Brendan Dwyer

All Publications

• A bivalent molecular glue linking lysine acetyltransferases to oncogene-induced cell death. Cell Nix, M. N., Gourisankar, S., Bowman, K. J., Nettles, S. A., Yang, H., Dwyer, B. G., Sarott, R. C., Abuzaid, H., Martinez, M. M., Phillips, N., Cabaud, V., Hakobyan, A., Arakelov, V., Petrosyan, G., Davtyan, A., Wang, Y., Simanauskaite, J. M., Romero, B. A., Jones, H. M., Krokhotin, A., Lowensohn, T. N., Chen, L., Low, C., Vogel, H., Davis, M. M., Fernandez, D., Zhang, T., Green, M. R., Hinshaw, S. M., Gray, N. S., Crabtree, G. R. 2026

  Abstract

  Developing cancer therapies that induce specific death of malignant cells is critical for preventing relapse. Highly effective strategies, such as immunotherapy, exemplify this principle. Here, we provide the mechanistic basis for a small-molecule approach that leverages chemically induced proximity (CIP) to kill diffuse large B cell lymphoma, the most common non-Hodgkin lymphoma. We developed lysine acetyltransferase (KAT)-based TCIPs (transcriptional/epigenetic chemical inducers of proximity), or KAT-TCIPs, which redirect p300/CREB-binding protein (CBP) to activate cell-death networks repressed by the oncogenic driver BCL6. Our lead KAT-TCIP reprograms the epigenome to initiate apoptosis. The crystal structure of the chemically induced p300-BCL6 complex reveals how chance protein-protein interactions may be exploited to confer the potency and selectivity of KAT-TCIPs. Thus, oncogenic drivers can be co-opted to activate robust cell death. Consistent with their gain-of-function mechanism, TCIPs recruiting different transcriptional activators-p300, BRD4, or CDK9-produce distinct genomic responses, suggesting specialized therapeutic uses.

  View details for DOI 10.1016/j.cell.2026.06.037

  View details for PubMedID 42476129

• A Type II CDK6 Degrader Enables Cellular Targeting beyond the Limits of Type II Inhibition. Journal of the American Chemical Society Kim, J. H., Mills, C. E., Kozicka, Z., Scott, D. C., Jin, C., Jiang, Z., Dwyer, B. G., Geng, Q., Toenjes, S. T., Byun, W. S., ElHarouni, D., Li, H., Ligon, K. L., Thornhill, A. M., Jones, H. M., Romero, B. A., Hinshaw, S. M., Ebert, B. L., Schulman, B. A., Donovan, K. A., Fischer, E. S., Gray, N. S. 2026

  Abstract

  PROTACs are commonly developed by linking E3 ligase-recruiting ligands to established inhibitors of a protein target, often resulting in degraders that retain enzymatic inhibition. Type II inhibition of cyclin-dependent kinases (CDKs) has been challenging, as reported compounds generally exhibit weak biochemical potency and limited cellular activity. Consistent with these limitations, most reported CDK degraders have been derived from type I ATP-competitive inhibitors. Here, we explored whether targeted protein degradation could enable functional CDK targeting from a type II kinase scaffold. Using the multikinase inhibitor regorafenib as a starting scaffold, we generated a focused library of CRL4CRBN-recruiting bifunctional molecules and profiled their degradation activity using quantitative mass spectrometry-based proteomics. This analysis unexpectedly revealed CDK5 and CDK6, kinases not inhibited by the parent scaffold, as degradation targets. Optimization of this series led to JHK-02-108-2, a selective CDK6 degrader that does not display a hook effect and promotes potent CDK6 degradation despite weak CDK6 binding and negligible CDK6 inhibition. In cellular models of acute myeloid leukemia (AML) and glioblastoma, JHK-02-108-2 induced sustained G1 arrest and reduced phosphorylation of the retinoblastoma protein. Interestingly, subtle modifications in PROTAC architecture redirected degradation selectivity, yielding JHK-02-102-1 as a selective type II CDK5 degrader derived from the same scaffold. Together, these findings establish the first type II inhibitor-derived selective CDK6 degrader and demonstrate that targeted protein degradation can enable functional CDK targeting from type II kinase scaffolds.

  View details for DOI 10.1021/jacs.6c10277

  View details for PubMedID 42358219

• The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue. Cell chemical biology Hinshaw, S. M., Yuan, L., Noman, M. A., Martinez, M. J., Colombo, G. M., Dwyer, B. G., Ji, W., Romero, B. A., Forrest, I., Lu, J., Bian, J., Dunn, T. B., Garvin, E. R., Fernandez, D., Zhang, T., Gray, N. S., Corsello, S. M. 2026

  Abstract

  Molecular glues that induce new protein interactions can be potent therapeutics. We and others recently discovered that the small molecule PRLX-93936 (PRLX), which was originally developed as an erastin derivative with antitumor activity, is a molecular glue that alters the substrate specificity of the TRIM21 ubiquitin ligase. PRLX causes TRIM21 to bind the nuclear pore protein NUP98, triggering nuclear pore complex (NPC) degradation. We present here the structural and biochemical basis of NUP98 recognition, finding that ternary complex assembly depends on the creation of a composite TRIM21-small molecule surface competent for NUP98 binding. A scarcity of direct small molecule-NUP98 contacts likely explains how multiple structurally diverse TRIM21 ligands can induce NPC degradation. We also report the discovery of an enhanced molecular glue, MAN-021, and describe its structure. Our findings provide a basis for rational development of next-generation small molecules with enhanced or differentiated activities.

