ABSTRACT
The field of targeted protein degradation (TPD) has grown exponentially over the past decade with the goal of developing therapies that mark proteins for destruction leveraging the ubiquitin-proteasome system. One common approach to achieve TPD is to employ a heterobifunctional molecule, termed as a degrader, to recruit the protein target of interest to the E3 ligase machinery. The resultant generation of an intermediary ternary complex (target-degrader-ligase) is pivotal in the degradation process. Understanding the ternary complex geometry offers valuable insight into selectivity, catalytic efficiency, linker chemistry, and rational degrader design. In this study, we utilize hydrogen-deuterium exchange mass spectrometry (HDX-MS) to identify degrader-induced protein-protein interfaces. We then use these data in conjunction with constrained protein docking to build three-dimensional models of the ternary complex. The approach was used to characterize complex formation between the E3 ligase CRBN and the first bromodomain of BRD4, a prominent oncology target. We show marked differences in the ternary complexes formed in solution based on distinct patterns of deuterium uptake for two degraders, CFT-1297 and dBET6. CFT-1297, which exhibited positive cooperativity, altered the deuterium uptake profile revealing the degrader-induced protein-protein interface of the ternary complex. For CFT-1297, the ternary complexes generated by the highest scoring HDX-constrained docking models differ markedly from those observed in the published crystal structures. These results highlight the potential utility of HDX-MS to provide rapidly accessible structural insights into degrader-induced protein-protein interfaces in solution. They further suggest that degrader ternary complexes exhibit significant conformation flexibility and that biologically relevant complexes may well not exhibit the largest interaction surfaces between proteins. Taken together, the results indicate that methods capable of incorporating linker conformation uncertainty may prove an important component in degrader design moving forward. In addition, the development of scoring functions modified to handle interfaces with no evolved complementarity, for example, through consideration of high levels of water infiltration, may prove valuable. Furthermore, the use of crystal structures as validation tools for novel degrader methods needs to be considered with caution.
Subject(s)
Cell Cycle Proteins/chemistry , Computer Simulation , Deuterium Exchange Measurement , Mass Spectrometry/methods , Transcription Factors/chemistry , Acetamides/chemistry , Acetamides/pharmacology , Gene Expression Regulation/drug effects , HEK293 Cells , Humans , Indoles/chemistry , Indoles/pharmacology , Models, Chemical , Models, Molecular , Molecular Structure , Piperidines/chemistry , Piperidines/pharmacology , Protein ConformationABSTRACT
Targeted, catalytic degradation of oncoproteins using heterobifunctional small molecules is an attractive modality, particularly for hematologic malignancies, which are often initiated by aberrant transcription factors and are challenging to drug with inhibitors. BRD4, a member of the bromodomain and extraterminal family, is a core transcriptional and epigenetic regulator that recruits the P-TEFb complex, which includes Cdk9 and cyclin T, to RNA polymerase II (pol II). Together, BRD4 and CDK9 phosphorylate serine 2 (pSer2) of heptad repeats in the C-terminal domain of RPB1, the large subunit of pol II, promote transcriptional elongation. Small-molecule degraders of BRD4 have shown encouraging efficacy in preclinical models for several tumor types but less efficacy in other cancers including small-cell lung cancer (SCLC) and pancreatic cancer. Here, we evaluated CFT-2718, a new BRD4-targeting degrader with enhanced catalytic activity and in vivo properties. In vivo, CFT-2718 has significantly greater efficacy than the CDK9 inhibitor dinaciclib in reducing growth of the LX-36 SCLC patient-derived xenograft (PDX) model and performed comparably to dinaciclib in limiting growth of the PNX-001 pancreatic PDX model. In vitro, CFT-2718 reduced cell viability in four SCLC and two pancreatic cancer models. In SCLC models, this activity significantly exceeded that of dinaciclib; furthermore, CFT-2718 selectively increased the expression of cleaved PARP, an indicator of apoptosis. CFT-2718 caused rapid BRD4 degradation and reduced levels of total and pSer2 RPB1 protein. These and other findings suggest that BRD-mediated transcriptional suppression merits further exploration in the setting of SCLC.
Subject(s)
Antineoplastic Agents/pharmacology , Cell Cycle Proteins/metabolism , Gene Expression Regulation, Neoplastic/drug effects , Lung Neoplasms/drug therapy , Pancreatic Neoplasms/drug therapy , Small Cell Lung Carcinoma/drug therapy , Small Molecule Libraries/pharmacology , Transcription Factors/metabolism , Animals , Apoptosis , Cell Movement , Cell Proliferation , Female , Humans , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mice , Mice, SCID , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/pathology , Small Cell Lung Carcinoma/metabolism , Small Cell Lung Carcinoma/pathology , Tumor Cells, Cultured , Xenograft Model Antitumor AssaysABSTRACT
A number of structurally and electronically diverse N-vinyl nitrones have been synthesized by a two-step method. The sequence consists of condensation of an α-chloroaldehyde or an α-phenoxy- or α-acetoxy ketone with a substituted benzyl hydroxylamine to provide the corresponding nitrone. Treatment of these species with a base induces a 1,4-elimination to provide the desired N-vinyl nitrone in good to excellent yields.
