Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells

Design and synthetic approaches to thalidomide based small molecule degraders

Thalidomide has been used as a repurposed drug for treating multiple myeloma since 1997. Several novel anticancer drugs containing thalidomide active moiety has been discovered since then. Many thalidomide drug candidates with tuned linker size have been instrumental in inhibiting histone deacetylase, kinase, transcription factors etc. and facilitate selective degradation of E3 ligase and other enzymes. Here we are focused on small molecule degraders that are being tailored with tweaking synthetic architectures around thalidomide chemical motif towards the development of promising drug candidates. Interesting biomedical applications of thalidomide-based degraders with recent developments including pharmacokinetic profiles, protein stability, activity studies, degradation assays, and antitumor response are elucidated.

ATF4:p52 complex activates oncogenic enhancers in multiple myeloma via p300/CBP recruitment to regulate BACH1

Multiple myeloma (MM) is a B-cell malignancy accounting for 20 % of all blood-associated cancers. MM patients with a poorer prognosis and high-risk stratification were previously observed to be causally linked to the constitutive activation of non-canonical NF-κB (ncNF-κB) pathway. Consistent with this, the ncNF-κB p52 transcription factor was earlier found to regulate the enhancer landscape of MM to potentiate oncogenic transcription. However, the mechanism by which aberrant p52 expression is involved in coordinating enhancer activity has not been well explored. In this study, we analysed H3K27ac ChIP-seq and ATAC-seq data from MM cell lines and patient samples to screen for putative transcription factors that cooperate with p52 to regulate enhancers activated in MM. We report that ATF4 interacts with p52 and together, this complex mediates the activity of a subset of MM-associated enhancers through the recruitment of histone acetyltransferases (HATs), p300 and CBP (CREB-binding protein). We also identified a ATF4:p52 regulated target gene BACH1 under the regulation of a proximal super-enhancer, which was found to drive oncogenesis in MM by promoting cell cycle progression and proliferation. Together, our findings provide further mechanistic insights into how aberrant enhancer activation observed in MM tumours could lead to disease progression.

Role of the bone marrow microenvironment in multiple myeloma: Impact of niches on drug resistance mechanisms

Multiple myeloma (MM) is a blood cancer characterized by the uncontrolled growth of plasma cells in the bone marrow. These malignant plasma cells can proliferate locally and spread to other tissues and organs. The M-protein they produce can lead to various clinical symptoms, including anemia, hypercalcemia, bone pain, bone destruction, and kidney dysfunction. Despite significant advancements in treatment over the past two decades that have improved survival and outcomes for many patients, drug resistance remains a significant therapeutic challenge. This resistance is largely driven by the complex interactions between MM cells and the bone marrow microenvironment (BMME), making long-term disease control difficult. To improve treatment outcomes, it is essential to understand how the BMME supports MM cell growth and survival, as well as how these cells evade therapies. Investigating these processes will help identify key mechanisms behind drug resistance, offering a pathway to develop targeted therapies that can overcome this challenge. This review will explore the intricate relationship between MM cells and the BMME, focusing on how both cellular and non-cellular components of the microenvironment contribute to resistance mechanisms and prompt disease progression. These insights aim to inform future therapeutic strategies to enhance treatment options for MM patients.

Proteolysis targeting chimera, molecular glue degrader and hydrophobic tag tethering degrader for targeted protein degradation: Mechanisms, strategies and application

Targeted protein degradation (TPD) represents a revolutionary approach to drug discovery, offering a novel mechanism that outperforms traditional inhibitors. This approach employs small molecule drugs to induce the ubiquitination and subsequent degradation of target protein via the proteasome or lysosomal pathways. Key strategies within TPD include proteolysis targeting chimeras (PROTACs), hydrophobic tag tethering degraders (HyTTDs), and molecular glue degraders (MGDs). PROTACs have been undergone clinical evaluations, MGDs have been used in the clinic, and HyTTDs have shown significant progress in cancer treatment. Each of these strategies presents unique advantages and approaches to target protein degradation. This review summarizes five years of research on PROTACs, HyTTDs, and MGDs, highlighting their design principles, advantages, limitations, and future challenges to provide clear guidance and in-depth insights for advancing drug development.

A phase I clinical trial of lenalidomide combined with bortezomib for acute myeloid leukemia or myelodysplastic syndrome relapsing after allogeneic stem cell transplantation

BACKGROUND

Allogeneic hematopoietic cell transplantation (HCT) may improve long-term survival in patients with MDS or AML but disease relapse following HCT is common, with limited subsequent treatment options and extremely poor post-relapse outcomes. Lenalidomide and bortezomib are therapies which, in this setting, may exert antiproliferative effects, enhance graft-vs-leukemia immune responses, and potentiate chemotherapeutic drugs.

OBJECTIVES

We sought to evaluate the safety and preliminary efficacy of bortezomib in combination with high dose lenalidomide in patients with AML or MDS relapsing after HCT.

STUDY DESIGN

We conducted a phase I, dose-escalation, multi-center study of bortezomib added to high dose lenalidomide in patients with AML or MDS relapsing after HCT. We enrolled adult patients with recurrent or progressive AML or MDS after transplant; patients were required to be off systemic immunosuppression, with no evidence of GVHD, and with adequate organ function. Escalating doses of bortezomib were administered on days 2, 5, 9, and 12 of each cycle, while lenalidomide was given at 50 mg daily on days 1-21 of a 28-day cycle. DLTs were assessed during the first 2 cycles of induction and responses were assessed within this period. After achieving a treatment response, patients could proceed to maintenance dosing. The primary endpoint was toxicity and to establish the maximally tolerated dose (MTD) of the combination, while secondary endpoints included response rate and duration of responses.

RESULTS

21 patients were enrolled, with a median age of 66 years (range 23-74). The majority of patients enrolled had AML (19/21). Three patients were enrolled at each bortezomib dose level of 0.7 mg/m2, 1.0 mg/m2 and 1.3 mg/m2. One patient experienced dose-limiting toxicity at 1.3 mg/m2 (received <50 % doses) and the cohort was expanded to 6 total patients, establishing this as the recommended phase two dose (RP2D); a maximum tolerated dose (MTD) was not reached. An additional 9 expansion patients were treated at this dose level for a total of 15 patients treated with lenalidomide 50 mg and bortezomib 1.3 mg/m2. During dose expansion, grade 4 toxicities attributed to study drug included grade 4 neutropenia (n = 5), thrombocytopenia (n = 3), and febrile neutropenia (n = 1). Across all cohorts (n = 21), 1 patient (4.8 %) achieved CR and 3 patients (14.3 %) achieved CRi (composite CR/CRi rate of 19 %). Of the 15 patients treated at the RP2D, 4 patients had progressive disease after the first induction cycle, and 2 patients stopped therapy during induction cycle 2. A total of 9 patients completed both induction cycles. Of the 15 patients treated at the RP2D, 1 achieved CR, 2 achieved CRi (composite CR/CRi 20 %, CI 5.7-44.0 %) and 4 patients had stable disease. Chimerism during treatment generally tracked with disease response and one patient with persistent low chimerism also achieved CRi. The single patient achieving CR harbored an NPM1 gene mutation. A total of 3 out of 13 patients tested harbored a TP53 gene mutation and 2 of these patients achieved CRi on study subsequent to receiving DLI before study entry.

CONCLUSIONS

Bortezomib can be combined with lenalidomide in patients with AML and MDS relapsing after HCT with overall 19 % of patients achieving composite remission. Toxicity was manageable and primarily related to cytopenias during induction. Responding patients included 1 with NPM1-mutated AML as well as 2 harboring TP53 gene mutations, suggesting possible therapeutic benefit in very high-risk disease. Bortezomib and lenalidomide could be safely used following donor lymphocyte infusion without evidence of graft failure or immune-related toxicity.