  View details for DOI 10.1016/j.chembiol.2026.04.016

  View details for PubMedID 42202785

• DNA damage chemical inducers of proximity (DD-CIP) for targeted cancer therapy Qiu, T., Lee, Y., Dwyer, B. G., Tan, Y., Chen, T., Romero, B. A., Wang, Y., Deng, J., Zhang, T., Crabtree, G. R., Hinshaw, S. M., Wong, K., Gray, N. S. AMER ASSOC CANCER RESEARCH. 2026: LB025

  View details for DOI 10.1158/1538-7445.AM2026-LB025

  View details for Web of Science ID 001744443300013

• Hijacking the BRD4-NUT fusion oncoprotein to activate programmed cell death Wang, K., Wang, Y., Qiu, T., Dwyer, B. G., Griffin, D., Shapiro, G. I., French, C. A., Gray, N. S., Crabtree, G. R. AMER ASSOC CANCER RESEARCH. 2026

  View details for DOI 10.1158/1538-7445.AM2026-7881

  View details for Web of Science ID 001734420600045

• A bivalent molecular glue linking lysine acetyltransferases to oncogene-induced cell death Nix, M., Gourisankar, S., Nettles, S., Bowman, K., Yang, H., Dwyer, B. G., Sarott, R. C., Abuzaid, H., Martinez, M., Krokhotin, A., Chen, L., Davis, M. M., Fernandez, D., Zhang, T., Green, M. R., Hinshaw, S. M., Gray, N. S., Crabtree, G. R. AMER ASSOC CANCER RESEARCH. 2026

  View details for DOI 10.1158/1538-7445.AM2026-3981

  View details for Web of Science ID 001734106300030

• Oncogenic SF3B1 mutations alter the splicing of mRNA noncoding regions to induce a novel therapeutic vulnerability. Blood Sekrecki, M., Sekrecka, A., Lattupally, R. R., Le, K., Jin, X., Mozes, C., Dwyer, B. G., Zhuang, Z., Romero, B. A., Pineda, J. M., Cao, X., Nguyen, L., Chen, V. W., Zhou, C., Wallace, J. A., Tanaka, K. L., Tiwari, C., Gabel, A., Kim, W. J., Stanley, R. F., Benbarche, S., Thind, J., Muruganandham, A., Zhang, T. Y., Greenberg, P. L., Gotlib, J., Mannis, G. N., Shomali, W., Salmasi, G. G., Kuo, C. J., Shanafelt, T. D., Singh, I., Inoue, D., Hansen, F. K., Gray, N. S., Van Rechem, C., Fakhri, B., Zhang, X., Lu, S. X. 2026

  Abstract

  Oncogenic mutations of SF3B1 are common in myeloid cancers, chronic lymphocytic leukemia (CLL) and select solid tumors. Their mechanistic basis for promoting oncogenesis has been investigated in detail, with the stereotyped missplicing of mRNA protein coding sequences most intensively studied. These changes, in genes such as MAP3K7, BRD9, and ABCB7, typically lead to loss-of-function, thus contributing to cancer pathogenesis.Here we systematically analyzed the impact of mutant SF3B1 on non-coding regions of mRNA transcripts across disease types, in both cell lines and primary patient specimens. This identified numerous novel and highly reproducible splicing alterations in such regions. Studies of one target gene, DCAF16, revealed multiple complex mutation-induced alterations in its 5' and 3' untranslated regions (5', 3' UTRs). Remarkably, these were mechanistically associated with increased DCAF16 protein levels in SF3B1 mutant cells, representing the first time that oncogenic SF3B1 has been shown to increase levels of a target protein in a gain-of-function manner. DCAF16 is a substrate recognition adapter for the DDB1/CUL4 E3 ubiquitin ligase complex. Novel protein degrader small molecules which co-opt DCAF16 to degrade BRD4 as a neosubstrate demonstrated preferential selectivity for SF3B1 mutant cancers and CLL primary patient specimens due to increased DCAF16 protein levels. In turn, this reveals the therapeutic relevance of mutant SF3B1 dysregulation of transcript untranslated regions and uncovers a novel strategy for the treatment of these important neoplasms.

  View details for DOI 10.1182/blood.2025029972

  View details for PubMedID 41587094

• Design and Development of DNA Damage Chemical Inducers of Proximity for Targeted Cancer Therapy. Journal of the American Chemical Society Qiu, T., Lee, Y. T., Dwyer, B. G., Tan, Y. J., Chen, T., Romero, B. A., Wang, Y., Deng, J., Zhang, T., Crabtree, G. R., Hinshaw, S. M., Wong, K., Gray, N. S. 2026

