Degrader Digest - Issue 4

Dear Protein Degradation Friends, Welcome to Issue 4 of the Targeted Protein Degradation (TPD) Digest! In this issue, we continue to provide a one-stop-shop for the most recent protein degradation updates. This TPD Digest contains the following sections: Upcoming TPD Industry Events - Spotlight on 4th Annual Targeted Protein Degradation Summit TPD Presentations Video Animations (complete list) Companies Working on Protein Degradation Media Articles (since Issue 3) Scientific Papers (since Issue 3) Sign Up for Degrader Digest Updates Link to Prior Issues If you have any questions, suggestions for improvement, presentations, or exciting animations you would like to share with the community, please email degraderdigest@gmail.com. Many thanks! -Marc

Upcoming TPD Industry Events

  • Targeted Protein Degradation Summit

    October 26-29, 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.

  • TPD Summit Summary

    With brand new data being shared including: • Georg Winter, Principal Investigator, CeMM – identification of new molecular glues and PROTACs that reprogram a new, not yet hijacked E3 ligase • Haojie Huang, Professor, Mayo Clinic – Workshop E where new anti-cancer efficacy data of O’PROTACs in mice will be disclosed • Ryan Potts, Head of Induced Proximity Platform, Amgen - Induced Proximity Medicines for Targeted Degradation of Proteins & RNAs • Harald Weinstabl, Head of Medicinal Chemistry, Boehringer Ingelheim - Identification of Selective & Orally Available VHL-Based PROTACs • Neil Bence, VP Oncology Discovery, BMS - Overcoming CRBN Resistance with the Aiolos/Ikaros Degrader CC-92480 for Multiple Myeloma & the Future of CELMoD Molecular Glues • David Millan, VP Chemistry, Foghorn Therapeutics - FHD-609: A Potent & Selective Intravenous Heterobifunctional Degrader of BRD9 • And more! Enquire here to find out more about the summit and the discounts available – info@hansonwade.com

  • Challenges and Opportunities in Protein Degradation

    October 21, 2021 at 4PM BDST, 11 AM EST. This is a free webinar hosted by DDW and supported by Cell Signaling Technology (CST). Dr. Nathanael Gray, Professor of Chemical and Systems Biology at the Stanford Cancer Institute, will discuss efforts to synthesise and characterise small molecule degraders of cancer targets, including kinases and transcriptional regulators.

  • 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 ​

TPD Presentations

Want to help the TPD community? Share presentations with us (degraderdigest@gmail.com) to consider including in the next issue.

  • 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.

  • 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…

Video Animations

Video exemplifications are incredibly helpful. If you have good examples to share, please forward the link to us (degraderdigest@gmail.com) be included in the TPD Digest.

  • 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)

  • 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, UBIQUITINATION, AND PROTEIN DESTRUCTION

    Sources: The best article:

  • 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

Private Companies

Working on Protein Degradation Candidates

  • *** NEW: PAQ Therapeutics

    PAQ Therapeutics Launches with $30 Million Series A to Develop Novel Therapies through Autophagy-Dependent Degradation

  • A-Alpha Bio

    A-Alpha Bio is accelerating drug development with synthetic biology and next-generation sequencing

  • Amphista Therapeutics

    Amphista Therapeutics is developing medicines for hard to treat diseases using next generation targeted protein degradation approaches. Our portfolio uses our own novel protein degrading mechanisms which build on the strengths of current protein degradation approaches whilst directly addressing their limitations. or why not drop us an email info@amphista.com Amphista Therapeutics is an exciting spin out company founded by Advent Life Sciences and built on groundbreaking science from the laboratory of Professor Alessio Ciulli (University of Dundee), a world leader in the field of targeted protein degradation.

  • BioTheryX

    BioTheryx is a clinical-stage company harnessing our 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.

Public Companies

Working on Protein Degradation Candidates

  • Arvinas

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

  • 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.

