Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation.

Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.

Pharmacological modulation of chloride channels as a therapeutic strategy for neurological disorders.

Chloride homeostasis is critical in the physiological functions of the central nervous system (CNS). Its concentration is precisely regulated by multiple ion-transporting proteins such as chloride channels and transporters that are widely distributed in the brain cells, including neurons and glia. Unlike ion transporters, chloride channels provide rapid responses to efficiently regulate ion flux. Some of chloride channels are also permeable to selected organic anions such as glutamate and γ-aminobutyric acid, suggesting neuroexcitatory and neuroinhibitory functions while gating. Dysregulated chloride channels are implicated in neurological disorders, e.g., ischemia and neuroinflammation. Modulation of chloride homeostasis through chloride channels has been suggested as a potential therapeutic approach for neurological disorders. The drug design for CNS diseases is challenging because it requires the therapeutics to traverse the blood-brain-barrier. Small molecules are a well-established modality with better cell permeability due to their lower molecular weight and flexibility for structure optimization compared to biologics. In this article, we describe the important roles of chloride homeostasis in each type of brain cells and introduce selected chloride channels identified in the CNS. We then discuss the contribution of their dysregulations towards the pathogenesis of neurological disorders, emphasizing the potential of targeting chloride channels as a therapeutic strategy for CNS disease treatment. Along with this literature survey, we summarize the small molecules that modulate chloride channels and propose the potential strategy of optimizing existing drugs to brain-penetrants to support future CNS drug discovery.

BRET measurement on CCD camera-based microtiter plate readers.

NanoBRET assays, which utilize bioluminescence energy resonance transfer (BRET), have been widely adopted in drug discovery for measuring both protein-protein interactions and drug target engagement. While the EnVision and other traditional well-scanning plate readers that measure a single well at a time are satisfactory for signal detection for smaller experiments, it becomes challenging to scale these assays to applications that require higher throughput. To address this, we explored the adaptation of the ViewLux and FLIPR plate readers for measuring NanoBRET signal. These plate readers utilize charge-coupled device (CCD) cameras for detection, which enable imaging of the entire assay plate simultaneously. We used tool compounds to generate data from each plate reader and found that the image-based plate readers can be used to measure NanoBRET signals with high S/B and Z´, resulting in comparable IC50 values to those obtained from the EnVision, while requiring less time to complete reads. Consequently, utilization of image-based plate readers for NanoBRET measurement may enable applications that require faster reads, such as for high-throughput screening or kinetics studies.

Cryo-EM structures of NPC1L1 reveal mechanisms of cholesterol transport and ezetimibe inhibition.

The intestinal absorption of cholesterol is mediated by a multipass membrane protein, Niemann-Pick C1-Like 1 (NPC1L1), the molecular target of a cholesterol lowering therapy ezetimibe. While ezetimibe gained Food and Drug Administration approval in 2002, its mechanism of action has remained unclear. Here, we present two cryo-electron microscopy structures of NPC1L1, one in its apo form and the other complexed with ezetimibe. The apo form represents an open state in which the N-terminal domain (NTD) interacts loosely with the rest of NPC1L1, leaving the NTD central cavity accessible for cholesterol loading. The ezetimibe-bound form signifies a closed state in which the NTD rotates ~60°, creating a continuous tunnel enabling cholesterol movement into the plasma membrane. Ezetimibe blocks cholesterol transport by occluding the tunnel instead of competing with cholesterol binding. These findings provide insight into the molecular mechanisms of NPC1L1-mediated cholesterol transport and ezetimibe inhibition, paving the way for more effective therapeutic development.

High-Throughput Implementation of the NanoBRET Target Engagement Intracellular Kinase Assay to Reveal Differential Compound Engagement by SIK2/3 Isoforms.

The real-time quantification of target engagement (TE) by small-molecule ligands in living cells remains technically challenging. Systematic quantification of such interactions in a high-throughput setting holds promise for identification of target-specific, potent small molecules within a pathophysiological and biologically relevant cellular context. The salt-inducible kinases (SIKs) belong to a subfamily of the AMP-activated protein kinase (AMPK) family and are composed of three isoforms in humans (SIK1, SIK2, and SIK3). They modulate the production of pro- and anti-inflammatory cytokines in immune cells. Although pan-SIK inhibitors are sufficient to reverse SIK-dependent inflammatory responses, the apparent toxicity associated with SIK3 inhibition suggests that isoform-specific inhibition is required to realize therapeutic benefit with acceptable safety margins. Here, we used the NanoBRET TE intracellular kinase assay, a sensitive energy transfer technique, to directly measure molecular proximity and quantify TE in HEK293T cells overexpressing SIK2 or SIK3. Our 384-well high-throughput screening of 530 compounds demonstrates that the NanoBRET TE intracellular kinase assay was sensitive and robust enough to reveal differential engagement of candidate compounds with the two SIK isoforms and further highlights the feasibility of high-throughput implementation of NanoBRET TE intracellular kinase assays for target-driven small-molecule screening.

Phase 1 investigation of lenalidomide/rituximab plus outcomes of lenalidomide maintenance in relapsed CNS lymphoma.

There is an unmet need for effective biological therapies for relapsed central nervous system (CNS) lymphoma. Lenalidomide is active in activated B-cell type diffuse large B-cell lymphoma and rituximab is effective in CNS lymphoma. These observations are the basis for this first trial of an immunomodulatory drug as monotherapy in CNS lymphoma, and, in patients with inadequate responses to lenalidomide, with rituximab. In an independent cohort, we evaluated lenalidomide maintenance after salvage with high-dose methotrexate or focal irradiation in relapsed primary CNS lymphoma (PCNSL). We determined safety, efficacy, and cerebrospinal fluid (CSF) penetration of lenalidomide at 10-, 15-, and 20-mg dose levels in 14 patients with refractory CD20+ CNS lymphoma. Nine subjects with relapsed, refractory CNS lymphoma achieved better than partial response with lenalidomide monotherapy, 6 maintained response ≥9 months, and 4 maintained response ≥18 months. Median progression-free survival for lenalidomide/rituximab was 6 months. In the independent cohort, response duration with lenalidomide maintenance after complete responses 2 through 5 were significantly longer than response durations after standard therapy. The CSF/plasma partition coefficient of lenalidomide was ≥20% at 15- and 20-mg dose levels. Change in CSF interleukin-10 at 1 month correlated with clinical response and response duration to lenalidomide. Metabolomic profiling of CSF identified novel biomarkers, including lactate, and implicated indoleamine-2,3 dioxygenase activity with CNS lymphoma progression on lenalidomide. We conclude that lenalidomide penetrates ventricular CSF and is active as monotherapy in relapsed CNS lymphomas. We provide evidence that maintenance lenalidomide potentiates response duration after salvage in relapsed PCNSL and delays whole brain radiotherapy (WBRT). This trial was registered at www.clinicaltrials.gov as #NCT01542918.