Degrader Digest - Issue 3

Last updated July 14, 2021 Dear Protein Degradation Friends, In this issue, we include an updated list of industry events, TPD companies, as well as recent media and scientific articles. You can also access Issues 1 and 2. We are focusing on providing the latest information with each issue. Speaking of recent news, congratulations to Monte Rosa Therapeutics on their IPO! It is wonderful to see continued interest from various investors in the field of targeted protein degradation. In a future issue, we would like to include short interview videos highlighting exciting TPD research. If you would like to present your work, please share with us an abstract describing your research to degraderdigest@gmail.com. We have also received positive comments on the video animations. I am personally a huge fan of animations to illustrate complex biological processes. If you have any exciting animations you would like to share with the community, please let us know at degraderdigest@gmail.com, along with any thoughts on how we can work together to improve this digest for the TPD community. Many thanks! -Marc Cover art: proteasome illustration

Video Animations (complete list)

Have good video animations to share? Forward the link to degraderdigest@gmail.com to include it in the next issue!

  • What is the proteasome?

    Cells are constantly building proteins to perform all kinds of different tasks inside a cell. But that also means that it can get quite crowded inside the cell, so it needs to get rid of proteins that are no longer needed. In a previous video, we've shown you how ubiquitin tags are attached to these unwanted proteins, flagging them for destruction. In this video, we're going into a bit more detail about how that destruction actually works, by looking at the cell's big protein shredder: the proteasome. Our video about ubiquitin: https://youtu.be/e29F7R3K_5A References: - Huang et al. Nature Structural & Molecular Biology (2016) - Koehler et al. Molecular Cell (2001) - Beck et al. PNAS (2012) - Unverdorben et al. PNAS (2014) - Aufderheide et al. PNAS (2015) - Schweitzer et al. PNAS (2016) - Wehmer et al. PNAS (2017)

  • THE PROTEASOME, UBIQUITINATION, AND PROTEIN DESTRUCTION

    Sources: The best article:

  • Proteasome Animation 3D Molecular Biology

    DEMO VIDEO | This video depicts the proteasome degradation pathway. Ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, and ubiquitin ligase (E3) are shown. We produce 3D, accurate, pedagogical cell and molecular biology animations for post-secondary education. For more information, please visit: www.smart-biology.com

  • The Proteasome: The Cell's Trash Processor in Action

    #NIGMS #NIH This animation shows how the proteasome breaks down damaged or unwanted proteins into bits that the cell can reuse to make new proteins. Learn more about NIGMS and the research we fund: https://www.nigms.nih.gov/ Credit: Andreas Martin, University of California, Berkeley.

  • What is ubiquitin?

    Ubiquitin is a small protein that is used in cell signalling: it can get attached to all kinds of proteins inside a cell in order to change their behaviour, location, or protein-protein interactions. In this video, we go into a bit more detail around the different kinds of ubiquitynation, and what enzymes are required to attach ubiquitin to a target protein. References: - Yau & Rape, Nature Cell Biology 2016 - Buetow & Huang, Nature Reviews Molecular Cell BIology 2016

TPD Presentations

Share presentations with us to consider including in the next issue (degraderdigest@gmail.com).

  • Protein degradation: Looking back and moving forward - Endpoints Webinars

    The 20th anniversary of the first paper published on the PROTAC® technology is July 17, 2021. In those 20 years, incredible progress and momentum has been generated, including the first benefit for patients demonstrated in multiple indications. Our panel will take a look back at 20 years of discovery and development in targeted protein degradation (TPD), assess the current and near-term state of the field, and look at what the future holds.