Media (since Issue 3)

Scientific Papers (since Issue 3)

  • Selective degradation-inducing probes for studying cereblon (CRBN) biology

    July 6, 2021 Abstract Targeted protein degradation represents a rapidly growing area in drug discovery and development. Moreover, small molecules that induce the targeted degradation of a given protein also represent an important addition to the chemical probes toolbox as these compounds can achieve selective protein knockdown, thus providing an approach that is orthogonal to genetic knockdowns. In order to develop degradation-inducing chemical probes for studying cereblon (CRBN) biology, we generated six CRBN–CRBN (homo-PROTAC) degraders and six CRBN–VHL (hetero-PROTAC) degraders. From these compounds we identified two potent and selective CRBN degraders (ZXH-4-130 and ZXH-4-137), both of which are CRBN–VHL compounds. We characterized these lead degraders by quantitative proteomics in five cell lines (MM1.S, Kelly, SK-N-DZ, HEK293T, and MOLT-4) and observed high selectivity for CRBN in all cell lines. Furthermore, we directly compared our compounds to current lead CRBN degraders and demonstrated how these probes can be used as chemical knockdown reagents for studying CRBN-dependent processes. Overall, our work provides a roadmap for thorough degrader characterization by combination western and proteomic analysis, as illustrated by the identification of ZXH-4-130 and ZXH-4-137 as CRBN-knockdown tool compounds suitable for cell-based studies.

  • Emerging protein degradation strategies: expanding the scope to extracellular and membrane proteins

    July 13, 2021 Abstract Classic small molecule inhibitors that directly target pathogenic proteins typically rely on the accessible binding sites to achieve prolonged occupancy and influence protein functions. The emerging targeted protein degradation (TPD) strategies exemplified by PROteolysis TArgeting Chimeras (PROTACs) are revolutionizing conventional drug discovery modality to target proteins of interest (POIs) that were categorized as "undruggable" before, however, these strategies are limited within intracellular POIs. The novel new degrader technologies such as LYsosome-TArgeting Chimaeras (LYTACs) and Antibody-based PROTACs (AbTACs) have been successfully developed to expand the scope of TPD to extracellular and membrane proteins, fulfilling huge unmet medical needs. Here, we systematically review the currently viable protein degradation strategies, emphasize that LYTACs and AbTACs turn a new avenue for the development of TPD, and highlight the potential challenges and directions in this vibrant field.

  • Targeted Protein Degradation: The New Frontier of Antimicrobial Discovery?

    July 14, 2021 Targeted protein degradation aims to hijack endogenous protein quality control systems to achieve direct knockdown of protein targets. This exciting technology utilizes event-based pharmacology to produce therapeutic outcomes, a feature that distinguishes it from classical occupancy-based inhibitor agents. Early degrader candidates display resilience to mutations while possessing potent nanomolar activity and high target specificity. Paired with the rapid advancement of our knowledge in the factors driving targeted degradation, the expansion of this style of therapeutic agent to a range of disease indications is eagerly awaited. In particular, the area of antibiotic discovery is sorely lacking in novel approaches, with the Antimicrobial Resistance (AMR) crisis looming as the next potential global health calamity. Here, the current advances in targeted protein degradation are highlighted, and potential approaches for designing novel antimicrobial protein degraders are proposed, ranging from adaptations of current strategies to completely novel approaches to targeted protein degradation.

  • Advances and opportunities in targeted protein degradation

    July 15, 2021 We are excited to welcome you to our special Review issue in Cell Chemical Biology on Advances and Opportunities in Targeted Protein Degradation. Over the past decade, targeted protein degradation (TPD) using proteolysis-targeting chimeras (PROTACs) and molecular glue degraders has become one of the hottest areas in drug discovery because of the potential for specifically degrading and eliminating any disease-causing protein. TPD using PROTACs or molecular glues employs heterobifunctional or monovalent molecules, respectively, to induce the proximity of E3 ubiquitin ligases to target proteins of interest for ubiquitination and proteasome-mediated degradation. Exciting aspects of TPD include the potential of this approach to therapeutically target “undruggable” disease-causing proteins, which have eluded classical drug discovery efforts, given small-molecule degraders only require an E3 ligase binder to the target protein, and not necessarily a consequential inhibitor. In contrast to small-molecule inhibitors that usually function by stoichiometrically occupying the active site of target proteins, TPD enables the catalytic degradation of target proteins resulting in sub-stoichiometric degradation of target proteins. In addition, for proteins that possess both enzymatic and scaffolding functions where inhibitors for the target protein may only partially alter the protein function, TPD and degrading the whole protein can confer added therapeutic properties beyond simple inhibitors. Despite the promise of TPD in drug discovery, several challenges still exist, including the necessity to discover more chemical matter for the >600 E3 ligases and developing approaches for the rational discovery of molecular glue degraders.