Cereblon E3 ligase complex genes are expressed in tissues sensitive to thalidomide in chicken and zebrafish embryos but are unchanged following thalidomide exposure

Thalidomide is an infamous drug used initially as a sedative until it was tragically discovered it has highly teratogenic properties. Despite this it is now being used to successfully treat a range of clinical conditions including erythema nodosum leprosum (ENL) and multiple myeloma (MM). Cereblon (CRBN), a ubiquitin ligase, is a binding target of thalidomide for both its therapeutic and teratogenic activities and forms part of an CRL4-E3 ubiquitin ligase complex with the proteins Damaged DNA Binding protein 1 (DDB1) and Cullin-4A (CUL4A). This complex mediates degradation of the zinc-finger transcription factors Ikaros (IKZF1) and Aiolos (IKZF3), to mediate thalidomide's anti-myeloma response. To better understand the importance of CRBN and its binding partners for thalidomide teratogenesis here we analysed the expression patterns of CRBN and some of its known E3 complex binding partners in wildtype and thalidomide-treated chicken and zebrafish embryos. CRBN and DDB1 are expressed in many tissues throughout development including those that are thalidomide-sensitive while CUL4A and targets of the CRL4-CRBN E3 Ligase Complex IKZF1 and IKZF3 are expressed at different timepoints and in fewer tissues in the body than CRBN. Furthermore, IKZF3 is expressed in tissues of the eye that CRBN is not. However, although we observed rapid changes to the chicken yolk-sac membrane vasculature following thalidomide exposure, we did not detect CRL4-CRBN E3 Ligase Complex expression in the yolk-sac membrane vessels. Furthermore, we did not detect any changes in CRBN, DDB1, CUL4, IKZF1 and IKZF3 expression following thalidomide exposure in chicken and zebrafish embryos. These findings demonstrate that the anti-angiogenic activities of thalidomide may occur independent of CRBN and that thalidomide does not regulate CRL4-CRBN E3 Ligase Complex gene expression at the mRNA level.

Targeted degradation of GOLM1 by CC-885 via CRL4-CRBN E3 ligase inhibits hepatocellular carcinoma progression

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, emphasizing the urgent need for novel therapeutic strategies. In this study, we investigate the anti-tumor potential of CC-885, a cereblon (CRBN) modulator known for its efficacy in targeting neoplastic cells through proteasomal degradation pathways. Our findings demonstrate that CC-885 exhibits potent anti-tumor activity against HCC. In vitro assays revealed that CC-885 significantly inhibits the proliferation, migration, and invasion of HCC cells. These effects were corroborated in vivo, where CC-885 markedly suppressed tumor growth and angiogenesis in chick embryos and impeded the progression of orthotopic liver tumors in murine models. Mechanistically, CC-885 selectively reduces GOLM1 protein levels via ubiquitin-mediated proteasomal degradation. Knockdown of GOLM1 recapitulated the anti-proliferative effects of CC-885, while overexpression of GOLM1 conferred resistance to CC-885-induced apoptosis and growth inhibition. Further investigation revealed that CC-885 facilitates the interaction between GOLM1 and the E3 ubiquitin ligase CRBN, promoting the ubiquitination and subsequent degradation of GOLM1. Transcriptomic analyses showed that both CC-885 treatment and GOLM1 knockdown modulate critical pathways involved in apoptosis. These findings position CC-885 as a promising therapeutic candidate for HCC, acting primarily through CRBN-dependent degradation of GOLM1, and support its further development for clinical application.

The contribution of cyclic imide stereoisomers on cereblon-dependent activity

Thalidomide, lenalidomide, and their derivatives mimic glutarimide and aspartimide protein modifications that give rise to a motif recognized by the E3 ligase substrate adapter cereblon (CRBN). These cyclic imides have a chiral center that, given the biological significance of chirality, may influence CRBN's function and therapeutic applications. Here, we systematically examine cyclic imides in small molecules, peptides, and proteins to assess their racemization, CRBN engagement, ternary complex formation in vitro, and resulting degradation outcomes in cells. While the thalidomide-binding domain of CRBN consistently favors the (S)-stereoisomer across all cyclic imide small molecule ligands and engineered proteins, we find that, in some cases, the (R)-stereoisomer can bind to CRBN, either enhancing or hindering the eventual target engagement and degradation. Lenalidomide and its derivatives racemize more rapidly (t 50%ee = 4-5 h) than the C-terminal cyclic imide under non-enzymatic conditions. These findings highlight that although the (S)-stereoisomer of the cyclic imide is the primary ligand for the thalidomide-binding domain of CRBN, the (R)-stereoisomer, if present, has the potential to contribute to CRBN-dependent cellular activity.

Computer-Aided Drug Discovery for Undruggable Targets

Undruggable targets are those of therapeutical significance but challenging for conventional drug design approaches. Such targets often exhibit unique features, including highly dynamic structures, a lack of well-defined ligand-binding pockets, the presence of highly conserved active sites, and functional modulation by protein-protein interactions. Recent advances in computational simulations and artificial intelligence have revolutionized the drug design landscape, giving rise to innovative strategies for overcoming these obstacles. In this review, we highlight the latest progress in computational approaches for drug design against undruggable targets, present several successful case studies, and discuss remaining challenges and future directions. Special emphasis is placed on four primary target categories: intrinsically disordered proteins, protein allosteric regulation, protein-protein interactions, and protein degradation, along with discussion of emerging target types. We also examine how AI-driven methodologies have transformed the field, from applications in protein-ligand complex structure prediction and virtual screening to de novo ligand generation for undruggable targets. Integration of computational methods with experimental techniques is expected to bring further breakthroughs to overcome the hurdles of undruggable targets. As the field continues to evolve, these advancements hold great promise to expand the druggable space, offering new therapeutic opportunities for previously untreatable diseases.

A highly selective and orally bioavailable casein kinase 1 alpha degrader through p53 signaling pathway targets B-cell lymphoma cells

The modest reduction in casein kinase 1 alpha (CK1α) by lenalidomide contributes to its clinical effectiveness in treating del(5q) myelodysplastic syndrome. However, the mechanism by which CK1α impacts lymphoma survival remains inadequately defined. We developed INNO-220, a CRBN-dependent CK1α degrader, by leveraging cytokine expression profiling in T cells. Unlike lenalidomide, INNO-220 is a highly selective and potent degrader of CK1α without affecting IKZF1/3. Screening across lymphoma cell lines revealed that cells harboring wild-type p53 and exhibiting constitutive NF-κB signaling were particularly sensitive to CK1α degradation yet resistant to Bruton tyrosine kinase inhibitors. Moreover, INNO-220 suppresses NF-κB signaling and activates p53 pathway, leading to complete inhibition of lymphoma tumor growth in vivo. Mechanistically, INNO-220 disrupts the assembly and function of the CARD11/BCL10/MALT1 complex, thereby inhibiting NF-κB signaling in stimulated T cells and lymphoma cells that harbor an activating mutation in CARD11. Moreover, we observed that activation of wild-type p53 upon INNO-220 treatment was sufficient to induce potent cancer cell death even in the absence of constitutive NF-κB activity. In summary, our findings introduce a selective CK1α degrader as a novel therapeutic approach for lymphoma, providing both mechanistic insights and a potential patient selection strategy in treating lymphoma and possibly other cancers.