  • Deshaies (Amgen) 1: A primer on the ubiquitin-proteasome system

    https://www.ibiology.org/cell-biology/primer-ubiquitin-proteasome-system/ Part 1: A primer on the ubiquitin-proteasome system: The ubiquitin-proteasome system is one of the principal means of degrading misfolded, mutated, or unwanted proteins in the cell. Part 2: Cullin-RING ubiquitin ligases: Over 200 types of cullin-RING ubiquitin ligases are formed by interchanging subunits. This carefully regulated system allows for great substrate specificity. Part 3: Targeting the ubiquitin-proteasome system in cancer: The ubiquitin-proteasome system is overworked in mutation-ridden cancer cells making it a potential target for anti-cancer drugs. https://www.ibiology.org/ibioseminars/cell-biology/primer-ubiquitin-proteasome-system.html Talk Overview: Neurons, blood cells and muscle cells have distinct morphologies and functions because they have different proteomes or collections of proteins. The proteome is maintained through the synthesis and degradation of different proteins. In his first talk, Dr. Deshaies explains that the ubiquitin-proteasome system (UPS) is the principal means of degrading proteins in the cytosol and therefore is key to maintaining the proteome. Ubiquitin is a small protein that can be added to, or removed from, other proteins altering their function or targeting them for degradation. Deshaies describes the multiple mechanisms for regulating ubiquitin ligase activity and the importance of protein degradation in many cell signaling pathways and in the removal of defective proteins. In Part 2, Deshaies delves more deeply into a specific group of ubiquitin ligases, the cullin-RING ligases (CRLs). By rearranging the subunits of CRLs in a combinatorial process, it is possible to generate more than 200 of these enzymes each with a specific substrate. The formation and activity of CRL complexes in the cell is regulated by the conjugation/deconjugation (Nedd8) or binding/dissociation (Cand1) of other proteins to the CRL complex, and this, in turn, is…

  • New Frontiers in Targeted Protein Degradation and Degrader Development

    Learn More about Targeted Protein Degradation: https://www.tocris.com/product-type/targeted-protein-degradation The use of heterobifunctional small molecule Degraders (e.g. PROTACs, SNIPERs etc) to elicit targeted protein degradation (TPD) is an area of increasing interest in chemical biology. They offer an attractive approach for inducing selective protein knockdown in a reversible and tuneable manner, without requiring genetic modification of cells. This is currently an area of tremendous interest, offering a potential new approach to tackle the ‘undruggable’ proteome and overcome common resistance mechanisms to current therapies. This webinar provides an introduction to Targeted Protein Degradation, discussing design and optimization of Degrader molecules and how structural biology and rational design can shed light on the Degrader development process. The second section of the webinar will present the dTAG platform for target validation. dTAG molecules specifically recognize and degrade FKBP12F36V fusion proteins, presenting a new platform for target validation studies.

Upcoming TPD Industry Events

  • Dana-Farber Targeted Protein Degradation - The Webinar Series

    Bi-weekly Seminars exploring different mechanisms of small molecule mediated protein degradation for the development of chemical probes and/or drugs. The Webinar Series will take place bi-weekly on: Thursdays 12 pm noon (Eastern Standard Time) 9 am (Pacific Standard Time) 5 pm (British Summer Time) 6 pm (Central European Summer Time) You can join webinar by Zoom. https://dfci.zoom.us/webinar/register/WN_m7JJaw52T8yZYt8-ykL6UQ ​

  • European Protein Degradation Congress 2021 | Kisaco Research

    SEPTEMBER 22-23, 2021 BASEL, SWITZERLAND Leading industry players from biotechs and big pharma will come together to exchange thoughts on how to best overcome obstacles to achieving reliable in vitro and in vivo data. Academic experts will be present their latest research to help build a deeper understanding of the mechanisms involved in the Ubiquitin pathway, providing a clearer picture on what makes a good, or not good, target for degradation.

  • Discovery on Target

    September 27-30, 2021 Discovery on Target (DOT) is the industry’s preeminent event on novel drug targets and technologies for drug discovery professionals. DOT highlights advances in current and emerging “hot” targets and technologies, as well as target validation strategies for the discovery and development of novel therapeutic agents, ranging from biologics to small molecules.

  • Undruggable Leaders Forum

    SEPTEMBER 2021 | EST The Undruggable Leaders Virtual Forum, the pan-undruggable meeting serving senior decision-makers from pharma and biotech who are striving to discover and advance undruggable targets.

  • Targeted Protein Degradation Summit

    October 2021 The 4th Targeted Protein Degradation Summit returns in October 2021 to once again explore the latest approaches, perspectives, and data-drive case studies that will continue to advance PROTACs, molecular glues, and other degrader modalities towards clinical success.

Private Companies

  • A-Alpha Bio | Measure more protein interactions

    AlphaSeq is a synthetic biology platform used to accelerate drug development by enabling library-on-library measurements of protein interactions.

  • Amphista Therapeutics

    Amphista Therapeutics is developing medicines for hard to treat diseases using next generation targeted protein degradation approaches.

  • BioTheryX

    BioTheryX is a clinical-stage company harnessing deep expertise in Targeted Protein Degradation to restore protein homeostasis in order to treat a wide range of diseases.

  • Captor Therapeutics

    Captor Therapeutics is a high-tech pharmaceutical company focused on targeting the undruggable proteome.