  Abstract

  Many chemotherapies are effective against cancers that display high levels of genome instability by disrupting or overwhelming the DNA damage response (DDR) to induce cell death. PARP inhibitors (PARPi) exploit this vulnerability by stalling DNA repair, particularly in homologous recombination-deficient cancer cells. Although PARPi are now used to treat BRCA1/2-mutated cancers such as ovarian and breast cancers, they are still limited to a narrow range of clinical indications and are susceptible to acquired resistance. Here, we introduce "DNA damage chemical inducers of proximity" (DD-CIPs), bivalent molecules that rewire the mechanism of action of conventional PARPi. The DD-CIPs function through chemically induced proximity between PARP1/2 and the chromatin remodeling protein, BRD4. From a candidate library of DD-CIPs, we identified DD-CIP1, which induces the DDR and apoptosis in cancer cells at two-digit nanomolar concentrations. Further optimization yielded DD-CIP2, which induces tumor cell death at nanomolar concentrations across diverse blood and solid cancer cells, including cancer types that are insensitive to PARPi. Using small-cell lung cancer (SCLC) as a model, we found that DD-CIP2 triggers DDR, cell cycle arrest, and apoptosis in vitro, leading to antitumor efficacy without substantial toxicity in preclinical SCLC xenograft models at well-tolerated doses. Our findings demonstrate that DD-CIPs may provide an opportunity to address the limitations of traditional PARPi and establish chemical-induced proximity as a strategy for modulating the DDR in cancer.

  View details for DOI 10.1021/jacs.5c17396

  View details for PubMedID 41480895

• Selective CDK6 Degradation via the KLHDC2 E3 Ubiquitin Ligase JOURNAL OF MEDICINAL CHEMISTRY Jeon, E., Kim, Y., Ahn, H., Martinez, M. J., Hwang, K., Cho, S., Dwyer, B. G., Romero, B. A., Hinshaw, S. M., Gray, N. S., Sim, T. 2025

  Abstract

  We discovered novel small molecule ligands of KLHDC2 and leveraged them to generate KLHDC2-mediated CDK6-selective degraders. Degrader 48a exhibited potent and selective CDK6 degradation (DC50 = 0.037 μM) over CDK4 (DC50 > 10 μM) in MOLM-14 cells, leading to pronounced G0/G1 cell-cycle arrest and apoptosis through inhibition of CDK6 downstream signaling. In addition, 48a demonstrated superior growth-inhibitory activity compared to the warhead, palbociclib, in several leukemia cells and displayed favorable microsomal stability. Proteomic profiling confirmed that 48a selectively degrades CDK6 with minimal effects on other CDK family members. Furthermore, 48a reduced tumor burden and CDK6 levels in an in vivo xenograft model. Collectively, these findings highlight the potential of KLHDC2-mediated degraders as a novel strategy for selective CDK6 degradation and underscore the promise of KLHDC2 as an alternative E3 ligase platform for targeted protein degradation.

  View details for DOI 10.1021/acs.jmedchem.5c02713

  View details for Web of Science ID 001630007800001

  View details for PubMedID 41329866

• Rewiring the Fusion Oncoprotein EWSR1::FLI1 in Ewing Sarcoma with Bivalent Small Molecules. Journal of the American Chemical Society Bond, M. J., Golden, R. P., DiGiovanni, G., Howard, B., Sarott, R. C., Karim, B. A., Gourisankar, S., Alexe, G., Ross, K., Jones, H. M., Dwyer, B. G., Gray, N. S., Stegmaier, K. 2025

  Abstract

  Dysregulated transcription is a defining hallmark of cancer. Recently, novel chemically induced proximity approaches have enabled the rewiring of transcriptional machinery to drive expression of pro-apoptotic genes using bivalent small molecules. In this work, we demonstrate that this strategy is amenable to relocalizing DNA bound transcriptional machinery, such as fusion transcription factors that commonly drive pediatric malignancies. Targeting fusion transcription factors, such as EWSR1::FLI1 in Ewing sarcoma, with these bivalent compounds may open new therapeutic avenues. Here, we develop a small molecule, EB-TCIP, that recruits FKBP12F36V-tagged EWSR1::FLI1 to DNA sites bound by the transcriptional regulator BCL6, leading to rapid chromatin remodeling and expression of BCL6 target genes. This proof-of-concept study demonstrates that DNA binding proteins with pioneering transcription factor activity, such as EWSR1::FLI1, can be relocalized on chromatin to induce expression of repressed genes. Insights herein will guide the development of future bivalent molecules that rewire DNA binding transcriptional machinery.

  View details for DOI 10.1021/jacs.5c05634

  View details for PubMedID 41307210

• Design and Development of DNA Damage Chemical Inducers of Proximity (DD-CIP) for Targeted Cancer Therapy. bioRxiv : the preprint server for biology Qiu, T., Lee, Y. T., Dwyer, B. G., Tan, Y. J., Chen, T., Romero, B. A., Wang, Y., Deng, J., Zhang, T., Crabtree, G. R., Hinshaw, S. M., Wong, K. K., Gray, N. S. 2025

  Abstract

  Many chemotherapies are effective against cancers that display high levels of genome instability by disrupting or overwhelming the DNA damage response to induce cell death. PARP inhibitors (PARPi) exploit this vulnerability by stalling DNA repair particularly in homologous recombination (HR)-deficient cancer cells. Although PARPi are now used to treat BRCA1/2-mutated cancers such as ovarian and breast cancers, they are still limited to a narrow range of clinical indications and are susceptible to acquired resistance. Here, we introduce "DNA Damage Chemical Inducers of Proximity" (DD-CIPs), bivalent molecules that rewire the mechanism of action of conventional PARPi. The DD-CIPs function through chemical induced proximity between PARP1/2 and the chromatin remodeling protein, BRD4. From a candidate library of DD-CIPs, we identified DD-CIP1 which induces the DNA damage response (DDR) and apoptosis to a range of cancer lines at two-digit nanomolar concentrations. Further optimization yielded DD-CIP2, which induces tumor cell death at nanomolar concentrations across diverse blood and solid cancer cells, including cancer types that are insensitive to PARPi. Using small-cell lung cancer (SCLC) as a model, we found that DD-CIP2 triggers DDR, cell cycle arrest, and apoptosis in vitro, leading to anti-tumor efficacy without substantial toxicity in preclinical SCLC xenograft models at well tolerated doses. Our findings demonstrate that DD-CIPs may provide an opportunity to address the limitations of traditional PARPi and establish chemical induced proximity as a strategy for modulating the DDR in cancer.

