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Kannan MP, Sreeraman S, Somala CS, Kushwah RB, Mani SK, Sundaram V, Thirunavukarasou A. Advancement of targeted protein degradation strategies as therapeutics for undruggable disease targets. Future Med Chem 2023; 15:867-883. [PMID: 37254917 DOI: 10.4155/fmc-2023-0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Targeted protein degradation (TPD) aids in developing novel bifunctional small-molecule degraders and eliminates proteins of interest. The TPD approach shows promising results in oncological, neurogenerative, cardiovascular and gynecological drug development. We provide an overview of technology advancements in TPD, including molecular glues, proteolysis-targeting chimeras (PROTACs), lysosome-targeting chimeras, antibody-based PROTAC, GlueBody PROTAC, autophagy-targeting chimera, autophagosome-tethering compound, autophagy-targeting chimera and chaperone-mediated autophagy-based degraders. Here we discuss the development and evolution of the TPD field, the variety of proteins that PROTACs target and the biological repercussions of their degradation. We particularly highlight the recent improvements in TPD research that utilize autophagy or the endolysosomal pathway, which enables the targeting of undruggable targets.
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Affiliation(s)
- Mayuri P Kannan
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
| | - Sarojini Sreeraman
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
- SRIIC Lab, Sri Ramachandra Institute for Higher Education & Research, Chennai, Tamil Nadu, 600116, India
| | - Chaitanya S Somala
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
| | - Raja Bs Kushwah
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX 77843, USA
| | - Saravanan K Mani
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600073, India
| | - Vickram Sundaram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
| | - Anand Thirunavukarasou
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
- SRIIC Lab, Sri Ramachandra Institute for Higher Education & Research, Chennai, Tamil Nadu, 600116, India
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Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A, Luke B. Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 2023; 14:1227. [PMID: 36869098 PMCID: PMC9984532 DOI: 10.1038/s41467-023-36866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free rNMP removal. In some pathological conditions, rNMP removal is impaired. If these rNMPs hydrolyze during, or prior to, S phase, toxic single-ended double-strand breaks (seDSBs) can occur upon an encounter with replication forks. How such rNMP-derived seDSB lesions are repaired is unclear. We expressed a cell cycle phase restricted allele of RNase H2 to nick at rNMPs in S phase and study their repair. Although Top1 is dispensable, the RAD52 epistasis group and Rtt101Mms1-Mms22 dependent ubiquitylation of histone H3 become essential for rNMP-derived lesion tolerance. Consistently, loss of Rtt101Mms1-Mms22 combined with RNase H2 dysfunction leads to compromised cellular fitness. We refer to this repair pathway as nick lesion repair (NLR). The NLR genetic network may have important implications in the context of human pathologies.
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Affiliation(s)
- Natalie Schindler
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Matthias Tonn
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Vanessa Kellner
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Jia Jun Fung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Arianna Lockhart
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Olga Vydzhak
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefanie Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anton Khmelinskii
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Brian Luke
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany. .,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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Sulimenko V, Dráberová E, Dráber P. γ-Tubulin in microtubule nucleation and beyond. Front Cell Dev Biol 2022; 10:880761. [PMID: 36158181 PMCID: PMC9503634 DOI: 10.3389/fcell.2022.880761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubules composed of αβ-tubulin dimers are dynamic cytoskeletal polymers that play key roles in essential cellular processes such as cell division, organelle positioning, intracellular transport, and cell migration. γ-Tubulin is a highly conserved member of the tubulin family that is required for microtubule nucleation. γ-Tubulin, together with its associated proteins, forms the γ-tubulin ring complex (γ-TuRC), that templates microtubules. Here we review recent advances in the structure of γ-TuRC, its activation, and centrosomal recruitment. This provides new mechanistic insights into the molecular mechanism of microtubule nucleation. Accumulating data suggest that γ-tubulin also has other, less well understood functions. We discuss emerging evidence that γ-tubulin can form oligomers and filaments, has specific nuclear functions, and might be involved in centrosomal cross-talk between microtubules and microfilaments.
