Biology subjects

Rankovic, Z.

Publications and source records attributed to Rankovic, Z..

6 recordsLinked to original sources

bioRxiv2026

Developing Potent and Selective TBK1 Molecular Glue Degraders for Cancer Immunotherapy

Immune checkpoint blockade (ICB) has transformed cancer therapy across multiple tumour types, yet primary and acquired resistance remain major barriers to durable benefit. TANK-binding kinase 1 (TBK1) has emerged as an attractive target to enhance anti-tumour immunity, acting as a serine/threonine kinase that restrains immunogenic cell death and downstream immune activation. Here we report the discovery of a first-in-class TBK1 molecular glue degrader (MGD), CCT412020, identified through high-throughput proteomics screening of a next-generation molecular glue library. CCT412020 induces rapid, potent and selective TBK1 degradation across a panel of breast cancer cell lines. A cryo-EM structure of CCT412020 in complex with CRBN/{Delta}BPB-DDB1 and TBK1-homodimer reveals an unexpected binding mode that bypasses the canonical G-loop and instead engages an unconventional site at the TBK1 homodimer interface. Functionally, TBK1 loss via CCT412020 sensitises tumour cells to TNF- and interferon-driven responses and reduced viability across a broad range of cancer cell lines. Together, these findings establish CCT412020 as a mechanistically distinct TBK1 degrader and provide a framework for developing TBK1-targeted degraders as immunomodulatory anti-cancer agents to overcome ICB resistance.

cancer biology↗

bioRxiv2025

LCK-targeting molecular glues overcome resistance to inhibitor-based therapy in T-cell acute lymphoblastic leukemia

Drug resistance is a major challenge in cancer therapy, especially in the context of kinase inhibitors. While targeted protein degradation (TPD) was a distinct mode of action compared to inhibition-based therapeutic targeting, the potential value of TPD in drug-resistant cancer remains unclear. Here, we report the discovery of cereblon-recruiting molecular glue degraders (MGDs) targeting LCK, an oncogenic kinase in T-cell acute lymphoblastic leukemia (T-ALL). By high-throughput screening and medicinal chemistry optimization, we developed a series of MGDs that induced CRBN-dependent degradation of LCK as well as potent cytotoxicity in T-ALL in vitro. Structure-activity relationship analysis and ternary complex modeling revealed a non-canonical degron at the LCK-CRBN interface involving the G-loop, whose mutation disrupts this interaction. Unlike inhibitors and inhibitor-based PROTACs, these MGDs engage LCK in regions distal to the ATP binding site and thus their activities in T-ALL are not affected by gate-keeper LCK mutations that drive resistance to inhibitor-based therapeutics. Taken together, our data underscore the potential of LCK-targeting MGDs as a strategy to overcome kinase inhibitor resistance in T-ALL, highlighting a potentially generalizable strategy in cancer therapy.

cancer biology↗

bioRxiv2024

Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics

Molecular glue degraders (MGDs) are small molecules that harness the ubiquitin-proteasome system to induce degradation of target proteins, including those lacking conventional druggable pockets. Given the challenges in their rational design, MGD discovery predominantly relies on screening-based approaches, such as cell viability assays. However, one potential limitation of such screening methods is the risk of overlooking non-essential neosubstrates of potential therapeutic value. To address this concern, we present a high-throughput proteome-wide MGD screening platform utilizing label-free, data-independent acquisition mass spectrometry (DIA-MS) for integrated proteomics and ubiquitinomics analysis. Processing a diverse set of 100 CRBN-ligands across two cancer cell lines reveals a broad array of neosubstrates, including 50 novel candidates validated by MS-based ubiquitinomics. These findings considerably expand the current landscape of CRBN-mediated neosubstrates. Comprehensive hit validation and structure-degradation relationship analyses guided by global proteomics, identifies highly selective and potent phenyl glutarimide-based degraders of novel neosubstrates, including KDM4B, G3BP2 and VCL, none of which contain the classical CRBN degron motif. This study demonstrates that comprehensive, high-throughput proteomic screening offers new opportunities in MGD drug discovery.