  View details for DOI 10.1101/2025.11.03.686423

  View details for PubMedID 41278667

  View details for PubMedCentralID PMC12637661

• Novel therapeutics for SF3B1 mutant cancers which exploit the missplicing of DCAF16 Sekrecki, M., Sekrecka, A., Lattupally, R., Le, K., Cao, X., Chen, V., Zhuang, Z., Dwyer, B., Zhou, C., Tiwari, C., Gabel, A., Kim, W., Stanley, R., Benbarche, S., Pineda, J., Gray, N., Zhang, T., Greenberg, P., Gotlib, J., Mannis, G., Shomali, W., Salmasi, G., Shanafelt, T., Van Rechem, C., Zhang, X., Fakhri, B., Lu, S. ELSEVIER. 2025: 1474-1475

  View details for DOI 10.1182/blood-2025-1474

  View details for Web of Science ID 001658978100025

• Therapeutic targeting of the nuclear pore complex with molecular glue degraders in pancreatic cancer Yuan, L., Ji, W., Dwyer, B. G., Lu, J., Bian, J., Colombo, G. M., Martinez, M. J., Fernandez, D., Phillips, N. A., Tang, M. T., Zhou, C. W., Jones, H. M., Calla, N., Huancas, C., Eckart, M., Tran, J., Qiu, T., Doench, J. G., Rees, M. G., Roth, J. A., Cameron, M. D., Charville, G. W., Kuo, C. J., Dixon, S. J., Zhang, T., Hinshaw, S. M., Gray, N. S., Corsello, S. M. AMER ASSOC CANCER RESEARCH. 2025

  View details for DOI 10.1158/1538-7445.PANCREATIC25-B003

  View details for Web of Science ID 001588114400040

• Defining the antitumor mechanism of action of a clinical-stage compound as a selective degrader of the nuclear pore complex. Cancer discovery Yuan, L., Ji, W., Dwyer, B. G., Lu, J., Bian, J., Colombo, G. M., Martinez, M. J., Fernandez, D., Phillips, N. A., Tang, M. T., Zhou, C. W., Quispe Calla, N. E., Guzman Huancas, C., Eckart, M., Tran, J., Jones, H. M., Qiu, T., Doench, J. G., Rees, M. G., Roth, J. A., Cameron, M. D., Charville, G. W., Kuo, C. J., Dixon, S. J., Zhang, T., Hinshaw, S. M., Gray, N. S., Corsello, S. M. 2025

  Abstract

  Cancer cells are acutely dependent on nuclear transport due to elevated transcriptional activity, suggesting an unrealized opportunity for selective therapeutic inhibition of the nuclear pore complex. Through large-scale phenotypic profiling of cancer cell lines, genome-scale functional genomic modifier screens, and mass spectrometry-based proteomics, we discovered that the clinical drug PRLX-93936 is a molecular glue that binds and reprograms the TRIM21 ubiquitin ligase to degrade the nuclear pore complex. Upon compound-induced TRIM21 recruitment, the nuclear pore is ubiquitylated and degraded, resulting in the loss of short-lived cytoplasmic mRNA transcripts and induction of cancer cell apoptosis. Direct compound binding to TRIM21 was confirmed via surface plasmon resonance and x-ray crystallography, while compound-induced TRIM21-nucleoporin complex formation was demonstrated through multiple orthogonal approaches in cells and in vitro. Phenotype-guided optimization yielded compounds with 10-fold greater potency and drug-like properties with robust pharmacokinetics and efficacy against pancreatic cancer xenografts and patient-derived organoids.

  View details for DOI 10.1158/2159-8290.CD-25-0271

  View details for PubMedID 40891634

• Rational Design of CDK12/13 and BRD4 Molecular Glue Degraders. Angewandte Chemie (International ed. in English) Gray, N. S., Zhuang, Z., Byun, W. S., Kozicka, Z., Donovan, K., Dwyer, B., Thornhill, A., Jones, H., Jiang, Z., Zhu, X., Fischer, E., Thomä, N. 2025: e202508427

  Abstract

  Targeted protein degradation (TPD) is an emerging therapeutic approach for the selective elimination of disease-related proteins. While molecular glue degraders exhibit drug-like properties, their discovery has traditionally been serendipitous and often requires post-hoc rationalization. In this study, we demonstrate the rational, mechanism-guided design of molecular glue degraders using gluing moieties. Building on established principles, by appending a chemical gluing moiety to several small molecule inhibitors, we successfully transformed them into degraders, obviating the need for a specific E3 ubiquitin ligase recruiter. Specifically, we found that incorporating a hydrophobic aromatic ring or a double bond into a cyclin-dependent kinase 12 and 13 (CDK12/13) dual inhibitor enabled the recruitment of DNA damage-binding protein 1 (DDB1), thereby transforming a high-molecular-weight bivalent CDK12 degrader into a potent monovalent CDK12/13 molecular glue degrader. We also showcase that attaching a cysteine-reactive warhead to a bromodomain-containing protein 4 (BRD4) inhibitor converts it into a degrader by recruiting the DDB1 and CUL4 associated factor 16 (DCAF16) E3 ligase.