  • Cedilla Therapeutics

    Cedilla is harnessing intrinsic protein stability mechanisms to broaden the reach of small molecule therapeutics. We work on cancer and other diseases caused by protein dysregulation.

  • Civetta Therapeutics

    Civetta Therapeutics was founded to advance new medicines through small molecule targeting of propeller domains with the goal of developing important therapeutics for cancers and other diseases.

  • Coho Therapeutics

    Coho Therapeutics is a nascent biotechnology company developing medicines within a new class of therapeutics called protein degraders.

  • Cullgen

    Cullgen is a privately held biopharmaceutical company dedicated to the development of first-in-class new chemical entities (NCEs) for the treatment of diseases lacking effective therapeutic approaches.

  • Dialectic Therapeutics

    Dialectic Therapeutics (DT) is a pre-clinical biotechnology company dedicated to the development of unique, impactful anti-cancer drugs that effectively treat patients with few to no other options.

  • Dunad Therapeutics

    Dunad Therapeutics is focusing on the development of next-generation targeted protein degradation therapies. Dunad’s platform enables selective degradation via direct target modification using tuneable mono-valent small molecules, unlocking new target space and allowing for the development of more drug-like, orally bioavailable and CNS-accessible protein degraders.

  • FIMECS, Inc.

    FIMECS is a protein degradation technology-based drug discovery biotech focused on developing first-in-class protein degradation therapeutics for cancers and other difficult-to-treat diseases.

  • Frontier Medicines

    Frontier Medicines’ integrated approach leverages chemoproteomics and machine learning to accelerate the development of medicines that drug the “undruggable” protein targets that drive human disease.

  • Hinova Pharmaceuticals

    Hinova Pharmaceuticals Inc. is a high-tech innovative drug discovery and development company dedicated to bring new medicines to patients worldwide.

  • Lycia Therapeutics

    Developing first-in-class therapeutics that degrade extracellular proteins to address difficult-to-treat diseases

  • Neomorph

    Advancing the science of targeted protein degradation to destroy ‘undruggable’ proteins and cure disease.

  • Orionis Biosciences

    Orionis Biosciences is a life sciences company pioneering technological innovation in genome-scale drug discovery and tunable molecular design of novel therapeutic drug modalities.

  • Orum Therapeutics

    Orum Therapeutics 오름테라퓨틱 is pioneering precision delivery of targeted protein degraders for the development of oncology and immuno-oncology treatments.

  • PhoreMost

    PhoreMost’s SITESEEKER® platform enables the inception of First-in-class drug discovery programmes. Using this unique approach, PhoreMost is developing an internal asset pipeline in oncology and other diseases of ageing.

  • Pin Therapeutics

    Pin Therapeutics aims to develop targeted protein degradation hijacking ubiquitin and/or UBL (ubiquitin-like) biology.

  • Plexium

    Plexium is implementing novel technologies and clinical approaches that enable the rapid and scalable development of first-in-class therapeutics.

Public Companies

  • Arvinas

    Arvinas is a pharmaceutical company focused on developing new small molecule strategies aimed at degrading disease-causing cellular proteins.

  • C4 Therapeutics

    C4 Therapeutics® is committed to transforming the treatment of cancer, neurological, and other important diseases with novel early stage therapies that eliminate disease-causing proteins.

  • Kymera

    Kymera is a biopharmaceutical company developing novel protein degrader therapeutics to treat disease in powerful new ways, which harness the body’s natural protein degradation system to selectively degrade disease causing proteins with the goal of completely removing them from the body.

  • Monte Rosa Therapeutics

    Monte Rosa's drug discovery platform is tailored to promote specific protein ubiquitination and subsequent proteasomal degradation of disease-causing, undruggable proteins, in essence leading to pharmacological protein knockout with high efficiency and accuracy.

  • Nurix Therapeutics

    Nurix Therapeutics discovers drugs that harness the body’s natural process to control protein levels.