  • Structure-Guided Design of a “Bump-and-Hole” Bromodomain-Based Degradation Tag

    July 19, 2021 Abstract Chemical biology tools to modulate protein levels in cells are critical to decipher complex biology. Targeted protein degradation offers the potential for rapid and dose-dependent protein depletion through the use of protein fusion tags toward which protein degraders have been established. Here, we present a newly developed protein degradation tag BRD4BD1L94V along with the corresponding cereblon (CRBN)-based heterobifunctional degrader based on a “bump-and-hole” approach. The resulting compound XY-06-007 shows a half-degradation concentration (DC50, 6 h) of 10 nM against BRD4BD1L94V with no degradation of off-targets, as assessed by whole proteome mass spectrometry, and demonstrates suitable pharmacokinetics for in vivo studies. We demonstrate that BRD4BD1L94V can be combined with the dTAG approach to achieve simultaneous degrader-mediated depletion of their respective protein fusions. This orthogonal system complements currently available protein degradation tags and enables investigation into the consequences resulting from rapid degradation of previously undruggable disease codependencies.

  • Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer

    July 20, 2021 Summary Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of—but not all—spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.

  • Exploring Ligand-Directed N-Acyl-N-alkylsulfonamide-Based Acylation Chemistry for Potential Targeted Degrader Development

    July 21, 2021 Ligand-directed bioconjugation strategies have been used for selective protein labeling in live cells or tissue samples in applications such as live-cell imaging. Here we hypothesized that a similar strategy could be used for targeted protein degradation. To test this possibility, we developed a series of CDK2-targeting N-acyl-N-alkylsulfonamide (NASA)-containing acylation probes. The probes featured three components: a CDK2 homing ligand, a CRL4CRBN E3 ligase recruiting ligand, and a NASA functionality. We determined that upon target binding, NASA-mediated reaction resulted in selective functionalization of Lys89 on purified or native CDK2. However, we were unable to observe CDK2 degradation, which is in contrast to the efficient degradation achieved by the use of a structurally similar reversible bivalent degrader. Our analysis suggests that the lack of degradation is due to the failure to form a productive CDK2:CRBN complex. Therefore, although this work demonstrates that NASA chemistry can be used for protein labeling, whether this strategy could enable efficient protein degradation remains an open question.

  • LYTACs: An Emerging Tool for the Degradation of Non-Cytosolic Proteins

    July 23, 2021 Abstract In the last two decades, targeted protein degradation has rapidly gained popularity as a technique to eliminate disease-causing undruggable proteins. Over the years, many tools have been devised to degrade proteins by exploiting natural protein homeostasis machinery available in our body, with LYTACs being the latest to come on board. LYTACs, or lysosome-targeting chimeras, make use of the lysosome degradation pathway by recruiting proteins to lysosome-shuttling receptors located at the cell surface. LYTACs are specifically meant for the degradation of membrane-bound and extracellular proteins, which account for the products of 40 % of all protein-encoding genes. In this highlight, we describe two studies that demonstrate the scope of LYTACs and its advantages over the other protein degradation platforms. In the first study, the LYTAC utilizes the cation-independent mannose-6-phosphate receptor (CI−M6PR), while the second study uses the asialoglycoprotein receptor (ASGPR) which is found only on the surface of liver cells.