  View details for DOI 10.1002/anie.202508427

  View details for PubMedID 40626960

• A Bivalent Molecular Glue Linking Lysine Acetyltransferases to Oncogene-induced Cell Death. bioRxiv : the preprint server for biology Nix, M. N., Gourisankar, S., Sarott, R. C., Dwyer, B. G., Nettles, S. A., Martinez, M. M., Abuzaid, H., Yang, H., Wang, Y., Simanauskaite, J. M., Romero, B. A., Jones, H. M., Krokhotin, A., Lowensohn, T. N., Chen, L., Low, C., Davis, M. M., Fernandez, D., Zhang, T., Green, M. R., Hinshaw, S. M., Gray, N. S., Crabtree, G. R. 2025

  Abstract

  Developing cancer therapies that induce robust death of the malignant cell is critical to prevent relapse. Highly effective strategies, such as immunotherapy, exemplify this observation. Here we provide the structural and molecular underpinnings for an approach that leverages chemical induced proximity to produce specific cell killing of diffuse large B cell lymphoma, the most common non-Hodgkin's lymphoma. We develop KAT-TCIPs (lysine acetyltransferase transcriptional/epigenetic chemical inducers of proximity) that redirect p300 and CBP to activate programmed cell death genes normally repressed by the oncogenic driver, BCL6. Acute treatment rapidly reprograms the epigenome to initiate apoptosis and repress c-MYC. The crystal structure of the chemically induced p300-BCL6 complex reveals how chance interactions between the two proteins can be systematically exploited to produce the exquisite potency and selectivity of KAT-TCIPs. Thus, the malignant function of an oncogenic driver can be co-opted to activate robust cell death, with implications for precision epigenetic therapies.

  View details for DOI 10.1101/2025.03.14.643404

  View details for PubMedID 40166243

  View details for PubMedCentralID PMC11956963

• Chemoproteomics-Enabled <i>De Novo</i> Proteolysis Targeting Chimera Discovery Platform Identifies a Metallothionein Degrader to Probe Its Role in Cancer JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Racioppo, B., Pechalrieu, D., Abegg, D., Dwyer, B., Ramseier, N., Hu, Y. S., Adibekian, A. 2025; 147 (9): 7817-7828

  Abstract

  Proteolysis targeting chimeras (PROTACs) represent powerful tools to modulate the activity of classically "undruggable" proteins, but their application has been limited to known ligands and a few select protein classes. Herein, we present our chemoproteomic strategy for simultaneous de novo discovery of novel degraders and ligands for challenging and previously "undruggable" targets. Using comparative PROTAC versus ligand global proteomics analyses, we rapidly identify proteins selectively downregulated by several "untargeted" PROTACs containing a VHL E3 ligase recruiter and various covalent and noncovalent ligands. We showcase our approach by identifying a first-in-class PROTAC for metallothionein 2A (MT2A), a small, cysteine-rich, metal-binding protein implicated in heavy metal detoxification, zinc homeostasis, and cellular invasion. Notably, isoform-specific MT overexpression has been shown to augment cellular migration and invasion across several cancer cell lines, although the precise mechanisms are unknown due to insufficient tools to study MTs. We show that optimized PROTAC AA-BR-157 covalently binds conserved C44, degrades overexpressed MT2A with nanomolar potency, and reduces the migration and invasion of MDA-MB-231 cells. We further demonstrate a time-dependent increase in intracellular zinc levels following MT2A degradation as well as downregulation of protein diaphanous homolog 3 (DIAPH3), a positive regulator of actin and cell motility. Super-resolution imaging of MDA-MB-231 cells shows that the downregulation of MT2A and DIAPH3 inhibits cell polarization and thereby migration, suggesting that MT2A may regulate motility via DIAPH3-dependent cytoskeletal remodeling. In summary, our strategy enables the de novo discovery of PROTACs and ligands for novel disease-related targets and lays the groundwork for expansion of the druggable proteome.

  View details for DOI 10.1021/jacs.4c17827

  View details for Web of Science ID 001432989100001

  View details for PubMedID 39989026

  View details for PubMedCentralID PMC12947296

• Relocalizing transcriptional kinases to activate apoptosis. Science (New York, N.Y.) Sarott, R. C., Gourisankar, S., Karim, B., Nettles, S., Yang, H., Dwyer, B. G., Simanauskaite, J. M., Tse, J., Abuzaid, H., Krokhotin, A., Zhang, T., Hinshaw, S. M., Green, M. R., Crabtree, G. R., Gray, N. S. 2024; 386 (6717): eadl5361

  Abstract

  Kinases are critical regulators of cellular function that are commonly implicated in the mechanisms underlying disease. Most drugs that target kinases are molecules that inhibit their catalytic activity, but here we used chemically induced proximity to convert kinase inhibitors into activators of therapeutic genes. We synthesized bivalent molecules that link ligands of the transcription factor B cell lymphoma 6 (BCL6) to inhibitors of cyclin-dependent kinases (CDKs). These molecules relocalized CDK9 to BCL6-bound DNA and directed phosphorylation of RNA polymerase II. The resulting expression of pro-apoptotic, BCL6-target genes caused killing of diffuse large B cell lymphoma cells and specific ablation of the BCL6-regulated germinal center response. Genomics and proteomics corroborated a gain-of-function mechanism in which global kinase activity was not inhibited but rather redirected. Thus, kinase inhibitors can be used to context-specifically activate transcription.