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Affiliation(s)
| | | | - Pavel Dráber
- *Correspondence: Vadym Sulimenko, ; Pavel Dráber,
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E3 ligases: a potential multi-drug target for different types of cancers and neurological disorders. Future Med Chem 2022; 14:187-201. [DOI: 10.4155/fmc-2021-0157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ubiquitylation is a posttranslational modification of proteins that is necessary for a variety of cellular processes. E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, and E3 ubiquitin ligase are all involved in transferring ubiquitin to the target substrate to regulate cellular function. The objective of this review is to provide an overview of different aspects of E3 ubiquitin ligases that can lead to major biological system failure in several deadly diseases. The first part of this review covers the important characteristics of E3 ubiquitin ligases and their classification based on structural domains. Further, the authors provide some online resources that help researchers explore the data relevant to the enzyme. The following section delves into the involvement of E3 ubiquitin ligases in various diseases and biological processes, including different types of cancer and neurological disorders.
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Yin C, Lui ESW, Jiang T, Qi RZ. Proteolysis of γ-tubulin small complex proteins is mediated by the ubiquitin-proteasome system. FEBS Lett 2021; 595:1987-1996. [PMID: 34107052 DOI: 10.1002/1873-3468.14146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/23/2021] [Accepted: 06/02/2021] [Indexed: 11/12/2022]
Abstract
Microtubule nucleation is mainly mediated by the γ-tubulin ring complex (γTuRC), whose core components are γ-tubulin and γ-tubulin complex proteins GCP2-6. A substantial fraction of γ-tubulin also exists with GCP2 and GCP3 in a tetramer called the γ-tubulin small complex (γTuSC). To date, the mechanisms underlying the turnover of γ-tubulin and GCPs have remained unclear. Here, we show that γ-tubulin, GCP2, and GCP3 are proteolyzed by the ubiquitin-proteasome system, and we identify cullin 1, cullin 4A, and cullin 4B as the E3 ligases that mediate the ubiquitination and, consequently, the degradation of γ-tubulin. Notably, we found that γTuSC disassembly promotes the degradation of γ-tubulin, GCP2, and GCP3, which indicates a role for γTuSCs in the stabilization of its components.
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Affiliation(s)
- Can Yin
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China
| | - Edna S W Lui
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China
| | - Taolue Jiang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China
| | - Robert Z Qi
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China
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Cheng J, Guo J, North BJ, Tao K, Zhou P, Wei W. The emerging role for Cullin 4 family of E3 ligases in tumorigenesis. Biochim Biophys Acta Rev Cancer 2018; 1871:138-159. [PMID: 30602127 DOI: 10.1016/j.bbcan.2018.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
As a member of the Cullin-RING ligase family, Cullin-RING ligase 4 (CRL4) has drawn much attention due to its broad regulatory roles under physiological and pathological conditions, especially in neoplastic events. Based on evidence from knockout and transgenic mouse models, human clinical data, and biochemical interactions, we summarize the distinct roles of the CRL4 E3 ligase complexes in tumorigenesis, which appears to be tissue- and context-dependent. Notably, targeting CRL4 has recently emerged as a noval anti-cancer strategy, including thalidomide and its derivatives that bind to the substrate recognition receptor cereblon (CRBN), and anticancer sulfonamides that target DCAF15 to suppress the neoplastic proliferation of multiple myeloma and colorectal cancers, respectively. To this end, PROTACs have been developed as a group of engineered bi-functional chemical glues that induce the ubiquitination-mediated degradation of substrates via recruiting E3 ligases, such as CRL4 (CRBN) and CRL2 (pVHL). We summarize the recent major advances in the CRL4 research field towards understanding its involvement in tumorigenesis and further discuss its clinical implications. The anti-tumor effects using the PROTAC approach to target the degradation of undruggable targets are also highlighted.
