bims-taprod Biomed News
on Targeted protein degradation
Issue of 2021–01–24
eleven papers selected by
Alessio Ciulli, University of Dundee
  1. 2020 biotech IPOs shatter all the records.
  2. The 2020 SLAS Technology Top Ten: Translating Life Sciences Innovation.
  3. Thalidomide and its metabolite 5-hydroxythalidomide induce teratogenicity via the cereblon neosubstrate PLZF.
  4. Evaluating and evolving a screening library in academia: the St Jude approach.
  5. Development of BODIPY FL VH032 as a High-Affinity and Selective von Hippel-Lindau E3 Ligase Fluorescent Probe and Its Application in a Time-Resolved Fluorescence Resonance Energy-Transfer Assay.
  6. The Giant HECT E3 Ubiquitin Ligase HERC1 Is Aberrantly Expressed in Myeloid Related Disorders and It Is a Novel BCR-ABL1 Binding Partner.
  7. Targeting TRIM Proteins: A quest towards drugging an emerging protein class.
  8. To Degrade a MicroRNA, Destroy Its Argonaute Protein.
  9. Maedi-visna virus Vif protein uses motifs distinct from HIV-1 Vif to bind zinc and the cofactor required for A3 degradation.
  10. Targeting the Ubiquitin Signaling Cascade in Tumor Microenvironment for Cancer Therapy.
  11. Discovery of a PROTAC targeting ALK with in vivo activity.
  1. Nat Rev Drug Discov. 2021 Jan 20.
    2020 biotech IPOs shatter all the records.
    Tess Cameron, Chris Morrison.
      
    DOI:  https://doi.org/10.1038/d41573-021-00019-5
  2. SLAS Technol. 2021 Feb;26(1): 37-41
    The 2020 SLAS Technology Top Ten: Translating Life Sciences Innovation.
    Edward Kai-Hua Chow.
      
    DOI:  https://doi.org/10.1177/2472630320982580
  3. EMBO J. 2021 Jan 20. e2020105375
    Thalidomide and its metabolite 5-hydroxythalidomide induce teratogenicity via the cereblon neosubstrate PLZF.
    Satoshi Yamanaka, Hidetaka Murai, Daisuke Saito, Gembu Abe, Etsuko Tokunaga, Takahiro Iwasaki, Hirotaka Takahashi, Hiroyuki Takeda, Takayuki Suzuki, Norio Shibata, Koji Tamura, Tatsuya Sawasaki.
      Thalidomide causes teratogenic effects by inducing protein degradation via cereblon (CRBN)-containing ubiquitin ligase and modification of its substrate specificity. Human P450 cytochromes convert thalidomide into two monohydroxylated metabolites that are considered to contribute to thalidomide effects, through mechanisms that remain unclear. Here, we report that promyelocytic leukaemia zinc finger (PLZF)/ZBTB16 is a CRBN target protein whose degradation is involved in thalidomide- and 5-hydroxythalidomide-induced teratogenicity. Using a human transcription factor protein array produced in a wheat cell-free protein synthesis system, PLZF was identified as a thalidomide-dependent CRBN substrate. PLZF is degraded by the ubiquitin ligase CRL4CRBN in complex with thalidomide, its derivatives or 5-hydroxythalidomide in a manner dependent on the conserved first and third zinc finger domains of PLZF. Surprisingly, thalidomide and 5-hydroxythalidomide confer distinctly different substrate specificities to mouse and chicken CRBN, and both compounds cause teratogenic phenotypes in chicken embryos. Consistently, knockdown of Plzf induces short bone formation in chicken limbs. Most importantly, degradation of PLZF protein, but not of the known thalidomide-dependent CRBN substrate SALL4, was induced by thalidomide or 5-hydroxythalidomide treatment in chicken embryos. Furthermore, PLZF overexpression partially rescued the thalidomide-induced phenotypes. Our findings implicate PLZF as an important thalidomide-induced CRBN neosubstrate involved in thalidomide teratogenicity.
