A Highly Selective and Orally Bioavailable CK1α Molecular Glue Degrader Targets B-Cell Lymphoma Cells
Authors: Kong Ran , Feng Shi , Wang Cong , Hao Qingbo , Zhang Yu , Han Jingjing , Xie Xiaoyu , Wang Haiyang , Elsner Jan , Mendy Derek , Haughey Michael , Krenitsky Paul , Plantevin-Krenitsky Veronique , Papa Patrick , Mercurio Frank , Xie Weilin , Zhou Xiangxiang 
Published: December 2024

Therapeutics for aggressive and high-risk lymphomas such as activated B-cell-like subtype of diffuse large B-cell lymphoma (ABC-DLBCL), which often develop resistance to treatment, remain unmet. Lenalidomide's clinical efficacy in del(5q) myelodysplastic syndrome is linked to CK1α degradation, though it more potently degrades IKZF1/3. Here, we report the discovery of a highly selective and orally active CK1α molecular glue degrader with strong activity against B-cell lymphomas, including those with acquired genetic resistance to BTK inhibitors.
To identify molecular glues other than degraders for IKZF1/3 and GSPT1, we rationally designed a cereblon (CRBN)-binding molecular glue library with unique chemical scaffolds distinct from traditional IMiDs drugs. The library was screened for compounds that suppress IL-2 expression following T-cell activation, as opposed to the IL-2 enhancement seen with IMiDs. Through this process, we identified INNO-220, a potent inhibitor of IL-2 secretion in a CRBN-dependent manner. Our proteomics analysis revealed a significant and selective downregulation of CK1α, along with an increase in p53 levels induced by INNO-220, both of which were CRBN-dependent. Notably, no impact on IKZF1, IKZF3, or GSPT1 was observed. Molecular dynamics modeling demonstrated that CK1α interacts with the CRBN-INNO-220 complex through the β-hairpin loop in the kinase N-lobe of CK1α β-strands 2 and 3.
INNO-220 treatment led to significant decrease in the phosphorylation of IκBα (Ser32) and p65 (Ser536) and inhibition of NF-κB signaling in activated T cells. Given the crucial role of NF-κB signaling in B-cell malignancies, we conducted a screen for INNO-220-sensitive lymphoma cell lines. DLBCL and mantle cell lymphoma (MCL) cell lines undergo apoptosis and cell cycle arrest at G0/G1 phase after INNO-220 treatment. Specifically, INNO-220 shows potent anti-proliferative activity in OCI-Ly3, an ABC-DLBCL cell line that harbors a CARD11 gain-of-function (GoF) mutation with constitutive NF-κB activation and is resistant to Bruton tyrosine kinase (BTK) inhibitors. In an OCI-Ly3 xenograft model, INNO-220 exhibits dose-dependent and more robust tumor inhibition compared to JNJ-67856633, a MALT1 inhibitor currently in clinical trials for lymphoma. Tumors from animals treated with INNO-220 showed a dose-dependent reduction in CK1α levels, increased p53 expression, and decreased Ki67 staining.
To understand the mechanism of action of INNO-220, we employed RNA sequencing in OCI-Ly3 and found INNO-220 activates p53 and inhibits NF-κB signaling. INNO-220 shows comparable anti-proliferative activity in OCI-Ly3 to the combination of MALT1 inhibitor and MDM2 antagonist, suggesting targeting both pathways is required for maximum anti-cancer activity. In Z-138 (MCL) and OCI-Ly19 (GCB-DLBCL) cells where NF-κB is not activated, INNO-220 demonstrates similar anti-proliferative activity with MDM2 antagonist, suggesting that activation of p53 is the primary mechanism driving their antiproliferative effects.
BTK inhibitors have minimal impact on NF-κB signaling in lymphoma with activating CARD11 mutations. The mechanism by which CARD11 mutations lead to the constitutive activation of NF-κB remains poorly defined. In OCI-Ly3, unlike what we observed in normal T cells, we found that CARD11/BCL10/MALT1 (CBM) complex is formed without stimulation. Degradation of CK1α by INNO-220 disrupts the existing CBM complex. The assembly of the CBM complex induced by BCR or TCR requires phosphorylation within the CARD11 linker region. In the absence of stimulation, the mutated CARD11 is already heavily phosphorylated at Ser652, which was significantly reduced by INNO-220. Our findings demonstrate that GoF CARD11 mutation is necessary, but not sufficient to form and maintain constitutively active CBM complex, for which CK1α is required.
In summary, our findings underscore the potential of INNO-220, a selective CK1α degrader that targets both the NF-κB and p53 pathways, in offering new treatment strategy for lymphoma, including those resistant to BTK inhibitors. The results from this study not only position INNO-220 as a promising anti-cancer agent for B-cell lymphomas but also suggest a potential strategy for patient stratification, a crucial aspect of personalized medicine.