Probing the E3 Ligase Adapter Cereblon with Chemical Biology

ConspectusThe E3 ligase substrate adapter cereblon (CRBN) has garnered widespread interest from the research laboratory to the clinic. CRBN was first discovered for its association with neurological development and subsequently identified as the target of thalidomide and lenalidomide, therapeutic agents used in the treatment of hematopoietic malignancies. Both thalidomide and lenalidomide have been repurposed as ligands for targeted protein degradation therapeutic modalities. These agents were proposed to mimic a naturally occurring ligand, although the native substrate recognition mechanism of CRBN remained elusive. Chemical biology, which involves the use of chemical tools to modulate and probe biological systems, can provide unique insights into the molecular mechanisms and interactions of proteins with their cognate ligands. Here we describe our use of chemical biology approaches, including photoaffinity labeling, chemical proteomics, and targeted protein degradation, to interrogate the biological activities of CRBN in the presence or absence of its ligands. Our development of a photoaffinity labeling probe derived from lenalidomide, termed photolenalidomide, enabled mapping of the binding site on CRBN and identification of a new target recruited to CRBN by lenalidomide through chemical proteomics. Further derivatization of the lenalidomide scaffold afforded DEG-77, a potent degrader with therapeutic efficacy against acute myeloid leukemia. Our parallel development of chemically defined probes that are inspired by heterobifunctional targeted protein degradation agents and functionally engage CRBN in cells revealed that thalidomide is a peptidomimetic of an underappreciated protein modification termed the C-terminal cyclic imide, which arises from intramolecular cyclization of asparagine or glutamine residues and represents a degron endogenously recognized by CRBN. Protein engineering and proteomic efforts validated the CRBN-dependent regulation of proteins bearing the C-terminal cyclic imide modification in vitro and in cells and the prevalence of the C-terminal cyclic imide in the biological system. Application of C-terminal cyclic imides as a class of cyclimid ligands for targeted protein degradation led to the development of a variety of heterobifunctional degraders with distinct efficacy and target selectivity, whereas examination of the occurrence of C-terminal cyclic imides as a form of protein damage uncovered the intrinsic and extrinsic factors that predispose peptides and proteins to C-terminal cyclic imide formation and the role of CRBN in mitigating the accumulation of damaged proteins with a propensity for aggregation. Future investigation of C-terminal cyclic imides, synthetic ligands, and their relationship to CRBN biology will illuminate regulatory mechanisms that are controlled by CRBN and drive the pursuit of additional functional chemistries on proteins and the biological pathways that intercept them.

Discovery of an LSD1 PROTAC degrader

Aberrant expression of lysine-specific demethylase 1 (LSD1) has been implicated in various cancers, including acute myeloid leukemia (AML). Recent studies have revealed both catalytic and noncatalytic oncogenic functions of LSD1, which cannot be effectively addressed by traditional small-molecule inhibitors. Therefore, to remove LSD1 and mitigate its oncogenic activity, we utilized the proteolysis-targeting chimera (PROTAC) approach and developed an LSD1 PROTAC degrader MS9117, which recruits the E3 ligase cereblon (CRBN). MS9117 induces LSD1 degradation in a concentration-, time-, CRBN-, and proteasome-dependent manner. Importantly, MS9117 effectively degrades LSD1 and demonstrates superior antiproliferative effects in AML cells, compared to the existing pharmacological LSD1 inhibitors. Furthermore, MS9117 also sensitized nonacute promyelocytic leukemia AML cells to all-trans retinoic acid treatment. Moreover, we developed two negative controls of MS9117, MS9117N1 and MS9117N2, which do not degrade LSD1 or inhibit leukemia cell growth, further confirming the mechanism of action of MS9117. Overall, MS9117 serves as a valuable chemical tool and a potential therapeutic to target both the catalytic and scaffolding functions of LSD1. With several LSD1 inhibitors already in clinical development, the LSD1 degraders such as MS9117 offer an additional option for future clinical studies.

Engineering ERα degraders with pleiotropic ubiquitin ligase ligands maximizes therapeutic efficacy by co-opting distinct effector ligases

Proximity-inducing compounds that modulate target protein homeostasis represent an emerging therapeutic strategy. While the inherent complexity of these bifunctional compounds presents certain challenges, their unique composition offers opportunities to co-opt specific cellular effectors to enhance therapeutic impact. In this study, we systematically evaluate a series of bifunctional degrader compounds engineered with the estrogen receptor-alpha (ERα) inhibitor endoxifen linked to various bioactive ubiquitin ligase ligands. Notably, ERα degraders containing pan-IAP antagonist ligands significantly reduced the proliferation of ERα-dependent cells compared to clinical-stage ERα degraders. These pan-IAP antagonist-based ERα degraders leverage distinct effector ligases to achieve dual therapeutic effects: They utilize XIAP within tumor cells to promote ERα degradation and activate cIAP1/2 in both tumor and immune cells to induce TNFα, which drives tumor cell death. Our findings illustrate a broader concept that co-opting the discrete functions of selected cellular effectors, while simultaneously modulating therapeutic target protein homeostasis, are dual strategies that can significantly enhance the efficacy of induced proximity therapeutics.

Discovery and Characterization of PVTX-321 as a Potent and Orally Bioavailable Estrogen Receptor Degrader for ER+/HER2- Breast Cancer

Estrogen receptor α (ERα) is a key therapeutic target in ER+/HER2- breast cancer, but ESR1 mutations drive resistance to endocrine therapies. Heterobifunctional degraders (HBDs) targeting ERα offer a promising strategy to overcome this resistance. Here, we report PVTX-321 (16a), a potent ER HBD derived from a novel spirocyclic cereblon ligand and an ERα binder. PVTX-321 achieves a DC50 of 0.15 nM in MCF-7 cells and acts as a strong antagonist (IC50 = 59 nM), suppressing proliferation in ERα+ cell lines, including mutant variants (Y537S, D538G). It demonstrates favorable oral bioavailability, dose-dependent ERα degradation in vivo and induces tumor regression at 10 mg/kg (QD) in MCF-7 xenografts. With minimal CYP inhibition and a strong preclinical safety profile, PVTX-321 is a promising candidate for advancing ER+/HER2- breast cancer treatment.

Acute lymphoblastic leukemia following lenalidomide therapy in multiple myeloma patients: Two case reports and review of the literature

BACKGROUND

Lenalidomide, as an immunomodulatory drug, has significantly contributed to advancements in hematologic malignancies. However, lenalidomide therapy has been associated with rare but severe complications, particularly therapy-related acute lymphoblastic leukemia (t-ALL). This study aims to contribute to understanding the clinical, genetic, and therapeutic characteristics of t-ALL following lenalidomide therapy. To achieve this, cases reported in the literature were reviewed, and a comprehensive evaluation was conducted with the addition of two new case reports.

METHODS

A comprehensive review of published cases was conducted using databases such as PubMed and Scopus. Inclusion criteria focused on patients who developed ALL following lenalidomide therapy. Clinical findings, cytogenetic data, treatment protocols, and outcomes were analyzed alongside two new cases from our institution.

RESULTS

The findings revealed a diverse genetic landscape among patients with lenalidomide-associated t-ALL, with common abnormalities including TP53 mutations and hypodiploidy. The latency period for developing t-ALL after lenalidomide therapy varied widely, with a median duration of approximately 50 months (range: 6-126). Treatment strategies, such as intensive chemotherapy and allogeneic hematopoietic stem cell transplantation, showed variable efficacy, heavily influenced by cytogenetic risk factors and the presence of infections.

CONCLUSION

Lenalidomide-associated t-ALL represents a rare but clinically significant complication. Vigilant monitoring, early detection, and personalized therapeutic strategies are crucial for improving outcomes. This study emphasizes the importance of balancing the therapeutic benefits of lenalidomide against its potential risks and advocates for further multicenter studies to refine management protocols and discover predictive biomarkers.

Post-Translational Modifications in Multiple Myeloma: Mechanisms of Drug Resistance and Therapeutic Opportunities

Multiple myeloma (MM) remains an incurable hematologic malignancy due to the inevitable development of drug resistance, particularly in relapsed or refractory cases. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, acetylation, and glycosylation, play pivotal roles in regulating protein function, stability, and interactions, thereby influencing MM pathogenesis and therapeutic resistance. This review comprehensively explores the mechanisms by which dysregulated PTMs contribute to drug resistance in MM, focusing on their impact on key signaling pathways, metabolic reprogramming, and the tumor microenvironment. We highlight how PTMs modulate drug uptake, alter drug targets, and regulate cell survival signals, ultimately promoting resistance to PIs, IMiDs, and other therapeutic agents. Furthermore, we discuss emerging therapeutic strategies targeting PTM-related pathways, which offer promising avenues for overcoming resistance to treatment. By integrating preclinical and clinical insights, this review underscores the potential of PTM-targeted therapies to enhance treatment efficacy and improve patient outcomes in MM.