  View details for DOI 10.1126/science.adl5361

  View details for PubMedID 39361741

• Discovery of electrophilic degraders that exploit SNAr chemistry. bioRxiv : the preprint server for biology Zhuang, Z., Byun, W. S., Kozicka, Z., Dwyer, B. G., Donovan, K. A., Jiang, Z., Jones, H. M., Abeja, D. M., Nix, M. N., Zhong, J., Słabicki, M., Fischer, E. S., Ebert, B. L., Gray, N. S. 2024

  Abstract

  Targeted covalent inhibition (TCI) and targeted protein degradation (TPD) have proven effective in pharmacologically addressing formerly 'undruggable' targets. Integration of both methodologies has resulted in the development of electrophilic degraders where recruitment of a suitable E3 ubiquitin ligase is achieved through formation of a covalent bond with a cysteine nucleophile. Expanding the scope of electrophilic degraders requires the development of electrophiles with tempered reactivity that enable selective ligase recruitment and reduce cross-reactivity with other cellular nucleophiles. In this study, we report the use of chemical moieties that enable nucleophilic aromatic substitution (SNAr) reactions in the rational design of electrophilic protein degraders. Appending an SNAr covalent warhead to several preexisting small molecule inhibitors transformed them into degraders, obviating the need for a defined E3 ligase recruiter. The SNAr covalent warhead is versatile; it can recruit various E3 ligases, including DDB1 and CUL4 associated factor 11 (DCAF11), DDB1 and CUL4 associated factor 16 (DCAF16), and possibly others. The incorporation of an SNAr covalent warhead into the BRD4 inhibitor led to the discovery of degraders with low picomolar degradation potency. Furthermore, we demonstrate the broad applicability of this approach through rational functional switching from kinase inhibitors into potent degraders.

  View details for DOI 10.1101/2024.09.25.615094

  View details for PubMedID 39386645

  View details for PubMedCentralID PMC11463635

• Proteomics-Based Discovery of First-in-Class Chemical Probes for Programmed Cell Death Protein 2 (PDCD2). Angewandte Chemie (International ed. in English) Ji, W., Byun, W. S., Lu, W., Zhu, X., Donovan, K. A., Dwyer, B., Che, J., Yuan, L., Abulaiti, X., Corsello, S. M., Fischer, E. S., Zhang, T., Gray, N. S. 2023: e202308292

  Abstract

  Chemical probes are essential tools for understanding biological systems and for credentialing potential biomedical targets. Programmed cell death 2 (PDCD2) is a member of the B-cell lymphoma 2 (Bcl-2) family of proteins, which are critical regulators of apoptosis. Here we report the discovery and characterization of 10e, a first-in-class small molecule degrader of PDCD2. We discovered PDCD2 degrader by serendipity using a chemical proteomics approach in contrast to the conventional approach for making bivalent degraders starting from a known binding ligand targeting the protein of interest. Using 10e as a pharmacological probe, we demonstrate that PDCD2 functions as a critical regulator of cell growth by modulating the progression of the cell cycle in T lymphoblasts. Our work provides a useful pharmacological probe for investigating PDCD2 function and highlights using chemical proteomics to discover selective small molecule degraders of unanticipated targets.

  View details for DOI 10.1002/anie.202308292

  View details for PubMedID 37658265

• Total Synthesis and Target Identification of the Curcusone Diterpenes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Cui, C., Dwyer, B. G., Liu, C., Abegg, D., Cai, Z., Hoch, D. G., Yin, X., Qiu, N., Liu, J., Adibekian, A., Dai, M. 2021; 143 (11): 4379-4386

  Abstract

  The curcusone natural products are complex diterpenes featuring a characteristic [6-7-5] tricyclic carbon skeleton similar to the daphnane and tigliane diterpenes. Among them, curcusones A-D demonstrated potent anticancer activity against a broad spectrum of human cancer cell lines. Prior to this study, no total synthesis of the curcusones was achieved and their anticancer mode of action remained unknown. Herein, we report our synthetic and chemoproteomics studies of the curcusone diterpenes which culminate in the first total synthesis of several curcusone natural products and identification of BRCA1-associated ATM activator 1 (BRAT1) as a cellular target. Our efficient synthesis is highly convergent, builds upon cheap and abundant starting materials, features a thermal [3,3]-sigmatropic rearrangement and a novel FeCl3-promoted cascade reaction to rapidly construct the critical cycloheptadienone core of the curcusones, and led us to complete the first total synthesis of curcusones A and B in only 9 steps, C and D in 10 steps, and dimericursone A in 12 steps. The chemical synthesis of dimericursone A from curcusones C and D provided direct evidence to support the proposed Diels-Alder dimerization and cheletropic elimination biosynthetic pathway. Using an alkyne-tagged probe molecule, BRAT1, an important but previously "undruggable" oncoprotein, was identified as a key cellular target via chemoproteomics. We further demonstrate for the first time that BRAT1 can be inhibited by curcusone D, resulting in impaired DNA damage response, reduced cancer cell migration, potentiated activity of the DNA damaging drug etoposide, and other phenotypes similar to BRAT1 knockdown.