    Keywords:  CRBN; protein degradation; thalidomide metabolite; thalidomide teratogenicity; ubiquitin
    DOI:  https://doi.org/10.15252/embj.2020105375
  4. Drug Discov Today. 2021 Jan 14. pii: S1359-6446(21)00005-2. [Epub ahead of print]
    Evaluating and evolving a screening library in academia: the St Jude approach.
    Gisele Nishiguchi, Sourav Das, Jason Ochoada, Heather Long, Richard E Lee, Zoran Rankovic, Anang A Shelat.
      The quality of lead compounds is a key factor for determining the success of chemical probe and drug discovery programs. Given that high-throughput screening (HTS) continues to be a dominant lead generation paradigm, access to high-quality screening libraries is crucial for such efforts in both industry and academia. Here, we discuss the strategy implemented a decade ago to build from scratch one of the largest compound collections in academia, containing ∼575 000 carefully annotated small molecules, and a recent multidisciplinary effort designed to further enhance the collection to meet our research demands for the next decade.
    DOI:  https://doi.org/10.1016/j.drudis.2021.01.005
  5. ACS Omega. 2021 Jan 12. 6(1): 680-695
    Development of BODIPY FL VH032 as a High-Affinity and Selective von Hippel-Lindau E3 Ligase Fluorescent Probe and Its Application in a Time-Resolved Fluorescence Resonance Energy-Transfer Assay.
    Wenwei Lin, Yongtao Li, Lei Yang, Taosheng Chen.
      The von Hippel-Lindau (VHL) tumor suppressor associates with transcription factors elongin-C and elongin-B to form the VHL-elongin-C-elongin-B protein complex and carry out its functions, such as degradation of hypoxia-inducible factors. VHL ligands are used not only to modulate hypoxia-signaling pathways and potentially treat chronic anemia or ischemia but also to form bivalent ligands as proteolysis-targeting chimeras to degrade proteins for potential therapeutic applications. Sensitive and selective VHL-based binding assays are critical for identifying and characterizing VHL ligands with high-throughput screening approaches. VHL ligand-binding assays, such as isothermal titration calorimetry, surface plasmon resonance, and fluorescence polarization assays, are reported but with limitations. Isothermal titration calorimetry requires higher protein concentrations with a lower throughput than fluorescence-based assays do. Surface plasmon resonance requires protein immobilization, which introduces variation and is not suitable for testing a large number of ligands. Fluorescence polarization can be sensitive with high-throughput capability but is susceptible to assay interference, and small-molecule-based fluorescent probes are not available. We developed the first small-molecule-based high-affinity VHL fluorescent probe BODIPY FL VH032 (5), with a K d of 3.01 nM, for a time-resolved fluorescence resonance energy-transfer assay. This new assay is sensitive, selective, resistant to assay interference, and capable of characterizing VHL ligands with a wide range of affinities. It is also suitable for VHL ligand identification and characterization with high-throughput screening.
    DOI:  https://doi.org/10.1021/acsomega.0c05221
  6. Cancers (Basel). 2021 Jan 19. pii: E341. [Epub ahead of print]13(2):
    The Giant HECT E3 Ubiquitin Ligase HERC1 Is Aberrantly Expressed in Myeloid Related Disorders and It Is a Novel BCR-ABL1 Binding Partner.
    Muhammad Shahzad Ali, Cristina Panuzzo, Chiara Calabrese, Alessandro Maglione, Rocco Piazza, Daniela Cilloni, Giuseppe Saglio, Barbara Pergolizzi, Enrico Bracco.
