoma 6 protein (BCL6) is a repressive transcription factor that is dysregulated in about 40 % of DLBCLs. As a rationale for pursuing BCL6 as a drug target, disrupting complexes between this protein and its co-repressors is thought to mitigate the downstream oncogenic effects of this pathway. However, drugging transcription factors presents a formidable undertaking since targeting protein-protein interactions has historically been challenging. In this study, we used X-ray structures of BCL6-SMRT (a silencing mediator for retinoid or thyroid-hormone receptors, also known as the nuclear receptor co-repressor 2, NCOR2) peptide and compound 79-6 to conduct a virtual screen of a library of 5.2 million compounds. Through this exercise, we identified the pyrrolopyridone 3 as a viable hit, which in turn led to the identification of pyrrolopyrimidone lead compound 4. The X-ray crystal structure of 4 bound to the BTB (Broad-Complex, Tramtrack, and Bric à brac) domain of BCL6 revealed a large back pocket as well as a left-hand channel adjacent to the ligand that could be leveraged to optimize these compounds. Sulfonamide side chains were therefore introduced to target this space, leading to compounds 11d and 11e having sub-micromolar binding to the BTB domain of BCL6.

Human DCAF1 is a multidomain protein that plays a critical role in protein homeostasis. Its WDR domain functions as a substrate recruitment module for RING-type CRL4 and HECT family EDVP E3 ubiquitin ligases, enabling the ubiquitination and proteasomal degradation of specific substrates. DCAF1's activity has been implicated in cell proliferation and is documented to promote tumorigenesis. Additionally, the DCAF1 WDR domain is hijacked by lentiviral accessory proteins to induce the degradation of host antiviral factors, such as SAMHD1 and UNG2. These diverse roles make DCAF1 an attractive target for therapeutic development in oncology and antiviral strategies. It is also a promising candidate for use in targeted protein degradation. We previously reported a novel ligand, OICR-8268, that targets the DCAF1 WDR domain. In this study, we present the development of OICR-41103, a potent, selective, and cell-active small molecule chemical probe for DCAF1, derived from OICR-8268. The co-crystal structure of the DCAF1-OICR-41103 complex reveals the ligand's binding mode within the WDR central pocket, demonstrating its potential for PROTAC design and development. Notably, OICR-41103 effectively displaces the lentiviral Vpr protein from DCAF1 in both biochemical and cellular settings, highlighting its potential for the development of HIV therapeutics.

Proteolysis-targeting chimeras (PROTACs) have been explored for the degradation of drug targets for more than two decades. However, only a handful of E3 ligase substrate receptors have been efficiently used. Downregulation and mutation of these receptors would reduce the effectiveness of such PROTACs. We recently developed potent ligands for DCAF1, a substrate receptor of EDVP and CUL4 E3 ligases. Here, we focus on DCAF1 toward the development of PROTACs for WDR5, a drug target in various cancers. We report four DCAF1-based PROTACs with endogenous and exogenous WDR5 degradation effects and high-resolution crystal structures of the ternary complexes of DCAF1-PROTAC-WDR5. The structures reveal detailed insights into the interaction of DCAF1 with various WDR5-PROTACs, indicating a significant role of DCAF1 loops in providing needed surface plasticity, and reflecting the mechanism by which DCAF1 functions as a substrate receptor for E3 ligases with diverse sets of substrates.

Compound full list of two libraries

BCL-2 immunohistochemistry validation

PDF file - 67KB, Supplementary Figure S2 shows results from the primary and validation screens with hits on sphere only or both sphere and monolayer, as well as sensitivity of HC11 cells.

Treatment of BCL-2 and IKKB inhibitor decreases cell growth and induces cell death in ENZ-resistant cell lines

PDF file - 44KB, Supplementary Table S2a and S2b list hits on Her2/Neu spheres and monolayer cells.

Abstract Small-molecule chemical “probes” complement the use of molecular biology techniques to explore, validate, and generate hypotheses on the function of proteins in diseases such as cancer. Unfortunately, the poor selection and use of small-molecule reagents can lead to incorrect conclusions. Here, we illustrate examples of poor chemical tools and suggest best practices for the selection, validation, and use of high-quality chemical probes in cancer research. We also note the complexity associated with tools for novel drug modalities, exemplified by protein degraders, and provide advice and resources to facilitate the independent identification of appropriate small-molecule probes by researchers. Significance: Validation of biological targets and pathways will be aided by a shared understanding of the criteria of potency, selectivity, and target engagement associated with small-molecule reagents (“chemical probes”) that enable that work. Interdisciplinary collaboration between cancer biologists, medicinal chemists, and chemical biologists and the awareness of available resources will reduce misleading data generation and interpretation, strengthen data robustness, and improve productivity in academic and industrial research.

PDF file - 51KB, Supplementary Table S4a lists gene sets enriched in TBK1-II treated HER2+ breast cancer cells.

Characterization of ENZ-resistant cell lines

Human G protein-coupled receptor 35 is regulated by agonist-mediated phosphorylation of a set of five phospho-acceptor amino acids within its C-terminal tail. Alteration of both Ser300 and Ser303 to alanine in the GPR35a isoform greatly reduces the ability of receptor agonists to promote interactions with arrestin adapter proteins. Here, we have integrated the use of cell lines genome edited to lack expression of combinations of G protein receptor kinases (GRKs), selective small molecule inhibitors of subsets of these kinases, and antisera able to specifically identify either human GPR35a or mouse GPR35 only when Ser300 and Ser303 (orce; the equivalent residues in mouse GPR35) have become phosphorylated to demonstrate that GRK5 and GRK6 cause agonist-dependent phosphorylation of these residues. Extensions of these studies demonstrated the importance of the GRK5/6-mediated phosphorylation of these amino acids for agonist-induced internalization of the receptor. Homology and predictive modeling of the interaction of human GPR35 with GRKs showed that the N terminus of GRK5 is likely to dock in the same methionine pocket on the intracellular face of GPR35 as the C terminus of the α5 helix of Gα13 and, that while this is also the case for GRK6, GRK2 and GRK3 are unable to do so effectively. These studies provide unique and wide-ranging insights into modes of regulation of GPR35, a receptor that is currently attracting considerable interest as a novel therapeutic target in diseases including ulcerative colitis.

Medulloblastomas (MBs) constitute the most common malignant brain tumor in children and adolescents. MYC-amplified Group 3 MBs are characterized by disease recurrence, specifically in the leptomeninges, whereby patients with these metastatic tumors have a mortality rate nearing 100

Pharmacological screens identify BCL-2 and IKKB inhibitor that specifically targets ENZ-resistant cell lines