Proteolysis-Targeting Chimera (PROTAC): A Revolutionary Tool for Chemical Biology Research

Proteolysis-targeting chimera (PROTAC) technology is a revolutionary tool for drug discovery that simultaneously recruits E3 ligase and the protein of interest to induce ubiquitination and subsequent proteasomal degradation. Since the inaugural PROTAC prototype emerged in 2001, this modality has garnered significant interest across academia and industry, catalyzing transformative applications in drug discovery and chemical biology. The field has evolved from foundational investigations into molecular design, structural optimization, and protein target extension to address more sophisticated challenges, such as structural analysis of ternary complexes, expansion of diversified therapeutic indications, and clinical translation studies. Recent progress across chemical, pharmaceutical, and biochemical sciences has reshaped PROTAC design paradigms, which in turn expanded the chemical biology toolkit. In this review, pivotal milestones are systematically chronicled in PROTAC development, evaluate emerging strategies for diversifying E3 ligase utilization and expanding the scope of degradable targets, and summarize a series of instrumental and biochemical methodologies that propelled sequential breakthroughs. Additionally, forward-looking trajectories are proposed to address current limitations and accelerate the clinical maturation of PROTAC-based therapeutics.

Gene regulation technologies for gene and cell therapy

Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased clinical utility due to various complications. Thus, many technologies for controlled gene expression are under development, including regulated transgenes, modulation of endogenous genes to leverage native biological regulation, mapping and repurposing of transcriptional regulatory networks, and engineered systems that dynamically react to cell state changes. Transformative therapies enabled by advances in tissue-specific promoters, inducible systems, and targeted delivery have already entered clinical testing and demonstrated significantly improved specificity and efficacy. This review highlights next-generation technologies under development to expand the reach of gene therapies by enabling precise modulation of gene expression. These technologies, including epigenome editing, antisense oligonucleotides, RNA editing, transcription factor-mediated reprogramming, and synthetic genetic circuits, have the potential to provide powerful control over cellular functions. Despite these remarkable achievements, challenges remain in optimizing delivery, minimizing off-target effects, and addressing regulatory hurdles. However, the ongoing integration of biological insights with engineering innovations promises to expand the potential for gene therapy, offering hope for treating not only rare genetic disorders but also complex multifactorial diseases.

Intrinsic/proximal cell surface marker logic-gated extracellular targeted protein degradation in specific cell population

Molecular tether-mediated extracellular targeted protein degradation (eTPD) presents an innovative technology and underlies a promising drug modality. However, to precisely implement eTPD within specific cell compartments remains a significant challenge. As eTPD depends on the degrader molecule expression and activity, we first seek to expand the panel of potential eTPD degraders. To this end, more than 50 receptors with variable tissue distributions are screened for identification of those with substantial endocytic rates. We subsequently assemble the bispecific, "Selected endocytic carrier-targeting chimeras (SecTAC)," and validate their efficacies to program the target cells to internalize membrane/extracellular protein cargos (or nucleic acids). Moreover, administration of a SecTAC for removal of excessive immunoglobulin G via a currently validated, emerging degrader (CD71) leads to evident therapeutic effect in a mouse lupus model. To further enhance cell-targeting specificity, we next develop logic-gated eTPD (LOG-eTPD) based on a combination of chimeras that indirectly couple cargo and degrader via another cell surface gating marker. Particularly, we find that a selective surface marker from the neighboring cells also may be exploited as input for LOG-eTPD in a therapeutically relevant context. Taken together, the present work has laid a strong foundation for developing eTPD agents that combine high potency with precision and safety.

Primed for degradation: How weak protein interactions enable molecular glue degraders

Molecular glues are small drug-like molecules that induce de novo protein-protein interactions or facilitate pre-existing weak interactions between proteins. In the context of a ubiquitin ligase, such binding events frequently result in ubiquitination by proximity. Rational development of these transformative modalities, however, remains a major challenge. Here we review recent insights into molecular glues and the emerging design principles. Protein surfaces can similarly be complemented by mutations or compounds inducing binding and a resulting gain of functionality. When the interaction surface between two proteins is relatively small, or when the affinity between the proteins is otherwise weak, proportionally more binding energy will have to be provided by the compound to glue the proteins together. We suggest a simple thermodynamic model to rationalize molecular glue action facilitated by compounds and mutations.

Niclosamide: CRL4AMBRA1 mediated degradation of cyclin D1 following mitochondrial membrane depolarization

Targeted protein degradation has emerged as a promising approach in drug discovery, utilizing small molecules like molecular glue degraders to harness the ubiquitin-proteasome pathway for selective degradation of disease-driving proteins. Based on results from proteomics screens we investigated the potential of niclosamide, an FDA-approved anthelmintic drug with a 50 year history in treating tapeworm infections, as a molecular glue degrader targeting the proto-oncogene cyclin D1. Proteomics screens in HCT116 colon carcinoma and KELLY neuroblastoma cells, found that niclosamide induces rapid cyclin D1 degradation through a mechanism involving the ubiquitin-proteasome pathway. A genetic CRISPR screen identified the E3 ligase CRL4AMBRA1 as a key player in this process. Structure-activity relationship studies highlighted critical features of niclosamide necessary for cyclin D1 degradation, demonstrating a correlation between mitochondrial membrane potential (MMP) disruption and cyclin D1 downregulation. Notably, various mitochondrial uncouplers and other compounds with similar drug sensitivity profiles share this correlation suggesting that MMP disruption can trigger cyclin D1 degradation, and that the cellular signal driving the degradation differs from previously described mechanism involving CRL4AMBRA1. Our findings underscore the complexities of proteostatic mechanisms and the multitude of mechanisms that contribute to degrader drug action.

Development of PVTX-405 as a potent and highly selective molecular glue degrader of IKZF2 for cancer immunotherapy

IKZF2 (Helios) is a transcription factor that is selectively expressed by Tregs and is essential for preserving the function and stability of Tregs in the tumor microenvironment (TME), where it suppresses the anti-tumor immune response. Targeted IKZF2 degradation by small molecules represents a promising strategy for the development of a new class of cancer immunotherapy. Herein, we describe the discovery of PVTX-405, a potent, effective, highly selective, and orally efficacious IKZF2 molecular glue degrader. PVTX-405 degrades IKZF2 (DC50 = 0.7 nM and Dmax = 91%) while sparing other CRBN neo-substrates. Degradation of IKZF2 by PVTX-405 increases production of inflammatory cytokine IL-2 and reduces the suppressive activity of Tregs, leading to an increase in Teff cell proliferation. Once-daily oral administration of PVTX-405 as single agent significantly delays the growth of MC38 tumors in a syngeneic tumor model using humanized CRBN mice. PVTX-405 in combination with anti-PD1 or anti-LAG3 significantly increases animal survival compared to anti-PD1 or anti-LAG3 alone. Together, these results demonstrate that PVTX-405 is a promising IKZF2 degrader for clinical development for the treatment of human cancers.

Targeted degradation of extracellular proteins: state of the art and diversity of degrader designs

Selective elimination of proteins associated with the pathogenesis of diseases is an emerging therapeutic modality with distinct advantages over traditional inhibitor-based approaches. This strategy, called targeted protein degradation (TPD), is based on hijacking the cellular proteolytic machinery using chimeric degrader molecules that physically link the target protein of interest with the degradation effectors. The TPD era began with the development of PROteolysis TAtrgeting Chimeras (PROTACs) in 2001, with various methods and applications currently available. Classical PROTAC molecules are heterobifunctional chimeras linking target proteins with E3 ubiquitin ligases. This induced interaction leads to the ubiquitylation of the target protein, which is needed for its recognition and subsequent degradation by the cellular proteasomes. However, this technology is limited to intracellular proteins since the effectors involved (E3 ubiquitin ligases and proteasomes) are located in the cytosol. The related methods for selective destruction of proteins present in the extracellular space have only emerged recently and are collectively termed extracellular TPD (eTPD). The prototypic eTPD technology utilizes LYsosomal TArgeting Chimeras (LYTACs) that link extracellular target proteins (secreted or membrane-associated) to lysosome-targeting receptors (LTRs) on the cell surface. The resulting complex is then internalized by endocytosis and trafficked to lysosomes, where the target protein is degraded. The successful elimination of various extracellular proteins via LYTACs and related approaches has been reported, including several important targets in oncology that drive tumor growth and dissemination. This review summarizes current progress in the eTPD field and focuses primarily on the respective technological developments. It discusses the design principles and diversity of degrader molecules and the landscape of available targets and effectors that can be employed for eTPD. Finally, it emphasizes current open questions, challenges, and perspectives of this technological platform to promote the expansion of the eTPD toolkit and further development of its therapeutic applications.