  View details for DOI 10.1021/jacs.1c00557

  View details for Web of Science ID 000634761500037

  View details for PubMedID 33705657

  View details for PubMedCentralID PMC8281983

• Chemoproteomics-Enabled De Novo Discovery of Photoswitchable Carboxylesterase Inhibitors for Optically Controlled Drug Metabolism ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Dwyer, B. G., Wang, C., Abegg, D., Racioppo, B., Qiu, N., Zhao, Z., Pechalrieu, D., Shuster, A., Hoch, D. G., Adibekian, A. 2021; 60 (6): 3071-3079

  Abstract

  Herein, we report arylazopyrazole ureas and sulfones as a novel class of photoswitchable serine hydrolase inhibitors and present a chemoproteomic platform for rapid discovery of optically controlled serine hydrolase targets in complex proteomes. Specifically, we identify highly potent and selective photoswitchable inhibitors of the drug-metabolizing enzymes carboxylesterases 1 and 2 and demonstrate their pharmacological application by optically controlling the metabolism of the immunosuppressant drug mycophenolate mofetil. Collectively, this proof-of-concept study provides a first example of photopharmacological tools to optically control drug metabolism by modulating the activity of a metabolizing enzyme. Our arylazopyrazole ureas and sulfones offer synthetically accessible scaffolds that can be expanded to identify specific photoswitchable inhibitors for other serine hydrolases, including lipases, peptidases, and proteases. Our chemoproteomic platform can be applied to other photoswitches and scaffolds to achieve optical control over diverse protein classes.

  View details for DOI 10.1002/anie.202011163

  View details for Web of Science ID 000596687000001

  View details for PubMedID 33035395

  View details for PubMedCentralID PMC12011475

• Combined Omics Approach Identifies Gambogic Acid and Related Xanthones as Covalent Inhibitors of the Serine Palmitoyltransferase Complex CELL CHEMICAL BIOLOGY Hoch, D. G., Abegg, D., Hannich, J., Pechalrieu, D., Shuster, A., Dwyer, B. G., Wang, C., Zhang, X., You, Q., Riezman, H., Adibekian, A. 2020; 27 (5): 586-+

  Abstract

  In this study, we identify the natural product gambogic acid as well as structurally related synthetic xanthones as first-in-class covalent inhibitors of the de novo sphingolipid biosynthesis. We apply chemoproteomics to determine that gambogic acid binds to the regulatory small subunit B of the serine palmitoyltransferase complex (SPTSSB). We then test structurally related synthetic xanthones to identify 18 as an equally potent but more selective binder of SPTSSB and show that 18 reduces sphingolipid levels in situ and in vivo. Finally, using various biological methods, we demonstrate that 18 induces cellular responses characteristic for diminished sphingosine-1-phosphate (S1P) signaling. This study demonstrates that SPTSSB may become a viable therapeutic target in various diseases with pathological S1P signaling. Furthermore, we believe that our compound will become a valuable tool for studying the sphingolipid metabolism and serve as a blueprint for the development of a new generation of sphingolipid biosynthesis inhibitors.

  View details for DOI 10.1016/j.chembiol.2020.03.008

  View details for Web of Science ID 000536032400011

  View details for PubMedID 32330443

• Ethynylation of Cysteine Residues: From Peptides to Proteins in Vitro and in Living Cells ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Tessier, R., Nandi, R., Dwyer, B. G., Abegg, D., Sornay, C., Ceballos, J., Erb, S., Cianferani, S., Wagner, A., Chaubet, G., Adibekian, A., Waser, J. 2020; 59 (27): 10961-10970

  Abstract

  Current approaches to introduce terminal alkynes for bioorthogonal reactions into biomolecules still present limitations in terms of either reactivity, selectivity, or adduct stability. We present a method for the ethynylation of cysteine residues based on the use of ethynylbenziodoxolone (EBX) reagents. The acetylene group is directly introduced onto the thiol group of cysteine and can be used for copper-catalyzed alkyne-azide cycloaddition (CuAAC) without further processing. Labeling proceeded with reaction rates comparable to or higher than the most often used iodoacetamide on peptides or maleimide on the antibody trastuzumab, and high cysteine selectivity was observed. The reagents were also used in living cells for cysteine proteomic profiling and displayed improved coverage of the cysteinome compared to previously reported iodoacetamide or hypervalent iodine reagents. Fine-tuning of the EBX reagents allows optimization of their reactivity and physical properties.

  View details for DOI 10.1002/anie.202002626

  View details for Web of Science ID 000531347300001

  View details for PubMedID 32233093

• Discovery and Evaluation of New Activity-Based Probes for Serine Hydrolases CHEMBIOCHEM Wang, C., Abegg, D., Dwyer, B. G., Adibekian, A. 2019; 20 (17): 2212-2216

  Abstract

  Serine hydrolases play crucial biological roles and are important therapeutic targets in many clinical applications. Activity-based protein profiling of serine hydrolases by using fluorophosphonate probes, pioneered by Cravatt and co-workers, has been a powerful tool for interrogating serine hydrolases in various biological systems. Herein, we present new phenyl phosphonate probes with an azide handle for click chemistry that offer remarkable improvements over the classical fluorophosphonate serine hydrolase activity-based probes including ease of preparation, excellent cell permeability, and distinct reactivity profiles, as controlled by the phenolate leaving group. Thus, these new activity-based serine hydrolase probes are valuable tools to further interrogate this important class of enzymes.