Media (since Issue 2)

Scientific Papers (since Issue 2)

  • Aptamer-PROTAC Conjugates (APCs) for Tumor-specific Targeting in Breast Cancer

    July 9, 2021 Shipeng He, Fei Gao, Junhui Ma, Haoqian Ma, Guoqiang Dong, Chunquan Sheng Abstract Development of proteolysis targeting chimeras (PROTACs) is emerging as a promising strategy for targeted protein degradation. However, the drug development using the heterobifunctional PROTAC molecules is generally limited by poor membrane permeability, low in vivo efficacy and indiscriminate distribution. Herein an aptamer-PROTAC conjugation approach was developed as a novel strategy to improve the tumor-specific targeting ability and in vivo antitumor potency of conventional PROTACs. As proof of concept, the first aptamer-PROTAC conjugate (APC) was designed by conjugating a BET-targeting PROTAC to the nucleic acid aptamer AS1411 (AS) via a cleavable linker. Compared with the unmodified BET PROTAC, the designed molecule (APR) showed improved tumor targeting ability in a MCF-7 xenograft model, leading to enhanced in vivo BET degradation and antitumor potency and decreased toxicity. Thus, the APC strategy may pave the way for the design of tumor-specific targeting PROTACs and have broad applications in the development of PROTAC-based drugs.

  • Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination

    July 6, 2021 Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlosser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf SPT6 is a histone chaperone that tightly binds RNA polymerase II (RNAPII) during transcription elongation. However, its primary role in transcription is uncertain. We used targeted protein degradation to rapidly deplete SPT6 in human cells and analyzed defects in RNAPII behavior by a multi-omics approach and mathematical modeling. Our data indicate that SPT6 is a crucial factor for RNAPII processivity and is therefore required for the productive transcription of protein-coding genes. Unexpectedly, SPT6 also has a vital role in RNAPII termination, as acute depletion induced readthrough transcription for thousands of genes. Long-term depletion of SPT6 induced cryptic intragenic transcription, as observed earlier in yeast. However, this phenotype was not observed upon acute SPT6 depletion and therefore can be attributed to accumulated epigenetic perturbations in the prolonged absence of SPT6. In conclusion, targeted degradation of SPT6 allowed the temporal discrimination of its function as an epigenetic safeguard and RNAPII elongation factor.

  • Proteolysis-Targeting Chimeras Enhance T Cell Bispecific Antibody-Driven T Cell Activation and Effector Function through Increased MHC Class I Antigen Presentation in Cancer Cells

    July 2, 2021 Vittoria Massafra, Sofia Tundo, Aline Dietzig, Axel Ducret, Christian Jost, Christian Klein, Roland E. Kontermann, Hendrik Knoetgen, Martin Steegmaier, Andrea Romagnani and Yvonne A. Nagel The availability of Ags on the surface of tumor cells is crucial for the efficacy of cancer immunotherapeutic approaches using large molecules, such as T cell bispecific Abs (TCBs). Tumor Ags are processed through intracellular proteasomal protein degradation and are displayed as peptides on MHC class I (MHC I). Ag recognition through TCRs on the surface of CD8+ T cells can elicit a tumor-selective immune response. In this article, we show that proteolysis-targeting chimeras (PROTACs) that target bromo- and extraterminal domain proteins increase the abundance of the corresponding target-derived peptide Ags on MHC I in both liquid and solid tumor–derived human cell lines. This increase depends on the engagement of the E3 ligase to bromo- and extraterminal domain protein. Similarly, targeting of a doxycycline-inducible Wilms tumor 1 (WT1)-FKBP12F36V fusion protein, by a mutant-selective FKBP12F36V degrader, increases the presentation of WT1 Ags in human breast cancer cells. T cell–mediated response directed against cancer cells was tested on treatment with a TCR-like TCB, which was able to bridge human T cells to a WT1 peptide displayed on MHC I. FKBP12F36V degrader treatment increased the expression of early and late activation markers (CD69, CD25) in T cells; the secretion of granzyme β, IFN-γ, and TNF-α; and cancer cell killing in a tumor-T cell coculture model. This study supports harnessing targeted protein degradation in tumor cells, for modulation of T cell effector function, by investigating for the first time, to our knowledge, the potential of combining a degrader and a TCB in a cancer immunotherapy setting.