Resistance to immunomodulatory drugs in multiple myeloma: the cereblon pathway and beyond

Acquired resistance to immunomodulatory drugs (IMiD) remains a significant unmet need in the treatment landscape of multiple myeloma (MM). The cereblon (CRBN) pathway-dependent mechanisms are known to be vital contributors to IMiD resistance; however, they may account for only a small proportion. Recent research has unveiled additional mechanisms of acquired IMiD resistance that are independent of the CRBN pathway. In this review, we provide a comprehensive overview of the existing work on IMiD resistance in MM, focusing specifically on the emerging evidence of CRBN pathway-independent mechanisms. Finally, we discuss the plausible actionable strategies and outlook for IMiD-based therapies moving forward.

IKAROS levels are associated with antigen escape in CD19- and CD22-targeted therapies for B-cell malignancies

Antigen escape relapse is a major challenge in targeted immunotherapies, including CD19- and CD22-directed chimeric antigen receptor (CAR) T-cell for B-cell acute lymphoblastic leukemia (B-ALL). To identify tumor-intrinsic factors driving antigen loss, we perform single-cell analyses on 61 B-ALL patient samples treated with CAR T cells. Here we show that low levels of IKAROS in pro-B-like B-ALL cells before CAR T treatment correlate with antigen escape. IKAROSlow B-ALL cells undergo epigenetic and transcriptional changes that diminish B-cell identity, making them resemble progenitor cells. This shift leads to reduced CD19 and CD22 surface expression. We demonstrate that CD19 and CD22 expression is IKAROS dose-dependent and reversible. Furthermore, IKAROSlow cells exhibit higher resistance to CD19- and CD22-targeted therapies. These findings establish a role for IKAROS as a regulator of antigens targeted by widely used immunotherapies and in the risk of antigen escape relapse, identifying it as a potential prognostic target.

Epigenetic Plasticity Drives Carcinogenesis and Multi-Therapy Resistance in Multiple Myeloma

We demonstrate that carcinogenesis and multi-therapy resistance in multiple myeloma (MM)-a treatable yet incurable plasma cell malignancy-are driven by epigenetic dysregulation. In this new paradigm, genomic and cytogenetic events unlock epigenetic plasticity, reshaping MM cell biology to evade tumor microenvironment constraints and therapeutic pressure. These conclusions are derived from a newly assembled cohort of nearly 1,000 patients, spanning premalignant to late-stage refractory MM, comprehensively characterized at molecular and clinical levels. Our findings provide a unifying framework to explain inter-patient genomic heterogeneity and the emergence of therapy resistance in sequential samples without new genomic alterations. In conclusion, we propose targeting epigenetic plasticity-mediated plasma cell evasion as a promising therapeutic strategy in MM.

The Importance of Cancer Stem Cells and Their Pathways in Endometrial Cancer: A Narrative Review

Endometrial cancer is one of the most common malignancies seen in women in developed countries. While patients in the early stages of this cancer show better responses to surgery, adjuvant hormonal therapy, and chemotherapy, patients with recurrence show treatment resistance. Researchers have recently focused on cancer stem cells (CSCs) in the treatment of gynecologic cancer in general but also specifically in endometrial cancer. CSCs have been investigated because of their resistance to conventional therapies, such as chemo- and radiotherapy, and their ability to induce the progression and recurrence of malignancy. The activation of alternative pathways, such as WNT, PI3K, NF-kB, or NOTCH, could be the basis of the acquisition of these abilities of CSCs. Their specific markers and signaling pathways could be treatment targets for CSCs. In this article, we discuss the importance of obtaining a better understanding of the molecular basis and pathways of CSCs in endometrial cancer and the role of CSCs, aiming to discover more specific therapeutic approaches.

Deubiquitinase-Targeting Chimeras (DUBTACs) as a Potential Paradigm-Shifting Drug Discovery Approach

Developing proteolysis-targeting chimeras (PROTACs) is well recognized through target protein degradation (TPD) toward promising therapeutics. While a variety of diseases are driven by aberrant ubiquitination and degradation of critical proteins with protective functions, target protein stabilization (TPS) rather than TPD is emerging as a unique therapeutic modality. Deubiquitinase-targeting chimeras (DUBTACs), a class of heterobifunctional protein stabilizers consisting of deubiquitinase (DUB) and protein-of-interest (POI) targeting ligands conjugated with a linker, can rescue such proteins from aberrant elimination. DUBTACs stabilize the levels of POIs in a DUB-dependent manner, removing ubiquitin from polyubiquitylated and degraded proteins. DUBTACs can induce a new interaction between POI and DUB by forming a POI-DUBTAC-DUB ternary complex. Herein, therapeutic benefits of TPS approaches for human diseases are introduced, and recent advances in developing DUBTACs are summarized. Relevant challenges, opportunities, and future perspectives are also discussed.

An updated review on the role of small molecules in mediating protein degradation

Targeted protein degradation (TPD) technologies, inspired by physiological processes, have recently provided new directions for drug development. Unlike conventional drug development focusing on targeting the active sites of disease-related proteins, TPD can utilize any nook or cranny of a protein to drive degradation through the cell's inherent destruction mechanism. It offers various advantages such as stronger pharmacological effects, an expanded range of drug targets, and higher selectivity. Based on the ubiquitin-proteasome system and the lysosomal degradation pathway, a variety of TPD strategies have been developed including PROTAC, PROTAB, and AUTOTAC. These TPD strategies have continuously enriched the toolbox for targeted protein degradation and expanded the scope of application, providing new ideas for biological research and drug discovery. This review attempts to introduce up-to-date research progress in the TPD strategies, focusing mainly on their design concepts, advantages, potential applications, and challenges, which may provide some inspiration for drug design, drug discovery, and clinical application for biologists and chemists.

Identification of E3 Ubiquitin Ligase Substrates Using Biotin Ligase-Based Proximity Labeling Approaches

Ubiquitylation is a post-translational modification originally identified as the first step in protein degradation by the ubiquitin-proteasome system. Ubiquitylation is also known to regulate many cellular processes without degrading the ubiquitylated proteins. Substrate proteins are specifically recognized and ubiquitylated by ubiquitin ligases. It is necessary to identify the substrates for each ubiquitin ligase to understand the physiological and pathological roles of ubiquitylation. Recently, a promiscuous mutant of a biotin ligase derived from Escherichia coli, BioID, and its variants have been utilized to analyze protein-protein interaction. In this review, we summarize the current knowledge regarding the molecular mechanisms underlying ubiquitylation, BioID-based approaches for interactome studies, and the application of BirA and its variants for the identification of ubiquitin ligase substrates.

The "three body solution": Structural insights into molecular glues

Molecular glues are small molecules that nucleate novel or stabilize natural, protein-protein interactions resulting in a ternary complex. Their success in targeting difficult to drug proteins of interest has led to ever-increasing interest in their use as therapeutics and research tools. While molecular glues and their targets vary in structure, inspection of diverse ternary complexes reveals commonalities. Whether of high or low molecular weight, molecular glues are often rigid and form direct hydrophobic interactions with their target protein. There is growing evidence that these hotspots can accommodate multiple ternary complex binding modes and enable targeting of traditionally undruggable targets. Advances in screening from the molecular glue degrader literature and insights in structure-based drug design, especially from the non-degrading tri-complex work, are likely intersectional.

Implications of frequent hitter E3 ligases in targeted protein degradation screens

Targeted protein degradation (TPD) offers a promising approach for chemical probe and drug discovery that uses small molecules or biologics to direct proteins to the cellular machinery for destruction. Among the >600 human E3 ligases, CRBN and VHL have served as workhorses for ubiquitin-proteasome system-dependent TPD. Identification of additional E3 ligases capable of supporting TPD would unlock the full potential of this mechanism for both research and pharmaceutical applications. This perspective discusses recent strategies to expand the scope of TPD and the surprising convergence of these diverse screening efforts on a handful of E3 ligases, specifically DCAF16, DCAF11 and FBXO22. We speculate that a combination of properties, including superficial ligandability, potential for promiscuous substrate interactions and high occupancy in Cullin-RING complexes, may position these E3 ligases as 'low-hanging fruit' in TPD screens. We also discuss complementary approaches that might further expand the E3 ligase landscape supporting TPD.