      HERC E3 subfamily members are parts of the E3 ubiquitin ligases and key players for a wide range of cellular functions. Though the involvement of the Ubiquitin Proteasome System in blood disorders has been broadly studied, so far the role of large HERCs in this context remains unexplored. In the present study we examined the expression of the large HECT E3 Ubiquitin Ligase, HERC1, in blood disorders. Our findings revealed that HERC1 gene expression was severely downregulated both in acute and in chronic myelogenous leukemia at diagnosis, while it is restored after complete remission achievement. Instead, in Philadelphia the negative myeloproliferative neoplasm HERC1 level was peculiarly controlled, being very low in Primary Myelofibrosis and significantly upregulated in those Essential Thrombocytemia specimens harboring the mutation in the calreticulin gene. Remarkably, in CML cells HERC1 mRNA level was associated with the BCR-ABL1 kinase activity and the HERC1 protein physically interacted with BCR-ABL1. Furthermore, we found that HERC1 was directly tyrosine phosphorylated by the ABL kinase. Overall and for the first time, we provide original evidence on the potential tumor-suppressing or -promoting properties, depending on the context, of HERC1 in myeloid related blood disorders.
    Keywords:  Bcr-Abl1; E3 ubiquitin ligases; HERC1; gene expression; myeloid neoplasms; protein–protein interaction; ubiquitin proteasome system
    DOI:  https://doi.org/10.3390/cancers13020341
  7. Chembiochem. 2021 Jan 22.
    Targeting TRIM Proteins: A quest towards drugging an emerging protein class.
    Francesca D'Amico, Rishov Mukhopadhyay, Huib Ovaa, Monique Priscilla Catharina Mulder.
      The ubiquitination machinery regulates several fundamental biological processes from protein homeostasis to a wide variety of cellular signalling pathways. As a consequence, its dysregulation is linked to diseases, including cancer, neurodegeneration, and autoimmunity. With this review, we aim to highlight the therapeutic potential of targeting E3 ligases with a special focus on an emerging class of RING ligases, named Tri-Partite Motif (TRIM) proteins, whose role as targets for drug development is currently gaining pharmaceutical attention. TRIM proteins exert their catalytic activity as scaffolds involved in many protein-protein interactions, whose multi-domains and adapter-like nature make their druggability very challenging. Here we report an overview of the current understanding of this class of single polypeptide RING E3 ligases and discuss potential targeting options.
    Keywords:  ligases inhibitors high throughput screening TRIM Ubiquitin
    DOI:  https://doi.org/10.1002/cbic.202000787
  8. Mol Cell. 2021 Jan 21. pii: S1097-2765(20)30964-3. [Epub ahead of print]81(2): 223-225
    To Degrade a MicroRNA, Destroy Its Argonaute Protein.
    Pei-Hsuan Wu, Phillip D Zamore.
      Han et al. (2020) and Shi et al. (2020) report that the E3 ubiquitin ligase ZSWIM8 senses when an RNA and an Argonaute protein-bound microRNA are extensively base paired and directs Argonaute destruction by the proteasome. The result is degradation of the microRNA.
    DOI:  https://doi.org/10.1016/j.molcel.2020.12.043
  9. J Biol Chem. 2020 Nov 24. pii: S0021-9258(20)00031-9. [Epub ahead of print]296 100045
    Maedi-visna virus Vif protein uses motifs distinct from HIV-1 Vif to bind zinc and the cofactor required for A3 degradation.
    Kirsten M Knecht, Yingxia Hu, Diana Rubene, Matthew Cook, Samantha J Ziegler, Stefán R Jónsson, Yong Xiong.
      The mammalian apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of cytidine deaminases restrict viral infections by mutating viral DNA and impeding reverse transcription. To overcome this antiviral activity, most lentiviruses express a viral accessory protein called the virion infectivity factor (Vif), which recruits A3 proteins to cullin-RING E3 ubiquitin ligases such as cullin-5 (Cul5) for ubiquitylation and subsequent proteasomal degradation. Although Vif proteins from primate lentiviruses such as HIV-1 utilize the transcription factor core-binding factor subunit beta as a noncanonical cofactor to stabilize the complex, the maedi-visna virus (MVV) Vif hijacks cyclophilin A (CypA) instead. Because core-binding factor subunit beta and CypA are both highly conserved among mammals, the requirement for two different cellular cofactors suggests that these two A3-targeting Vif proteins have different biochemical and structural properties. To investigate this topic, we used a combination of in vitro biochemical assays and in vivo A3 degradation assays to study motifs required for the MVV Vif to bind zinc ion, Cul5, and the cofactor CypA. Our results demonstrate that although some common motifs between the HIV-1 Vif and MVV Vif are involved in recruiting Cul5, different determinants in the MVV Vif are required for cofactor binding and stabilization of the E3 ligase complex, such as the zinc-binding motif and N- and C-terminal regions of the protein. Results from this study advance our understanding of the mechanism of MVV Vif recruitment of cellular factors and the evolution of lentiviral Vif proteins.