  • Chemical-Mediated Targeted Protein Degradation in Neurodegenerative Diseases

    June 24, 2021 Soonsil Hyun and Dongyun Shin Neurodegenerative diseases, including Alzheimer’s disease, Huntington’s disease, and Parkinson’s disease, are a class of diseases that lead to dysfunction of cognition and mobility. Aggregates of misfolded proteins such as β-amyloid, tau, α-synuclein, and polyglutamates are known to be among the main causes of neurodegenerative diseases; however, they are considered to be some of the most challenging drug targets because they cannot be modulated by conventional small-molecule agents. Recently, the degradation of target proteins by small molecules has emerged as a new therapeutic modality and has garnered the interest of the researchers in the pharmaceutical industry. Bifunctional molecules that recruit target proteins to a cellular protein degradation machinery, such as the ubiquitin–proteasome system and autophagy–lysosome pathway, have been designed. The representative targeted protein degradation technologies include molecular glues, proteolysis-targeting chimeras, hydrophobic tagging, autophagy-targeting chimeras, and autophagosome-tethering compounds. Although these modalities have been shown to degrade many disease-related proteins, such technologies are expected to be potentially important for neurogenerative diseases caused by protein aggregation. Herein, we review the recent progress in chemical-mediated targeted protein degradation toward the discovery of drugs for neurogenerative diseases.

  • Opportunities and Challenges of Small Molecule Induced Targeted Protein Degradation

    June 22, 2021 Ming He, Wenxing Lv and Yu Rao Proteolysis targeting chimeras (PROTAC) represents a new type of small molecule induced protein degradation technology that has emerged in recent years. PROTAC uses bifunctional small molecules to induce ubiquitination of target proteins and utilizes intracellular proteasomes for chemical knockdown. It complements the gene editing and RNA interference for protein knockdown. Compared with small molecule inhibitors, PROTAC has shown great advantages in overcoming tumor resistance, affecting the non-enzymatic function of target proteins, degrading undruggable targets, and providing new rapid and reversible chemical knockout tools. At the same time, its challenges and problems also need to be resolved as a fast-developing new chemical biology technology.

  • PROTACs technology for targeting non-oncoproteins: advances and perspectives

    June 21, 2021 Chao Wanga, Yujing Zhang, Dongming Xing, Renshuai, Zhang Proteolysis targeting chimeras (PROTACs) have been developed to be an effective technology for targeted protein degradation. Each PROTAC contains three key components: a protein-of-interest (POI) ligand, an E3 ligase ligand, and a linker. These bifunctional molecules can hijack the intracellular inherent ubiquitin–proteasome system to degrade different POIs. With several advantages over other therapeutic strategies, PROTACs have set off a new upsurge of drug discovery in recent years. PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, fatty liver disease, immune diseases, neurodegenerative diseases, and viral infections. In this review, we aim to summarize the rapid progress from 2010 to 2021 in PROTACs targeting various non-oncoproteins and elucidate the advantages of PROTACs technology. Finally, the potential challenges of this dynamic field are also discussed.

  • Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors

    June 20, 2021 Gabriel LaPlante and Wei Zhang The ubiquitin-proteasome system (UPS) is a critical regulator of cellular protein levels and activity. It is, therefore, not surprising that its dysregulation is implicated in numerous human diseases, including many types of cancer. Moreover, since cancer cells exhibit increased rates of protein turnover, their heightened dependence on the UPS makes it an attractive target for inhibition via targeted therapeutics. Indeed, the clinical application of proteasome inhibitors in treatment of multiple myeloma has been very successful, stimulating the development of small-molecule inhibitors targeting other UPS components. On the other hand, while the discovery of potent and selective chemical compounds can be both challenging and time consuming, the area of targeted protein degradation through utilization of the UPS machinery has seen promising developments in recent years. The repertoire of proteolysis-targeting chimeras (PROTACs), which employ E3 ligases for the degradation of cancer-related proteins via the proteasome, continues to grow. In this review, we will provide a thorough overview of small-molecule UPS inhibitors and highlight advancements in the development of targeted protein degradation strategies for cancer therapeutics.

  • Advancing targeted protein degradation for cancer therapy

    June 15, 2021 Brandon Dale, Meng Cheng, Kwang-Su Park, H. Ümit Kaniskan, Yue Xiong & Jian Jin The development of small-molecule degraders such as proteolysis-targeting chimeras (PROTACs) has made it possible to target oncoproteins previously considered undruggable. This Review discusses recent advances in the field, with a focus on opportunities and challenges for future development.

  • Targeted Protein Degradation through Fast Optogenetic Activation and Its Application to the Control of Cell Signaling

    June 13, 2021 Amy Ryan, Jihe Liu, and Alexander Deiters Development of methodologies for optically triggered protein degradation enables the study of dynamic protein functions, such as those involved in cell signaling, that are difficult to be probed with traditional genetic techniques. Here, we describe the design and implementation of a novel light-controlled peptide degron conferring N-end pathway degradation to its protein target. The degron comprises a photocaged N-terminal amino acid and a lysine-rich, 13-residue linker. By caging the N-terminal residue, we were able to optically control N-degron recognition by an E3 ligase, consequently controlling ubiquitination and proteasomal degradation of the target protein. We demonstrate broad applicability by applying this approach to a diverse set of target proteins, including EGFP, firefly luciferase, the kinase MEK1, and the phosphatase DUSP6 (also known as MKP3). The caged degron can be used with minimal protein engineering and provides virtually complete, light-triggered protein degradation on a second to minute time scale.

  • mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution

    June 11, 2021 Christopher M. Weber, Antonina Hafner, Jacob G. Kirkland, Simon M. G. Braun, Benjamin Z. Stanton, Alistair N. Boettiger & Gerald R. Crabtree The mammalian SWI/SNF complex, or BAF complex, has a conserved and direct role in antagonizing Polycomb-mediated repression. Yet, BAF also promotes repression by Polycomb in stem cells and cancer. How BAF both antagonizes and promotes Polycomb-mediated repression remains unknown. Here, we utilize targeted protein degradation to dissect the BAF–Polycomb axis in mouse embryonic stem cells on short timescales. We report that rapid BAF depletion redistributes Polycomb repressive complexes PRC1 and PRC2 from highly occupied domains, like Hox clusters, to weakly occupied sites normally opposed by BAF. Polycomb redistribution from highly repressed domains results in their decompaction, gain of active epigenomic features and transcriptional derepression. Surprisingly, through dose-dependent degradation of PRC1 and PRC2, we identify a conventional role for BAF in Polycomb-mediated repression, in addition to global Polycomb redistribution. These findings provide new mechanistic insight into the highly dynamic state of the Polycomb–Trithorax axis.

  • Optical control of targeted protein degradation

    June 10, 2021 Martin Reynders, Dirk Trauner Molecular glues and proteolysis targeting chimeras (PROTACs) have emerged as small-molecule tools that selectively induce the degradation of a chosen protein and have shown therapeutic promise. Recently, several approaches employing light as an additional stimulus to control induced protein degradation have been reported. Here, we analyze the principles guiding the design of such systems, provide a survey of the literature published to date, and discuss opportunities for further development. Light-responsive degraders enable the precise temporal and spatial control of protein levels, making them useful research tools but also potential candidates for human precision medicine.

  • Rational Control of Molecular Properties Is Mandatory to Exploit the Potential of PROTACs as Oral Drugs

    June 8, 2021 Giuseppe Ermondi, Diego Garcia Jimenez, Matteo Rossi Sebastiano, and Giulia Caron To obtain new oral drugs in the beyond rule of five space, PROTACs among others, molecular properties should be optimized in early drug discovery. Degraders call for design strategies which focus on intramolecular interaction and chameleonicity. In parallel, tailored revalidation of permeability assessment and prediction methods becomes fundamental in this innovative chemical space.

  • TF-PROTACs Enable Targeted Degradation of Transcription Factors

    June 8, 2021 Jing Liu, He Chen, H. Ümit Kaniskan, Ling Xie, Xian Chen, Jian Jin, and Wenyi We Transcription factors (TFs) represent a major class of therapeutic targets for the treatment of human diseases including cancer. Although the biological functions and even crystal structures of many TFs have been clearly elucidated, there is still no viable approach to target the majority of TFs, thus rendering them undruggable for decades. PROTACs (proteolysis targeting chimeras) emerge as a powerful class of therapeutic modalities, which rely on induced protein–protein interactions between the proteins of interest (POIs) and E3 ubiquitin ligases to aid the degradation of POIs by the ubiquitin-proteasome system (UPS). Here, we report the development of a platform termed TF-PROTAC, which links an DNA oligonucleotide to an E3 ligase ligand via a click reaction, to selectively degrade the TF of interest. The selectivity of these TF-PROTACs depends on the DNA oligonucleotides utilized that can be specific to the TFs of interest. We have developed two series of VHL-based TF-PROTACs, NF-κB-PROTAC (dNF-κB) and E2F-PROTAC (dE2F), which effectively degrade endogenous p65 and E2F1 proteins in cells, respectively, and subsequently display superior antiproliferative effects in cells. Collectively, our results suggest that TF-PROTACs provide a generalizable platform to achieve selective degradation of TFs and a universal strategy for targeting most “undruggable” TFs.