Research advancements in molecular glues derived from natural product scaffolds: Chemistry, targets, and molecular mechanisms

The mechanism of action of traditional Chinese medicine (TCM) remains unclear. Historically, research on TCM has mainly focused on exploring the mechanisms of active components acting on single targets. However, it is insufficient to explain the complex mechanisms by which these active components in TCM treat diseases. In recent years, the emergence of molecular glues (MGs) theory has provided new strategies to address this issue. MGs are small molecules that can promote interactions between proteins at their interface. The characteristic of MGs is to establish connections between diverse protein structures, thereby enabling a chemically-mediated proximity effect that triggers a wide spectrum of biological functions. Natural products are the result of billions of years of evolutionary processes in the natural environment. Thus, the extensive structural diversity of natural products renders them a rich source of MGs, including polyketides, terpenoids, steroids, lignans, organic acids, alkaloids and other classes. Currently, several well-known natural MGs, including the immunosuppressants cyclosporin A (CsA) and tacrolimus (FK506), as well as the anticancer agent taxol, have been incorporated into clinical practice. Meanwhile, the advancement of new technologies is propelling the discovery of novel MGs from natural products. Thus, we primarily summarize a growing variety of MGs from natural origins reported in recent years and categorize them based on the chemical structural types. Moreover, the main sources of TCM are natural products. The discovery of natural MGs promises to provide a new perspective for the elucidation of the molecular mechanism behind the efficiency of TCM. In summary, this review aims to provide insights from the perspective of natural products that could potentially influence TCM and modern drug development.

Advancing brain tumor therapy: unveiling the potential of PROTACs for targeted protein degradation

The long-term treatment of malignancies, particularly brain tumors, is challenged by abnormal protein expression and drug resistance. In terms of potency, selectivity, and overcoming drug resistance, Proteolysis Targeting Chimeras (PROTACs), a cutting-edge method used to selectively degrade target proteins, beats traditional inhibitors. This review summarizes recent research on using PROTACs as a therapeutic strategy for brain tumors, focusing on their mechanism, benefits, limitations, and the need for optimization. The review draws from a comprehensive search of peer-reviewed literature, scientific databases, and clinical trial databases. Articles published up to the knowledge cutoff date up to 14 April 2023 were included. Inclusion criteria covered PROTAC-based brain tumor therapies, including preclinical and early clinical studies, with no restrictions on design or publication type. We included studies using in vitro, in vivo brain tumor models, and human subjects. Eligible treatments involved PROTACs targeting proteins linked to brain tumor progression. We evaluated the selected studies for methodology, including design, sample size, and data analysis techniques. A narrative synthesis summarized key outcomes and trends in PROTAC-based brain tumor therapy. Recent research shows PROTACs selectively degrade brain tumor-related proteins with minimal off-target effects. They offer enhanced potency, selectivity, and the ability to combat resistance compared to traditional inhibitors. PROTACs hold promise for brain tumor treatment offering advantages over traditional inhibitors, but more research is needed to refine their mechanisms, efficacy, and safety. Larger-scale trials and translational studies are essential for assessing their clinical utility.

RBM39 Functions as a Potential Oncogene Through the NF-κB Signaling Pathway in Colorectal Cancer Cells

Colorectal cancer (CRC) ranks as the third most frequently diagnosed cancer and is the second leading cause of cancer-related deaths globally. Recently, RNA-binding protein 39(RBM39), a critical factor in tumor-targeted mRNA and protein expression, has played a vital role in tumorigenesis and has broad development prospects in clinical treatment and drug research. However, the functional roles of RBM39 in the progression of CRC remain largely unexplored. This study found that RBM39 is notably overexpressed at both the mRNA and protein levels in CRC tissues compared with normal adjacent tissues. RBM39 was identified as a potential therapeutic target for colorectal cancer. Elevated RBM39 mRNA levels in CRC patients indicated worse survival probabilities. We show that RBM39 enhances the proliferation, migration, and invasion ability of CRC cells. Furthermore, we have made an innovative discovery that increased RBM39 inhibits apoptosis in CRC cells. Mechanistically, RNA-seq analysis indicated that RBM39 activates the NF-κB pathway, which plays a pivotal role in driving the malignant biological behaviors of colorectal cancer. Notably, these findings represent a novel contribution to our understanding of the mechanistic underpinnings of CRC, as they have not been previously documented in the literature. In the in vivo nude mouse xenograft model, our study demonstrates that the targeted knockdown of RBM39 markedly suppresses tumor formation, highlighting a novel therapeutic strategy for combating colorectal cancer. In conclusion, RBM39 emerges as a promising candidate for clinical diagnosis and targeted treatment of colorectal cancer, with implications for future research in tumor biology and therapeutic strategies.

A method for the detection and enrichment of endogenous cereblon substrates

C-Terminal cyclic imides are posttranslational modifications on proteins that are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN). Despite the observation of these modifications across the proteome by mass spectrometry-based proteomics, an orthogonal and generalizable method to visualize the C-terminal cyclic imide would enhance detection, sensitivity, and throughput of endogenous CRBN substrate characterization. Here we develop an antibody-like reagent, termed "cerebody," for visualizing and enriching C-terminal cyclic imide-modified proteins. We describe the engineering of CRBN derivatives to produce cerebody and use it to identify CRBN substrates by Western blot and enrichment from whole cell and tissue lysates. CRBN substrates identified by cerebody enrichment are mapped, validated, and further characterized for dependence on the C-terminal cyclic imide modification. These methods will accelerate the characterization of endogenous CRBN substrates and their regulation.

Progress of immune senescence in multiple myeloma treatment resistance

Multiple myeloma has become the second most common hematologic malignancy threatening human health with the increasing incidence in the population, and the emergence of drug resistance in its treatment has become a problem that needs to be solved urgently. Recent studies have shown that the immune system is closely related to the development of multiple myeloma, and immune senescence plays an extremely critical role in MM treatment resistance. In this paper, we review the connection between immune senescence and the development of MM and its possible role in the drug resistance of MM treatment, to provide new research ideas for the in-depth study of the mechanism of immune senescence and the search for new immunotherapeutic targets to overcome the phenomenon of drug resistance in the immunotherapy of MM patients.

PCMT1 generates the C-terminal cyclic imide degron on CRBN substrates

The E3 ligase substrate adapter cereblon (CRBN), the primary target of clinical agents thalidomide and lenalidomide, recognizes endogenous substrates bearing the C-terminal cyclic imide modification. Although C-terminal cyclic imides can form spontaneously, an enzyme that regulates the formation of these modifications and thereby promotes a biological pathway connecting substrates to CRBN is unknown. Here, we report that protein carboxymethyltransferase (PCMT1) promotes formation of the C-terminal cyclic imide on C-terminal asparagine residues of CRBN substrates. PCMT1 and CRBN co-regulate the levels of metabolic enzymes glutamine synthetase (GLUL) and inorganic pyrophosphatase 1 (PPA1) in vitro, in cells, and in vivo, and this regulation is associated with the proepileptic phenotype of CRBN knockout mouse models. The discovery of an enzyme that regulates CRBN substrates through the C-terminal cyclic imide modification reveals a previously unknown biological pathway that is perturbed by thalidomide derivatives and provides a biochemical basis for the connection between multiple biological processes and CRBN.