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Affiliation(s)
- Ji Cheng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Govindarajalu G, Selvam M, Palchamy E, Baluchamy S. N-terminal truncations of human bHLH transcription factor Twist1 leads to the formation of aggresomes. Mol Cell Biochem 2017; 439:75-85. [PMID: 28779345 DOI: 10.1007/s11010-017-3137-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/01/2017] [Indexed: 01/25/2023]
Abstract
In the cell, misfolded proteins are processed by molecular chaperone-mediated refolding or through ubiquitin-mediated proteosome system. Dysregulation of these mechanisms facilitates the aggregation of misfolded proteins and forms aggresomes in the juxta nuclear position of the cell which are removed by lysosome-mediated autophagy pathway in the subsequent cell division. Accumulation of misfolded proteins in the cell is hallmark of several neurological disorders and other diseases including cancer. However, the exact mechanism of aggresome formation and clearance is not thoroughly understood. Reports have shown that several proteins including p300, p53, TAU, α-synuclein, SOD, etc. contain intrinsically disordered region (IDR) which has the tendency to form aggresome. To study the nature of aggresome formation and stability of the aggresome, we have chosen Twist1 as a model protein since it has IDR regions. Twist1 is a bHLH transcription factor which plays a major role in epithelial mesenchymal transition (EMT) and shown to interact with HAT domain of p300 and p53. In the present study, we generated several deletion mutants of human Twist1 with different fluorescent tags and delineated the regions responsible for aggresome formation. The Twist1 protein contains two NLS motifs at the N-terminal region. We showed that the deletions of regions spanning the amino acids 30-46 (Twist1Δ30-46) which lacks the first NLS motif form larger and intense aggregates while the deletion of residues from 47 to 100 (Twist1Δ47-100) which lacks the second NLS motif generates smaller and less intense aggregates in the juxta nuclear position. This suggests that both the NLS motifs are needed for the proper nuclear localization of Twist1. The aggresome formation of the Twist1 deletion mutants was confirmed by counterstaining with known aggresome markers: Vimentin, HDAC6, and gamma tubulin and further validated by MG-132 treatment. In addition, it was found that the aggresomes generated by the Twist1Δ30-46 construct are more stable than the aggresome produced by the Twist1Δ47-100 construct as well as the wild-type Twist1 protein. Taken together, our data provide an important understanding on the role of IDR regions on the formation and stability of aggresomes.
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Affiliation(s)
- Gokulapriya Govindarajalu
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Elango Palchamy
- Translational Gerontology Branch, National Institute ON Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India.
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miR-181a-2 downregulates the E3 ubiquitin ligase CUL4A transcript and promotes cell proliferation. Med Oncol 2017; 34:146. [PMID: 28730334 DOI: 10.1007/s12032-017-1006-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/15/2017] [Indexed: 10/25/2022]
Abstract
MiR-181a-2 plays a major role in cell proliferation both positively and negatively depending on tissue type by targeting several regulators 3'UTR regions. We have predicted several targets for miR-181a-2 through computational approaches and characterized one its interesting target, CUL4A, an E3 ubiquitin ligase. CUL4A regulates diverse functions in the cells including DNA repair, DNA replication, cell cycle, genomic stability through polyubiquitination of target proteins. Deregulation of both miR-181a-2 and CUL4A are reported in many cancerous cells, but the functional link between them is unknown. We show that miR-181a-5p binds to 3'UTR of CUL4A and regulates its transcripts levels in HEK293 cells through overexpression studies. In addition, by using MTT and Neutral red assays, we showed that miR-181a-2 overexpression increased the proliferation in HEK293 cells. Moreover, cell cycle analysis using flow cytometer revealed that an increase in S-phase cells upon the overexpression of miR-181a-2. Though several miRNAs are known to downregulate the CUL4A levels, here we show that miR-181a-2 also participates in the downregulation of CUL4A. Taken together, our data demonstrated that miR-181a-2 increases the cell proliferation in HEK293 cells possibly through the downregulation of CUL4A.