  • Selective autophagy as the basis of autophagy-based degraders

    June 3, 2021 Daiki Takahashi, Hirokazu Arimoto Degrader technologies, which enable the chemical knockdown of disease-causing proteins, are promising for drug discovery. After two decades of research, degraders using the ubiquitin-proteasome system (UPS) are currently in clinical trials. However, the UPS substrates are mainly limited to soluble proteins. Autophagy-targeting chimeras and autophagosome-tethering compounds are degraders that use autophagy, which has functions complementary to the UPS. They can degrade organelles and aggregate-prone proteins, making them promising treatments against age-related conditions such as mitochondrial dysfunction and neurodegenerative diseases. The molecular mechanism of selective autophagy is an ongoing research topic, which explains why autophagy-based degraders were not available until recently. In this review, we introduce four classifications of selective autophagy mechanisms to facilitate the understanding of the degrader design.

  • Reviewing the toolbox for degrader development in oncology

    May 28, 2021 Joel O.Cresser-Brown, Graham P. Marsh, Hannah J. Maple The field of targeted protein degradation encompasses a growing number of modalities that achieve potent and selective knockdown of target proteins at the post-translational level. Among the most clinically advanced are bifunctional small-molecule degraders, also referred to as PROteolysis Targeting Chimeras, Degronimids, SNIPERs, or uSMITEs. Although applicable to many disease indications, oncology stands to be the first to benefit from this promising therapeutic approach, with the first investigational new drugs (INDs) filed in 2019 and a proliferation of research specifically focused on harnessing degraders for cancer treatment. In this review, we consider the toolbox of guidelines, reagents, and technologies that has evolved alongside the field to support degrader research and development.

  • PROTACs, molecular glues and bifunctionals from bench to bedside: Unlocking the clinical potential of catalytic drugs

    June 2021 M. Maneiro E. De Vita, D. Conole, C.S. Kounde, Q. Zhang, E.W. Tate The vast majority of currently marketed drugs rely on small molecules with an ‘occupancy-driven’ mechanism of action (MOA). Therefore, the efficacy of these therapeutics depends on a high degree of target engagement, which often requires high dosages and enhanced drug exposure at the target site, thus increasing the risk of off-target toxicities (Churcher, 2018 [1]). Although small molecule drugs have been successfully used as treatments for decades, tackling a variety of disease-relevant targets with a defined binding site, many relevant therapeutic targets remain challenging to drug due, for example, to lack of well-defined binding pockets or large protein-protein interaction (PPI) interfaces which resist interference (Dang et al., 2017 [2]). In the quest for alternative therapeutic approaches to address different pathologies and achieve enhanced efficacy with reduced side effects, ligand-induced targeted protein degradation (TPD) has gained the attention of many research groups both in academia and in industry in the last two decades. This therapeutic modality represents a novel paradigm compared to conventional small-molecule inhibitors. To pursue this strategy, heterobifunctional small molecule degraders, termed PROteolysis TArgeting Chimeras (PROTACs) have been devised to artificially redirect a protein of interest (POI) to the cellular protein homeostasis machinery for proteasomal degradation (Chamberlain et al., 2019 [3]). In this chapter, the development of PROTACs will first be discussed providing a historical perspective in parallel to the experimental progress made to understand this novel therapeutic modality. Furthermore, common strategies for PROTAC design, including assays and troubleshooting tips will be provided for the reader, before presenting a compendium of all PROTAC targets reported in the literature to date. Due to the recent advancement of these molecules…

  • Selective targeting of non-centrosomal AURKA functions through use of a targeted protein degradation tool

    May 28, 2021 Richard Wang, Camilla Ascanelli, Ahmed Abdelbaki, Alex Fung, Tim Rasmusson, Iacovos Michaelides, Karen Roberts & Catherine Lindon Targeted protein degradation tools are becoming a new therapeutic modality, allowing small molecule ligands to be reformulated as heterobifunctional molecules (PROteolysis Targeting Chimeras, PROTACs) that recruit ubiquitin ligases to targets of interest, leading to ubiquitination and destruction of the targets. Several PROTACs against targets of clinical interest have been described, but detailed descriptions of the cell biology modulated by PROTACs are missing from the literature. Here we describe the functional characterization of a PROTAC derived from AURKA inhibitor MLN8237 (alisertib). We demonstrate efficient and specific destruction of both endogenous and overexpressed AURKA by Cereblon-directed PROTACs. At the subcellular level, we find differential targeting of AURKA on the mitotic spindle compared to centrosomes. The phenotypic consequences of PROTAC treatment are therefore distinct from those mediated by alisertib, and in mitotic cells differentially regulate centrosome- and chromatin- based microtubule spindle assembly pathways. In interphase cells PROTAC-mediated clearance of non-centrosomal AURKA modulates the cytoplasmic role played by AURKA in mitochondrial dynamics, whilst the centrosomal pool is refractory to PROTAC-mediated clearance. Our results point to differential sensitivity of subcellular pools of substrate, governed by substrate conformation or localization-dependent accessibility to PROTAC action, a phenomenon not previously described for this new class of degrader compounds.