Dual CARM1-and IKZF3-targeting: A novel approach to multiple myeloma therapy synergy between CARM1 inhibition and IMiDs

Advancements in the treatment of multiple myeloma (MM) have resulted in an improvement in the survival rate. However, there continues to be an urgent need for improved therapies. The protein arginine methyltransferase, CARM1 (coactivator associated arginine methyltransferase 1), is emerging as a potential cancer therapy target and inhibitors have been developed. MM cell lines are particularly dependent on CARM1 for cell survival. Here, we show that targeting of CARM1 through small molecule inhibition potentiates the activity of immunomodulatory drugs (IMiDs) in cell line models of MM. This likely occurs through synergistic targeting of Aiolos (IKZF3) and MYC expression. Rational design of a new molecule, 074, which consists of a CARM1 inhibitor linked to the IMiD pomalidomide, was carried out and treatment with this agent led to more potent killing of MM cells than either the CARM1 inhibitor or the IMiD as single agents. Importantly, 074 was able to override IMiD resistance. Taken together, our results demonstrate that dual CARM1/IKZF3-targeting agents represent a promising novel therapeutic strategy for MM and IMiD-resistant disease.

Structure-guided design of a truncated heterobivalent chemical probe degrader of IRE1α

IRE1α is an ER protein involved in the unfolded protein response (UPR) and dysregulation of the ER stress pathway has been implicated in several diseases. Inhibitors of the cytoplasmic endonuclease or kinase domains of the enzyme have limited utility and targeted degradation would address additional scaffolding functions of the protein. Here, we describe the design and development of IRE1α proteolysis targeting chimeras (PROTACs) based on a lysine-reactive salicylaldehyde RNase inhibitor, and present the structure-activity relationships (SARs) that delivered the first highly selective degraders of a native ER-membrane associated protein. Medicinal chemistry optimization exploited ternary complex computational modelling to inform design, HiBiT-SpyTag IRE1α degradation and NanoBRET cereblon occupancy cell-based assays to generate SARs, and mass spectrometry-based proteomics to assess broad selectivity in an unbiased manner. Merging IRE1α and CRBN ligand chemotypes provided the truncated chimera CPD-2828 with physicochemical properties more akin to an oral molecular glue degrader than a traditional PROTAC.

Development of Ethyl-Hydrazide-Based Selective Histone Deacetylase 6 (HDAC6) PROTACs

Histone deacetylases (HDACs) are promising targets for epigenetic drug discovery. Additionally, targeted degradation of HDACs has emerged as a novel approach in medicinal chemistry and chemical biology. However, most inhibitors and degraders rely on the potentially genotoxic hydroxamate as a zinc-binding group (ZBG). In this study, we present the development of HDAC6-directed proteolysis-targeting chimeras (PROTACs) featuring an ethyl hydrazide moiety as an alternative ZBG. This approach avoids the genotoxicity concerns of hydroxamates while maintaining potent HDAC6 degradation. We synthesized a series of CRBN- and VHL-recruiting PROTACs and identified several potent HDAC6 degraders (HDAC6 D max > 80%). Among these, 17c was the most effective, achieving an HDAC6 degradation of 91% and a DC50 value of 14 nM. Further characterization proved that 17c acts via the ubiquitin-proteasome system and chemoproteomics confirmed selective HDAC6 degradation over other HDAC isoforms.

Discovery of AK-1690: A Potent and Highly Selective STAT6 PROTAC Degrader

STAT6 is an attractive therapeutic target for human cancers and other human diseases. Starting from a STAT6 ligand with Ki = 3.5 μM binding affinity, we obtained AK-068 with Ki = 6 nM to STAT6 and at least >85-fold binding selectivity over STAT5. Using AK-068 and cereblon ligands, we discovered AK-1690 as the first, potent and selective PROTAC STAT6 degrader. AK-1690 effectively induces degradation of STAT6 protein in cells with DC50 values of as low as 1 nM while showing minimal effect on other STAT members up to 10 μM. A single dose of AK-1690 effectively depletes STAT6 in mouse tissues. Determination of the first cocrystal structure of STAT6 in complex with AK-1690 provides a structural basis for their interactions. AK-1690 is a powerful tool with which to investigate the roles of STAT6 in human diseases and biological processes and a promising lead compound for further optimization.

The ADAR1-regulated cytoplasmic dsRNA-sensing pathway is a novel mechanism of lenalidomide resistance in multiple myeloma

ABSTRACT

Immunomodulatory drugs (IMiDs) are a major class of drugs for treating multiple myeloma (MM); however, acquired resistance to IMiDs remains a significant clinical challenge. Although alterations in cereblon and its pathway are known to contribute to IMiD resistance, they account for only 20% to 30% of cases, and the underlying mechanisms in the majority of the resistance cases remain unclear. Here, we identified adenosine deaminase acting on RNA1 (ADAR1) as a novel driver of lenalidomide resistance in MM. We showed that lenalidomide activates the MDA5-mediated double-stranded RNA (dsRNA)-sensing pathway in MM cells, leading to interferon (IFN)-mediated apoptosis, with ADAR1 as the key regulator. Mechanistically, ADAR1 loss increased lenalidomide sensitivity through endogenous dsRNA accumulation, which in turn triggered dsRNA-sensing pathways and enhanced IFN responses. Conversely, ADAR1 overexpression reduced lenalidomide sensitivity, attributed to increased RNA editing frequency, reduced dsRNA accumulation, and suppression of the dsRNA-sensing pathways. In summary, we report the involvement of ADAR1-regulated dsRNA sensing in modulating lenalidomide sensitivity in MM. These findings highlight a novel RNA-related mechanism underlying lenalidomide resistance and underscore the potential of targeting ADAR1 as a novel therapeutic strategy.

Effect of metachronous primary and secondary solid cancers in patients with multiple myeloma: a retrospective study from a single-center

Statement of translational relevance

Effects of metachronous primary malignant solid tumor (MPMST) on survival risk and prognosis of multiple myeloma (MM) and differences between MPMST occurring before and after MM remains unclear. Use of well-characterized clinical information of individual patient, we found that older patients with MM (≥ 65 years) had a higher risk of developing MPMST. Patients with MM and MPMST including male patients, aged ≥ 65 years and those with ISS stage III had a worse prognosis. The top three solid cancers occurred before and after MM were the lung, thyroid, and breast cancer. These findings provide detailed information for the precise treatment of patients with MM and MPMST.

Objective

To analyze the effects of MPMST on MM and the risk difference of MPMSTs occurring before and after MM.

Methods

Retrospective data from patients with MM and MPMST, including sex, age, immunoglobulin isotype, ISS stage, and therapy, were collected from 2015 to 2023. Differences in variables, risk, and survival were compared using the χ² test, logistic regression analysis and the Cox model, respectively.

Results

The 34 (1.57%) patients with MM and MPMST identified from a total of 2167 MM patients had a shorter overall survival. The survival risk was higher in male patients with MM and MPMST (HR: 3.96, 95% CI: 1.05 -14.96), in those aged ≥ 65 years (HR: 3.30, 95% CI: 1.41 -7.71), and with ISS stage III (HR: 4.08, 95% CI: 0.81-20.65). Patients with MM subsequent to CAR-T cell therapy had neither enhanced incidence rates of second solid cancers nor had longer overall survival time. Furthermore, the top three solid cancers occurred before or after MM were lung, thyroid, and breast cancer.

Conclusion

Male patients, aged ≥ 65 years and MM patients with ISS stage III and MPMST had a worse prognosis.

Lasalocid A selectively induces the degradation of MYD88 in lymphomas harboring the MYD88 L265P mutation

ABSTRACT

Myeloid differentiation primary response protein 88 (MYD88) is a key adaptor molecule in the signaling pathways of toll-like receptor and interleukin-1 receptor. A somatic mutation resulting in a leucine-to-proline change at position 265 of the MYD88 protein (MYD88 L265P) is one of the most prevalent oncogenic mutations found in patients with hematological malignancies. In this study, we used high-throughput screening to identify lasalocid A as a potent small molecule that selectively inhibited the viability of lymphoma cells expressing MYD88 L265P and the associated activation of NF-κB. Further investigations using CRISPR-CRISPR-associated protein 9 genetic screening, proteomics, and biochemical assays revealed that lasalocid A directly binds to the MYD88 L265P protein, enhancing its interaction with the ubiquitin ligase RNF5. This interaction promotes MYD88 degradation through the ubiquitin-dependent proteasomal pathway, specifically in lymphomas with the MYD88 L265P mutation. Lasalocid A exhibited strong antitumor efficacy in xenograft mouse models, induced disease remission in ibrutinib-resistant lymphomas, and showed synergistic activity with the B-cell lymphoma 2 inhibitor venetoclax. This study highlights the potential of inducing MYD88 L265P degradation using small molecules, offering promising strategies for treating lymphomas that harbor the MYD88 L265P mutation.