  • Molecular Glues for Targeted Protein Degradation: From Serendipity to Rational Discovery

    July 28, 2021 Abstract Targeted protein degradation is a promising area in the discovery and development of innovative therapeutics. Molecular glues mediate proximity-induced protein degradation and have intrinsic advantages over heterobifunctional proteolysis-targeting chimeras, including unprecedented mechanisms, distinct biological activities, and favorable physicochemical properties. Classical molecular glue degraders have been identified serendipitously, but rational discovery and design strategies are emerging rapidly. In this review, we aim to highlight the recent advances in molecular glues for targeted protein degradation and discuss the challenges in developing molecular glues into therapeutic agents. In particular, discovery strategies, action mechanisms, and representative case studies will be addressed.

  • Chemo-proteomics exploration of HDAC degradability by small molecule degraders

    July 26, 2021 Summary Targeted protein degradation refers to the use of small molecules that recruit a ubiquitin ligase to a target protein for ubiquitination and subsequent proteasome-dependent degradation. While degraders have been developed for many targets, key questions regarding degrader development and the consequences of acute pharmacological degradation remain, specifically for targets that exist in obligate multi-protein complexes. Here, we synthesize a pan-histone deacetylase (HDAC) degrader library for the chemo-proteomic exploration of acute degradation of a key class of chromatin-modifying enzymes. Using chemo-proteomics, we not only map the degradability of the zinc-dependent HDAC family identifying leads for targeting HDACs 1–8 and 10 but also explore important aspects of degrading epigenetic enzymes. We discover cell line-driven target specificity and that HDAC degradation often results in collateral loss of HDAC-containing repressive complexes. These findings potentially offer a new mechanism toward controlling chromatin structure, and our resource will facilitate accelerated degrader design and development for HDACs.

  • An astonishing wealth of new proteasome homologs

    July 29, 2021 Abstract Motivation The proteasome is the main proteolytic machine for targeted protein degradation in archaea and eukaryotes. While some bacteria also possess the proteasome, most of them contain a simpler and more specialized homolog, the HslV protease. In recent years, three further homologs of the proteasome core subunits have been characterized in prokaryotes: Anbu, BPH, and connectase. With the inclusion of these members, the family of proteasome-like proteins now exhibits a range of architectural and functional forms, from the canonical proteasome, a barrel-shaped protease without pronounced intrinsic substrate specificity, to the monomeric connectase, a highly specific protein ligase. Results We employed systematic sequence searches to show that we have only seen the tip of the iceberg so far and that beyond the hitherto known proteasome homologs lies a wealth of distantly related, uncharacterized homologs. We describe a total of 22 novel proteasome homologs in bacteria and archaea. Using sequence and structure analysis, we analyze their evolutionary history and assess structural differences that may modulate their function. With this initial description, we aim to stimulate the experimental investigation of these novel proteasome-like family members. Availability The protein sequences in this study are searchable in the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) with ProtBLAST/PSI-BLAST and with HHpred (database "proteasome_homologs"). The following data are available at https://data.mendeley.com/datasets/t48yhff7hs/3: (I) sequence alignments for each proteasome-like homolog, (II) the coordinates for their structural models, and (III) a cluster-map file, which can be navigated interactively in CLANS and gives direct access to all the sequences in this study.

  • Protein degradation: a novel computational approach to design protein degrader probes for main protease of SARS-CoV-2 - PubMed

    July 30, 2021 Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has afflicted many lives and led to approvals of drugs and vaccines for emergency use. Even though vaccines have emerged, the high mortality of COVID-19 and its insurgent proliferation throughout the masses commands an innovative therapeutic proposition for the treatment. Targeted protein degradation has been applied to various disease domains and we propose that it could be incredibly beneficial to tackle the current pandemic. In this study, we have attempted to furnish insights on the design of suitable PROTACs for the main protease (Mpro) of SARS-CoV-2, a protein that is considered to be an essential target for viral replication. We have employed protein-protein docking to predict the possible complementarity between a cereblon E3 ligase and Mpro of SARS-CoV-2, and estimate possible linker length. Molecular Dynamic simulation and analysis on generated ternary complexes demonstrated stable interactions that suggested that designed PROTAC has a potential to cause degradation. The superior characteristics rendered by PROTACS led us to propose them as possibly the next-generation antiviral drugs for SARS-CoV-2.

