Understanding Molecular Glue Mechanisms

Today in @ScienceMagazine, together with my former colleagues at the Novartis Institutes for BioMedical Research, we report the discovery and characterization of first molecular glue degraders of the WIZ transcription factor (TF) for fetal hemoglobin derepression and therapeutic consideration in Sickle Cell Disease. Chemical Biologists may appreciate the CRBN-directed glue degrader library, here used in phenotypic screening of erythropoietic progenitors for HbF induction w/o effect on viability or differentiation. WIZ was discovered by proteomic study of hits and validated by CRISPR. Globin Biologists will enjoy the discovery of WIZ as a repressor of fetal hemoglobin (HbF). This biology has been intently studied, and here we find WIZ loss derepresses HbF by a local decrease in repressive H3K9me2, attributable to the association of WIZ and EHMT1/2. Medicinal chemists will appreciate the potent and selective activity of dWIZ-1 and dWIZ-2, the excellent drug-like properties, oral bioavailability and importantly the excellent tolerability in rodents and monkeys. For Biochemists, we show recruitment to CRBN as dependent on WIZ zinc finger 7, and biophysically characterize association by surface plasmon resonance. The CRBN:dWIZ: WIZ ternary complex buries 413 sq-A of surface area. Drug hunters like me might reflect on molecules that potently target a transcription factor with no pockets – effectively no tertiary structure predicted by @AlphaFold. This chemistry targets instead targets the ZnF secondary structure – truly marking the conceptual end of “undruggable” (if still in doubt). Hematologists will enjoy pharmacologic target validation in multiple pre-clinical models, a relatively selective impact on gene expression, the wide open therapeutic index, and the ease of end-game medicinal chemistry to produce investigational agents. Most importantly, for patients with Sickle Cell Disease. The advance of CRISPR-edited stem cells for transplantation, from our group and others, is a major advance. But patients need more accessible, safe, oral medicines especially in Sub-Saharan Africa. We welcome your feedback on this study, and hope dWIZ-1 and dWIZ-2 immediately prove valuable tools to the community and an inspiration for targeting disordered proteins. Finally, I thank all former colleagues in the NIBR TPD Initiative, and in particular this program’s true champion – Dr. Pamela Ting. Pam, working with you on this brave idea and on the collaborative assembly of the manuscript this last year are treasures I will always cherish, like our friendship. Article: https://lnkd.in/es6k87up Perspective: https://lnkd.in/ewn4eZNT

Targeted protein degradation (TPD) uses small molecules to induce the selective degradation of proteins by recruiting ubiquitin E3 ligases to target proteins of interest, resulting in their ubiquitylation and proteasomal degradation. There are two main classes of TPD therapeutics: bifunctional PROTACs and molecular glue degraders, each with their own advantages and challenges. A new review written by Jonathan Tsai and larger team at the Brigham and Women's Hospital covers the current landscape of TPD approaches, their parallels in biological processes, the ongoing clinical exploration of novel degraders, and future directions of the field. Checkout the link to the full paper and a brief summary below: Targeted protein degradation from mechanisms to clinic. https://lnkd.in/dYZufUHt Serendipitous discovery of new protein degraders: A key catalyzing event for the TPD field was the clinical proof of concept provided by the unexpected discovery that thalidomide derivatives like lenalidomide induce degradation of the transcription factors IKZF1 and IKZF3, which underlies their efficacy in multiple myeloma. Structural studies revealed thalidomide derivatives bind to cereblon and reshape its surface to enable recruitment of neo-substrates containing a glycine degron. This led to the development of many new cereblon-based molecular glues and PROTACs. Discovery of novel molecular glues: Given the clinical success of molecular glue degraders, there is high interest in discovering new molecular glues beyond thalidomide derivatives. One rational approach identified small molecules that enhance the interaction between beta-catenin and its natural E3 ligase SCF-beta-TrCP. Another approach is diversifying known molecular glue scaffolds like thalidomide to identify new neo-substrates, which has led to selective degraders of the transcription factor IKZF2. Clinical perspectives: Despite the mechanistic diversity of TPD, relatively few degrader drugs are currently FDA-approved. However, many molecular glues and PROTACs are now in clinical development for indications like cancer and autoimmune disorders. Molecular glues are being tested in hematologic and solid tumors, while PROTACs are being developed for a wider range of targets like kinases, nuclear receptors, and apoptotic proteins. The clinical success of thalidomide derivatives has established TPD as a viable therapeutic modality, but also revealed some potential safety concerns like embryotoxicity that must be monitored. Resistance mechanisms to degraders are starting to be uncovered, including mutations in E3 ligases or upregulation of efflux pumps. TPD is also being explored in other diseases beyond cancer, such as neurodegenerative and infectious diseases. Ultimately, the versatility of TPD approaches has greatly expanded the druggable proteome and is poised to deliver many novel therapeutics in the years ahead.