Targeting ABCD1-ACOX1-MET/IGF1R axis suppresses multiple myeloma

Multiple myeloma (MM) remains an incurable hematological malignancy that necessitates the identification of novel therapeutic strategies. Here, we report that intracellular levels of very long chain fatty acids (VLCFAs) control the cytotoxicity of MM chemotherapeutic agents. Inhibition of VLCFA biosynthesis reduced cell death in MM cells caused by the proteasome inhibitor, bortezomib. Conversely, inhibition of VLCFA degradation via suppression of peroxisomal acyl-CoA oxidase 1 (ACOX1) increased the cytotoxicity of bortezomib, its next-generation analog, carfilzomib, and the immunomodulatory agent lenalidomide. Furthermore, treatment with an orally available ACOX1 inhibitor cooperated with bortezomib in suppressing the growth of bortezomib-resistant MM xenografts in mice. Increased VLCFA levels caused by genetic or pharmacological inhibition of VLCFA degradation reduced the activity of two major kinases involved in MM pathogenesis, MET proto-oncogene (MET) and insulin-like growth factor 1 receptor (IGF1R). Mechanistically, inhibition of ACOX1 promoted the accumulation of VLCFA-containing cerebrosides, altered MET and IGF1R interaction with a cerebroside analog, and selectively inhibited the association of these kinases with the plasma membrane signaling platforms, importantly, without disrupting the platforms' integrity. Our study revealed a specific metabolic vulnerability of MM cells and identified a targetable axis linking VLCFA metabolism to the regulation of MET and IGF1R activity.

Can we develop effective direct or indirect inhibitors of transcription factors? On the clinical evolution of protein degraders for multiple myeloma therapy

INTRODUCTION

Transcription factors (TFs) are master regulators of cellular function and orchestrate diverse signaling pathways and processes. Acting as convergence points of signaling pathways, they integrate extracellular stimuli with intracellular responses to regulate cell functions. Dysregulation of TFs drives tumorigenesis including proliferation, drug resistance, and immune evasion of multiple myeloma (MM), the second most-common hematologic malignancy.

AREAS COVERED

The discovery that IMiDs are molecular glue degraders, which reprogram the E3-ligase cereblon (CRBN) to ubiquitinate and degrade IKZF1 and IKZF3, two otherwise un-druggable crucial TFs in MM, gave rise to the widespread interest in proximity-induced protein-degradation as an exciting novel therapeutic strategy. This review summarizes our up-to-date knowledge on the pre/clinical development of IMiD-related, more potent CRBN E3-Ligase Modulatory Drugs (CELMoDs), directed PROteolysis TArgeting Chimeras (PROTACs) and degronomids as well as on promising future avenues in the field of targeted protein-degradation (TPD).

EXPERT OPINION

TPD is an emerging field to treat cancer, including MM. CELMoDs are already reshaping the treatment landscape of MM. Preclinical data on PROTACs are promising. Nevertheless, a deeper understanding of TF biology as well as further advancements in screening methodologies and chemoproteomics are crucial to further spur the transformative potential of targeted TF degradation in MM.

SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation

Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable." This strategy induces the degradation of target proteins rather than inhibiting their activity, achieving desirable therapeutic outcomes. Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) are the primary small molecules that induce TPD. Both types of molecules form a ternary complex linking an E3 ubiquitin ligase with a target protein, a crucial step for drug discovery. While significant advances have been made in in-silico binary structure prediction for proteins and small molecules, ternary structure prediction remains challenging due to obscure interaction mechanisms and insufficient training data. Traditional methods relying on manually assigned rules perform poorly and are computationally demanding due to extensive random sampling. In this work, we introduce DeepTernary, a novel deep learning-based approach that directly predicts ternary structures in an end-to-end manner using an encoder-decoder architecture. DeepTernary leverages an SE(3)-equivariant graph neural network (GNN) with both intra-graph and ternary inter-graph attention mechanisms to capture intricate ternary interactions from our collected high-quality training dataset, TernaryDB. The proposed query-based Pocket Points Decoder extracts the 3D structure of the final binding ternary complex from learned ternary embeddings, demonstrating state-of-the-art accuracy and speed in existing PROTAC benchmarks without prior knowledge from known PROTACs. It also achieves notable accuracy on the more challenging MGD benchmark under the blind docking protocol. Remarkably, our experiments reveal that the buried surface area calculated from DeepTernary-predicted structures correlates with experimentally obtained degradation potency-related metrics. Consequently, DeepTernary shows potential in effectively assisting and accelerating the development of TPDs for previously undruggable targets.

Combinatorial mapping of E3 ubiquitin ligases to their target substrates

E3 ubiquitin ligases (E3s) confer specificity of protein degradation through ubiquitination of substrate proteins. Yet, the vast majority of the >600 human E3s have no known substrates. To identify proteolytic E3-substrate pairs at scale, we developed combinatorial mapping of E3 targets (COMET), a framework for testing the role of many E3s in degrading many candidate substrates within a single experiment. We applied COMET to SCF ubiquitin ligase subunits that mediate degradation of target substrates (6,716 F-box-ORF [open reading frame] combinations) and E3s that degrade short-lived transcription factors (TFs) (26,028 E3-TF combinations). Our data suggest that many E3-substrate relationships are complex rather than 1:1 associations. Finally, we leverage deep learning to predict the structural basis of E3-substrate interactions and probe the strengths and limits of such models. Looking forward, we consider the practicality of transposing this framework, i.e., computational structural prediction of all possible E3-substrate interactions, followed by multiplex experimental validation.

Cullin-RING ligase BioE3 reveals molecular-glue-induced neosubstrates and rewiring of the endogenous Cereblon ubiquitome

BACKGROUND

The specificity of the ubiquitination process is mediated by the E3 ligases. Discriminating genuine substrates of E3s from mere interacting proteins is one of the major challenges in the field. We previously developed BioE3, a biotin-based approach that uses BirA-E3 fusions together with ubiquitin fused to a low-affinity AviTag to obtain a site-specific and proximity-dependent biotinylation of the substrates. We proved the suitability of BioE3 to identify targets of RING and HECT-type E3 ligases.

METHODS

BioE3 experiments were performed in HEK293FT and U2OS stable cell lines expressing TRIPZ-bioGEFUb transiently transfected with BirA-cereblon (CRBN). Cells were seeded using biotin-free media, followed later by a short-biotin pulse. We evaluated the applicability of the BioE3 system to CRBN and molecular glues by Western blot and confocal microscopy, blocking the proteasome with bortezomib, inhibiting NEDDylation with MLN4924 and treating the cells with pomalidomide. For the identification of endogenous substrates and neosubstrates we analyzed the eluates of streptavidin pull-downs of BioE3 experiments by LC-MS/MS. Analysis of targets for which ubiquitination changes significantly upon treatment was done using two-sided Student's t-test. Orthogonal validations were performed by histidine pull-down, GFP-trap and computational modelling.

RESULTS

Here we demonstrate that BioE3 is suitable for the multi-protein complex Cullin-RING E3s ligases (CRLs), the most utilized E3-type for targeted protein degradation (TPD) strategies. Using CRBN as proof of concept, one of the substrate receptors of CRL4 E3 ligase, we identified both endogenous substrates and novel neosubstrates upon pomalidomide treatment, including CSDE1 which contains a G-loop motif potentially involved in the binding to CRBN in presence of pomalidomide. Importantly, we observed a major rearrangement of the endogenous ubiquitination landscape upon treatment with this molecular glue.

CONCLUSIONS

The ability of BioE3 to detect and compare both substrates and neosubstrates, as well as how substrates change in response to treatments, will facilitate both on-target and off-target identifications and offer a broader characterization and validation of TPD compounds, like molecular glues and PROTACs.