  • A Phenotypic Approach for the Identification of New Molecules for Targeted Protein Degradation Applications

    May 27, 2021 Peter Stacey, Hannah Lithgow, Xiao Lewell, Agnieszka Konopacka, Stephen Besley, Georgina Green, Ryan Whatling, Robert Law, Sascha Röth, Gopal P. Sapkota, Ian E. D. Smith, Glenn A. Burley, John Harling, Andrew B. Benowitz, Markus A. Queisser, Marcel Muelbaier Targeted protein degradation is an emerging new strategy for the modulation of intracellular protein levels with applications in chemical biology and drug discovery. One approach to enable this strategy is to redirect the ubiquitin–proteasome system to mark and degrade target proteins of interest (POIs) through the use of proteolysis targeting chimeras (PROTACs). Although great progress has been made in enabling PROTACs as a platform, there are still a limited number of E3 ligases that have been employed for PROTAC design. Herein we report a novel phenotypic screening approach for the identification of E3 ligase binders. The key concept underlying this approach is the high-throughput modification of screening compounds with a chloroalkane moiety to generate HaloPROTACs in situ, which were then evaluated for their ability to degrade a GFP-HaloTag fusion protein in a cellular context. As proof of concept, we demonstrated that we could generate and detect functional HaloPROTACs in situ, using a validated Von Hippel–Lindau (VHL) binder that successfully degraded the GFP-HaloTag fusion protein in living cells. We then used this method to prepare and screen a library of approximately 2000 prospective E3 ligase-recruiting molecules.

  • A PROTAC targets splicing factor 3B1

    May 27, 2021 Rodrigo A. Gama-Brambila, Jie Chen, Jun Zhou, Georg Tascher, Christian Münch, Xinlai Cheng The proteolysis-targeting chimeras (PROTACs) are a new technology to degrade target proteins. However, their clinical application is limited currently by lack of chemical binders to target proteins. For instance, it is still unknown whether splicing factor 3B subunit 1 (SF3B1) is targetable by PROTACs. We recently identified a 2-aminothiazole derivative (herein O4I2) as a promoter in the generation of human pluripotent stem cells. In this work, proteomic analysis on the biotinylated O4I2 revealed that O4I2 targeted SF3B1 and positively regulated RNA splicing. Fusing thalidomide—the ligand of the cereblon ubiquitin ligase—to O4I2 led to a new PROTAC-O4I2, which selectively degraded SF3B1 and induced cellular apoptosis in a CRBN-dependent manner. In a Drosophila intestinal tumor model, PROTAC-O4I2 increased survival by interference with the maintenance and proliferation of stem cell. Thus, our finding demonstrates that SF3B1 is PROTACable by utilizing noninhibitory chemicals, which expands the list of PROTAC target proteins.

  • Development of Agonist-Based PROTACs Targeting Liver X Receptor

    May 26, 2021 Hanqiao Xu, Nobumichi Ohoka, Hidetomo Yokoo, Kanako Nemoto, Takashi Ohtsuki, Hiroshi Matsufuji, Mikihiko Naito, Takao Inoue, Genichiro Tsuji and Yosuke Demizu Liver X receptors (LXRs) belong to the nuclear hormone receptor superfamily and function as ligand-dependent transcription factors that regulate cholesterol homeostasis, lipid homeostasis, and immune responses. LXR antagonists are promising treatments for hypercholesterolemia and diabetes. However, effective LXR antagonists and inhibitors are yet to be developed. Thus, we aimed to develop LXR degraders (proteolysis targeting chimeras PROTACs against LXR) as a complementary strategy to provide a similar effect to LXR inhibition. In this study, we report the development of GW3965-PEG5-VH032 (3), a PROTAC capable of effectively degrading LXRβ protein. Compound 3 induced the ubiquitin-proteasome system-dependent degradation of the LXRβ protein, which requires VHL E3 ligase. We hope that PROTACs targeting LXR proteins will become novel therapeutic agents for LXR-related diseases.

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