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Blondelle J, Shapiro P, Domenighetti AA, Lange S. Cullin E3 Ligase Activity Is Required for Myoblast Differentiation. J Mol Biol 2017; 429:1045-1066. [PMID: 28238764 DOI: 10.1016/j.jmb.2017.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 01/06/2023]
Abstract
The role of cullin E3-ubiquitin ligases for muscle homeostasis is best known during muscle atrophy, as the cullin-1 substrate adaptor atrogin-1 is among the most well-characterized muscle atrogins. We investigated whether cullin activity was also crucial during terminal myoblast differentiation and aggregation of acetylcholine receptors for the establishment of neuromuscular junctions in vitro. The activity of cullin E3-ligases is modulated through post-translational modification with the small ubiquitin-like modifier nedd8. Using either the Nae1 inhibitor MLN4924 (Pevonedistat) or siRNA against nedd8 in early or late stages of differentiation on C2C12 myoblasts, and primary satellite cells from mouse and human, we show that cullin E3-ligase activity is necessary for each step of the muscle cell differentiation program in vitro. We further investigate known transcriptional repressors for terminal muscle differentiation, namely ZBTB38, Bhlhe41, and Id1. Due to their identified roles for terminal muscle differentiation, we hypothesize that the accumulation of these potential cullin E3-ligase substrates may be partially responsible for the observed phenotype. MLN4924 is currently undergoing clinical trials in cancer patients, and our experiments highlight concerns on the homeostasis and regenerative capacity of muscles in these patients who often experience cachexia.
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Affiliation(s)
- Jordan Blondelle
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA
| | - Paige Shapiro
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA
| | - Andrea A Domenighetti
- Rehabilitation Institute of Chicago, Chicago, IL-60611 USA; Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL-60611, USA
| | - Stephan Lange
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA.
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Arkwright R, Pham TM, Zonder JA, Dou QP. The preclinical discovery and development of bortezomib for the treatment of mantle cell lymphoma. Expert Opin Drug Discov 2016; 12:225-235. [PMID: 27917682 DOI: 10.1080/17460441.2017.1268596] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Mantle cell lymphoma (MCL) is an incurable, often aggressive B-cell malignancy. Bortezomib (BTZ), the 20S proteasome inhibitor was originally developed and approved for treatment of relapsed refractory multiple myeloma, and subsequently approved for treatment of MCL. BTZ's single-agent activity induces clinical responses in approximately one-third of relapsed MCL patients. BTZ-containing combination therapies have further improved the quality and duration of clinical responses compared to standard chemotherapies in previously untreated MCL patients. Areas covered: This review summarizes the discovery, mechanisms of -action and resistance, preclinical- clinical-developments, and FDA approval of BTZ for treatments of MCL. Expert opinion: Preclinical MCL models demonstrated the apoptotic effect of BTZ through multiple mechanisms, as well as synergistic anti-MCL activity between BTZ and other chemotherapeutics. Single-agent and combinational clinical trials have validated the therapeutic potential of targeting the ubiquitin proteasome system (UPS) in MCL. However, inherent and acquired drug resistance remains a significant clinical problem and multiple potential mechanisms have been identified. Next-generation proteasome inhibitors with different pharmacodynamic properties from BTZ may partially address the issue of inherent resistance, with increased response rates noted in some diseases. In addition, upstream UPS components, e.g., E3 ligases or deubiquitinating enzymes, may also be targetable in MCL.
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Affiliation(s)
- Richard Arkwright
- a Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan , USA.,b Barbara Ann Karmanos Cancer Institute , Detroit , Michigan , USA
| | - Tri Minh Pham
- c Department of Pathology , Wayne State University School of Medicine , Detroit , Michigan , USA
| | - Jeffrey A Zonder
- a Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan , USA.,b Barbara Ann Karmanos Cancer Institute , Detroit , Michigan , USA
| | - Q Ping Dou
- a Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan , USA.,b Barbara Ann Karmanos Cancer Institute , Detroit , Michigan , USA.,c Department of Pathology , Wayne State University School of Medicine , Detroit , Michigan , USA
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