  View details for DOI 10.1002/cbic.201900126

  View details for Web of Science ID 000479688100001

  View details for PubMedID 30968522

• The Hairpin Form of r(G₄C₂)<SUP>exp</SUP> in c9ALS/FTD Is Repeat-Associated Non-ATG Translated and a Target for Bioactive Small Molecules CELL CHEMICAL BIOLOGY Wang, Z., Ursu, A., Childs-Disney, J. L., Guertler, R., Yang, W., Bernat, V., Rzuczek, S. G., Fuerst, R., Zhang, Y., Gendron, T. F., Yildirim, I., Dwyer, B. G., Rice, J. E., Petrucelli, L., Disney, M. D. 2019; 26 (2): 179-+

  Abstract

  The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is an expanded G4C2 repeat [(G4C2)exp] in C9ORF72. ALS/FTD-associated toxicity has been traced to the RNA transcribed from the repeat expansion [r(G4C2)exp], which sequesters RNA-binding proteins (RBPs) and undergoes repeat-associated non-ATG (RAN) translation to generate toxic dipeptide repeats. Using in vitro and cell-based assays, we identified a small molecule (4) that selectively bound r(G4C2)exp, prevented sequestration of an RBP, and inhibited RAN translation. Indeed, biophysical characterization showed that 4 selectively bound the hairpin form of r(G4C2)exp, and nuclear magnetic resonance spectroscopy studies and molecular dynamics simulations defined this molecular recognition event. Cellular imaging revealed that 4 localized to r(G4C2)exp cytoplasmic foci, the putative sites of RAN translation. Collectively, these studies highlight that the hairpin structure of r(G4C2)exp is a therapeutically relevant target and small molecules that bind it can ameliorate c9ALS/FTD-associated toxicity.

  View details for DOI 10.1016/j.chembiol.2018.10.018

  View details for Web of Science ID 000460048700004

  View details for PubMedID 30503283

  View details for PubMedCentralID PMC6386614

• Drugging the RNA World COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY Disney, M. D., Dwyer, B. G., Childs-Disney, J. L. 2018; 10 (11)

  Abstract

  Although we live in the remnants of an RNA world, the world of drug discovery and chemical probes is firmly protein-centric. Developing highly selective small molecules targeting RNA is often considered to be an insurmountable challenge. Our goal is to demystify the design of such compounds. In this review, we describe various approaches to design small molecules that target RNA from sequence and the application of these compounds in RNA biology, with a focus on inhibition of human RNA-protein complexes. We have developed a library-versus-library screening approach to define selective RNA-small-molecule binding partners and applied them to disease-causing RNAs, in particular noncoding oncogenic RNAs and expanded RNA repeats, to modulate their biology in cells and animals. We also describe the design of new types of small-molecule probes that could broadly decipher the mysteries of RNA in cells.

  View details for DOI 10.1101/cshperspect.a034769

  View details for Web of Science ID 000448987500001

  View details for PubMedID 30385607

  View details for PubMedCentralID PMC6211391

• Ruthenium anticancer agent KP1019 binds more tightly than NAMI-A to tRNA<SUP>Phe</SUP> JOURNAL OF INORGANIC BIOCHEMISTRY Dwyer, B. G., Johnson, E., Cazares, E., Holman, K., Kirk, S. R. 2018; 182: 177-183

  Abstract

  The ruthenium-based anticancer agent NAMI-A (ImH[trans-RuCl4(dmso)(Im)], where Im = imidazole) has been shown to interact with RNA in vivo and in vitro. We hypothesized that the similarly structured drug KP1019 (IndH[trans-RuCl4(Ind)2], where Ind = indazole) binds to RNA as well. Fluorescence spectroscopy was employed to assay the interactions between either NAMI-A or KP1019 and tRNAPhe through an intrinsic fluorophore wybutosine (Y) base and by extrinsic displacement of the intercalating agent ethidium bromide. In both the intrinsic Y-base and extrinsic ethidium bromide studies, KP1019 exhibited tighter binding to phenylalanine-specific tRNA (tRNAPhe) than NAMI-A. In the ethidium bromide study, reducing both drugs from RuIII to RuII resulted in a significant decrease in binding. Our findings suggest that the relatively large heteroaromatic indazole ligands of KP1019 intercalate in the π-stacks of tRNAPhe within structurally complex binding pockets. In addition, NAMI-A appears to be sensitive to destabilizing electrostatic interactions with the negative phosphate backbone of tRNAPhe. Interactions with additional tRNA molecules and other types of RNA require further evaluation to determine the role of RNA in the mechanisms of action for KP1019 and to better understand how Ru drugs fundamentally interact with biomolecules that are more structurally sophisticated than short DNA oligonucleotides. To the best of our knowledge, this is the first study to report KP1019 binding interactions with RNA.

  View details for DOI 10.1016/j.jinorgbio.2018.02.019

  View details for Web of Science ID 000430157000019

  View details for PubMedID 29501978