  • A Universal Chemical Method for Rational Design of Protein-Based Nanoreactors

    August 2, 2021 Abstract Self-assembly of a monomeric protease to form a multi-subunit protein complex “proteasome” enables targeted protein degradation in living cells. Naturally occurring proteasomes serve as an inspiration and blueprint for the design of artificial protein-based nanoreactors. Here we disclose a general chemical strategy for the design of proteasome-like nanoreactors. Micelle-assisted protein labeling (MAPLab) technology along with the N-terminal bioconjugation strategy is utilized for the synthesis of a well-defined monodisperse self-assembling semi-synthetic protease. The designed protein is programmed to self-assemble into a proteasome-like nanostructure which preserves the functional properties of native protease.

  • Targeted protein degradation and regulation with molecular glue: past and recent discoveries

    August 5, 2021 Abstract The evolution in research and clinical settings of targeted therapies has been inspired by the progress of cancer chemotherapy to use small molecules and monoclonal antibodies for targeting specific disease-associated genes and proteins for noninfectious chronic diseases. In addition to conventional protein inhibition and activation strategies as drug discovery modalities, new methods of targeted protein degradation and regulation using molecular glues have become an attractive approach for drug discovery. Mechanistically, molecular glues trigger interactions between the proteins that originally did not interact by forming ternary complexes as protein-protein interaction (PPI) modulators. New molecular glues and their mechanisms of action have been actively investigated in the past decades. An immunomodulatory imide drug, thalidomide, and its derivatives have been used in the clinic and are a class of molecular glue that induces degradation of several neo-substrates. In this review, we summarize the development of molecular glues and share our opinions on the identification of novel molecular glues in an attempt to promote the concept and inspire further investigations.

  • [Induced degradation of proteins by PROTACs and other strategies: towards promising drugs] - PubMed

    August 16, 2021 Targeted protein degradation (TPD), discovered twenty years ago through the PROTAC technology, is rapidly developing thanks to the implication of many scientists from industry and academia. PROTAC chimeras are heterobifunctional molecules able to link simultaneously a protein to be degraded and an E3 ubiquitin ligase. This allows the protein ubiquitination and its degradation by 26S proteasome. PROTACs have evolved from small peptide molecules to small non-peptide and orally available molecules. It was shown that PROTACs are capable to degrade proteins considered as "undruggable" i.e. devoid of well-defined pockets and deep grooves possibly occupied by small molecules. Among these "hard to drug" proteins, several can be degraded by PROTACs: scaffold proteins, BAF complex, transcription factors, Ras family proteins. Two PROTACs are clinically tested for breast (ARV471) and prostate (ARV110) cancers. The protein degradation by proteasome is also induced by other types of molecules: molecular glues, hydrophobic tagging (HyT), HaloPROTACs and homo-PROTACs. Other cellular constituents are eligible to induced degradation: RNA-PROTACs for RNA binding proteins and RIBOTACs for degradation of RNA itself (SARS-CoV-2 RNA). TPD has recently moved beyond the proteasome with LYTACs (lysosome targeting chimeras) and MADTACs (macroautophagy degradation targeting chimeras). Several techniques such as screening platforms together with mathematical modeling and computational design are now used to improve the discovery of new efficient PROTACs.

  • [Induced degradation of proteins by PROTACs and other strategies: towards promising drugs]. - Abstract - Europe PMC

    Europe PMC is an archive of life sciences journal literature.

  • Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase

    August 16, 2021 Abstract Ubiquibodies (uAbs) are a customizable proteome editing technology that utilizes E3 ubiquitin ligases genetically fused to synthetic binding proteins to steer otherwise stable proteins of interest (POIs) to the 26S proteasome for degradation. The ability of engineered uAbs to accelerate the turnover of exogenous or endogenous POIs in a post-translational manner offers a simple yet robust tool for dissecting diverse functional properties of cellular proteins as well as for expanding the druggable proteome to include tumorigenic protein families that have yet-to-be successfully drugged by conventional inhibitors. Here, we describe the engineering of uAbs composed of human carboxyl-terminus of Hsc70-interacting protein (CHIP), a highly modular human E3 ubiquitin ligase, tethered to differently designed ankyrin repeat proteins (DARPins) that bind to nonphosphorylated (inactive) and/or doubly phosphorylated (active) forms of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Two of the resulting uAbs were found to be global ERK degraders, pan-specifically capturing all endogenous ERK1/2 protein forms and redirecting them to the proteasome for degradation in different cell lines, including MCF7 breast cancer cells. Taken together, these results demonstrate how the substrate specificity of an E3 ubiquitin ligase can be reprogrammed to generate designer uAbs against difficult-to-drug targets, enabling a modular platform for remodeling the mammalian proteome.

  • Bifunctional small molecules that mediate the degradation of extracellular proteins

    August 19, 2021 Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy. Most TPD technologies use the ubiquitin–proteasome system, and are therefore limited to targeting intracellular proteins. To address this limitation, we developed a class of modular, bifunctional synthetic molecules called MoDE-As (molecular degraders of extracellular proteins through the asialoglycoprotein receptor (ASGPR)), which mediate the degradation of extracellular proteins. MoDE-A molecules mediate the formation of a ternary complex between a target protein and ASGPR on hepatocytes. The target protein is then endocytosed and degraded by lysosomal proteases. We demonstrated the modularity of the MoDE-A technology by synthesizing molecules that induce depletion of both antibody and proinflammatory cytokine proteins. These data show experimental evidence that nonproteinogenic, synthetic molecules can enable TPD of extracellular proteins in vitro and in vivo. We believe that TPD mediated by the MoDE-A technology will have widespread applications for disease treatment.

  • Harnessing the E3 Ligase KEAP1 for Targeted Protein Degradation

    September 14, 2021 Abstract Proteolysis targeting chimeras (PROTACs) represent a new class of promising therapeutic modalities. PROTACs hijack E3 ligases and the ubiquitin-proteasome system (UPS), leading to selective degradation of the target proteins. However, only a very limited number of E3 ligases have been leveraged to generate effective PROTACs. Herein, we report that the KEAP1 E3 ligase can be harnessed for targeted protein degradation utilizing a highly selective, noncovalent small-molecule KEAP1 binder. We generated a proof-of-concept PROTAC, MS83, by linking the KEAP1 ligand to a BRD4/3/2 binder. MS83 effectively reduces protein levels of BRD4 and BRD3, but not BRD2, in cells in a concentration-, time-, KEAP1- and UPS-dependent manner. Interestingly, MS83 degrades BRD4/3 more durably than the CRBN-recruiting PROTAC dBET1 in MDA-MB-468 cells and selectively degrades BRD4 short isoform over long isoform in MDA-MB-231 cells. It also displays improved antiproliferative activity than dBET1. Overall, our study expands the limited toolbox for targeted protein degradation.

  • Redefining the Scope of Targeted Protein Degradation: Translational Opportunities in Hijacking the Autophagy–Lysosome Pathway

    September 27, 2021 Abstract The advent of multi-specific targeted protein degradation (TPD) therapies has made it possible to drug targets that have long been considered to be inaccessible. For this reason, the foremost TPD modalities - molecular glues and proteolysis targeting chimeras (PROTACs) -have been widely adopted and developed in therapeutic programs across the pharmaceutical and biotechnology industries. While there are many clear advantages to these two approaches, there are also blind spots. Specifically, PROTACs and molecular glues are inherently mechanistically analogous in that targets of both are degraded via the 26s proteasome; however, not all disease-relevant targets are suitable for ubiquitin proteasome system (UPS)-mediated degradation. The alternative mammalian protein degradation pathway, the autophagy–lysosome system (or ALS), is capable of degrading targets that elude the UPS such as long-lived proteins, insoluble protein aggregates, and even abnormal organelles. Emerging TPD strategies- such as ATTEC, AUTAC, and LYTAC- take advantage of the substrate diversity of the ALS to greatly expand the clinical utility of TPD. In this Perspective, we will discuss the array of current TPD modalities, with a focus on critical evaluation of these novel ALS-mediated degradation techniques.

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