Small-molecule drugs are effective and thus most widely used. However, their applications are limited by their reliance on active high-affinity binding sites, restricting their target options. A breakthrough approach involves molecular glues, a novel class of small-molecule compounds capable of inducing protein-protein interactions. This opens avenues to target conventionally undruggable proteins, overcoming limitations seen in conventional small-molecule drugs. Molecular glues play a key role in targeted protein degradation (TPD) techniques, including ubiquitin-proteasome system-based approaches such as Proteolysis Targeting Chimeras (PROTACs) and Molecular Glue Degraders and recently emergent lysosome system-based techniques like Molecular Degraders of Extracellular proteins through the Asialoglycoprotein receptors (MoDE-As) and Macroautophagy Degradation Targeting Chimeras (MADTACs). These techniques enable an innovative targeted degradation strategy for prolonged inhibition of pathology-associated proteins. This review provides an overview of them, emphasizing the clinical potential of molecular glues and guiding the development of molecular-glue-mediated TPD techniques.

How can AI + Physics Accelerate #Molecular #Glue Discovery? Designing molecular glues requires prior knowledge of specific protein conformations that reveal binding pockets at protein-protein interfaces. These pockets are critical targets for small molecules that induce proximity between proteins. However, identifying such pockets using traditional AI-based protein structure prediction models is challenging because the necessary conformational dynamics occur on microsecond to millisecond timescales. Combining AI and Physics to Identify Targetable Pockets Can we combine AI with physics-based simulations to capture these elusive pockets? Indeed, we can. The interaction between BRAF and MEK1 serves as an example. Under normal conditions, BRAF interacts with MEK1, and both proteins adopt inactive conformations, leading to normal cell growth and division. The BRAF V600E gene mutation is associated with more rapid cancer growth and a higher death rate in papillary thyroid cancer. Impact of the BRAF V600E Mutation: So how does the BRAF V600E mutation affect the BRAF-MEK1 interaction? The V600E mutation shifts BRAF from an inactive to an active state, which in turn activates MEK1 and the MAPK pathway. This activation leads to increased cell proliferation and tumorigenesis. Counteracting Activation with Molecular Glues: To counter this activation, we need to stabilize the BRAF(V600E)-MEK1 complex where both proteins adopt inactive conformations. One way to achieve this is by targeting these proteins with molecular glues that can stabilize their interaction. Our Approach and Findings Using a combination of AI and physics-based simulations, we managed to sample the conformational ensemble of the BRAF(V600E)-MEK1 complex in its native state. This allowed us to find druggable binding pockets at the protein-protein interface that can be targeted by molecular glues. Advancing #Molecular #Glue Discovery Traditionally, molecular glue discovery has been led by serendipity. Our results demonstrate how we can use AI and physics to discover druggable binding pockets in protein-protein interfaces. This method opens new avenues for developing molecular glues that can alter conformational ensembles and restore normal cellular function. Data To build a molecular glue targeting BRAF(V600E)-MEK1, you can utilize our conformational ensemble data and corresponding pocket analysis. Link: https://osf.io/ehx2b/ Connect with Us If you are working on molecular glues and want to understand how the dynamics of protein-protein interactions play a role in cellular signaling—or if you wish to discover druggable pockets that can be targeted by small-molecule glues—please feel free to reach out. #AI #ProteinDynamics #compchem #molecularglue #cancer #CancerResearch