    Keywords:  E3 ubiquitin ligase; HIV; cyclophilin; lentivirus; metalloprotein; protein complex; protein–protein interaction; viral protein; zinc
    DOI:  https://doi.org/10.1074/jbc.RA120.015828
  10. Int J Mol Sci. 2021 Jan 14. pii: E791. [Epub ahead of print]22(2):
    Targeting the Ubiquitin Signaling Cascade in Tumor Microenvironment for Cancer Therapy.
    Qi Liu, Bayonle Aminu, Olivia Roscow, Wei Zhang.
      Tumor microenvironments are composed of a myriad of elements, both cellular (immune cells, cancer-associated fibroblasts, mesenchymal stem cells, etc.) and non-cellular (extracellular matrix, cytokines, growth factors, etc.), which collectively provide a permissive environment enabling tumor progression. In this review, we focused on the regulation of tumor microenvironment through ubiquitination. Ubiquitination is a reversible protein post-translational modification that regulates various key biological processes, whereby ubiquitin is attached to substrates through a catalytic cascade coordinated by multiple enzymes, including E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes and E3 ubiquitin ligases. In contrast, ubiquitin can be removed by deubiquitinases in the process of deubiquitination. Here, we discuss the roles of E3 ligases and deubiquitinases as modulators of both cellular and non-cellular components in tumor microenvironment, providing potential therapeutic targets for cancer therapy. Finally, we introduced several emerging technologies that can be utilized to develop effective therapeutic agents for targeting tumor microenvironment.
    Keywords:  E3 ligase; cancer-associated fibroblasts; deubiquitinase; extracellular matrix; hypoxia; immune cells; inhibitors; tumor microenvironment; ubiquitin variants; ubiquitination
    DOI:  https://doi.org/10.3390/ijms22020791
  11. Eur J Med Chem. 2021 Jan 02. pii: S0223-5234(20)31122-3. [Epub ahead of print]212 113150
    Discovery of a PROTAC targeting ALK with in vivo activity.
    Guoyi Yan, Xinxin Zhong, Lin Yue, Chunlan Pu, Huifang Shan, Suke Lan, Meng Zhou, Xueyan Hou, Jie Yang, Rui Li.
      Anaplastic lymphoma kinase (ALK) was involved in the development of various cancer types. Although several ALK inhibitors have been advanced to clinical trials, the emergence of drug resistance has limited the clinical application of them. To overcome the drug resistance, proteolysis targeting chimeras (PROTACs) could be an alternative strategy. In this study, a series of ALK degraders were designed and synthesized. The degraders were developed through the conjugation of LDK378 and CRBN E3 ubiquitin ligase ligands. Among all the molecules, compound B3 showed potent selective inhibitory activity to ALK and can decrease the cellular levels of ALK fusion proteins in a concentration- and time-dependent manner in H3122 cell line. Meanwhile, B3 showed improved anticancer activity in vitro comparing with LDK378 and the antiproliferative activity to xenograft tumor model was acceptable. All the results demonstrated that ALK degrader B3 with in vitro and in vivo anti-cancer activities was valuable for further investigation.
    Keywords:  ALK; Degrader; Oral anticancer bioactivities; PROTAC
    DOI:  https://doi.org/10.1016/j.ejmech.2020.113150
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