biochemistry↗

bioRxiv2022

Morphogen Directed Coordination of GPCR Activity Promotes Primary Cilium Function for Downstream Signaling

Sonic Hedgehog (SHH) signaling is an essential driver of embryonic patterning that, when corrupted, leads to developmental disorders and cancers. SHH effector responses are organized through nonmotile primary cilia that grow and retract with the cell cycle and in response to distinct extracellular cues. Destabilization of primary cilium length corrupts SHH pathway regulation, which places significant pressure on SHH to maintain ciliary architecture. Herein, we investigate whether SHH signaling promotes ciliary length control. We reveal a signal crosstalk circuit induced by SHH activation of Phospholipase A2 (cPLA2) that drives ciliary EP4 signaling to stabilize primary cilium length. We demonstrate that chemical or genetic blockade of SHH-EP4 crosstalk leads to destabilized primary cilium cyclic AMP (cAMP) control, reduced ciliary length, and attenuated SHH pathway induction. Accordingly, we find that Ep -/- mice display shortened neuroepithelial primary cilia and altered SHH-dependent neuronal cell fate specification. Thus, SHH initiates a signaling crosstalk circuit that maintains primary cilium length for a robust downstream signaling response.

cell biology↗

bioRxiv2020

Patient-Derived Orthotopic Xenografts and Cell Lines from Pediatric High-Grade Glioma Recapitulate the Heterogeneity of Histopathology, Molecular Signatures, and Drug Response

Pediatric high-grade glioma (pHGG) is a major contributor to cancer-related death in children. In vitro and in vivo disease models reflecting the intimate connection between developmental context and pathogenesis of pHGG are essential to advance understanding and identify therapeutic vulnerabilities. We established 21 patient-derived pHGG orthotopic xenograft (PDOX) models and eight matched cell lines from diverse groups of pHGG. These models recapitulated histopathology, DNA methylation signatures, mutations and gene expression patterns of the patient tumors from which they were derived, and included rare subgroups not well-represented by existing models. We deployed 16 new and existing cell lines for high-throughput screening (HTS). In vitro HTS results predicted variable in vivo response to inhibitors of PI3K/mTOR and MEK signaling pathways. These unique new models and an online interactive data portal to enable exploration of associated detailed molecular characterization and HTS chemical sensitivity data provide a rich resource for pediatric brain tumor research.

cancer biology↗

bioRxiv2019

Geldanamycin inhibits Jumonji histone lysine demethylase KDM4 and targets chimeric transcription factor PAX3-FOXO1

Histone lysine demethylases (KDMs) are emerging as therapeutic targets in cancer. Development of potent KDM inhibitors may provide additional options for epigenomics-oriented therapies. Using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) functional demethylation assay, in combination with a high-content immunofluorescence imaging phenotypic screen, Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance mass spectrometry (MALDI-FTICR MS) and Amplified Luminescent Proximity Homogeneous Assay (ALPHA), we identified geldanamycin, an inhibitor of heat shock protein 90 (Hsp90), as a novel inhibitor of JmjC-domain containing demethylases such as KDM4B. We further found that geldanamycin can destabilize the PAX3-FOXO1 fusion oncoprotein, an Hsp90 client, which is a driver of clinically unfavorable alveolar rhabdomyosarcoma (aRMS). We then hypothesized that dual inhibition of PAX3-FOXO1 and epigenetic modifiers of aRMS would have synergistic antitumor activity. We repurposed the geldanamycin analog 17-DMAG to target aRMS and found that 17-DMAG significantly delays tumor growth, extends survival in xenograft mouse models, and inhibits expression of PAX3-FOXO1 targets and multiple oncogenic pathways including MYC, E2F and NOTCH. In addition, the combination of 17-DMAG with conventional chemotherapy or the bromodomain inhibitor JQ1 significantly enhances therapeutic efficacy. In summary, we have identified geldanamycin and 17-DMAG as dual KDM/Hsp90 inhibitors and 17-DMAG is efficacious against PAX3-FOXO1-driven rhabdomyosarcoma.

cancer biology↗