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Current Status of Oligonucleotide-Based Protein Degraders. Pharmaceutics 2023; 15:pharmaceutics15030765. [PMID: 36986626 PMCID: PMC10055846 DOI: 10.3390/pharmaceutics15030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Transcription factors (TFs) and RNA-binding proteins (RBPs) have long been considered undruggable, mainly because they lack ligand-binding sites and are equipped with flat and narrow protein surfaces. Protein-specific oligonucleotides have been harnessed to target these proteins with some satisfactory preclinical results. The emerging proteolysis-targeting chimera (PROTAC) technology is no exception, utilizing protein-specific oligonucleotides as warheads to target TFs and RBPs. In addition, proteolysis by proteases is another type of protein degradation. In this review article, we discuss the current status of oligonucleotide-based protein degraders that are dependent either on the ubiquitin–proteasome system or a protease, providing a reference for the future development of degraders.
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Sosič I, Bricelj A, Steinebach C. E3 ligase ligand chemistries: from building blocks to protein degraders. Chem Soc Rev 2022; 51:3487-3534. [PMID: 35393989 DOI: 10.1039/d2cs00148a] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, proteolysis-targeting chimeras (PROTACs), capable of achieving targeted protein degradation, have proven their great therapeutic potential and usefulness as molecular biology tools. These heterobifunctional compounds are comprised of a protein-targeting ligand, an appropriate linker, and a ligand binding to the E3 ligase of choice. A successful PROTAC induces the formation of a ternary complex, leading to the E3 ligase-mediated ubiquitination of the targeted protein and its proteasomal degradation. In over 20 years since the concept was first demonstrated, the field has grown substantially, mainly due to the advancements in the discovery of non-peptidic E3 ligase ligands. Development of small-molecule E3 binders with favourable physicochemical profiles aided the design of PROTACs, which are known for breaking the rules of established guidelines for discovering small molecules. Synthetic accessibility of the ligands and numerous successful applications led to the prevalent use of cereblon and von Hippel-Lindau as the hijacked E3 ligase. However, the pool of over 600 human E3 ligases is full of untapped potential, which is why expanding the artillery of E3 ligands could contribute to broadening the scope of targeted protein degradation. In this comprehensive review, we focus on the chemistry aspect of the PROTAC design process by providing an overview of liganded E3 ligases, their chemistries, appropriate derivatisation, and synthetic approaches towards their incorporation into heterobifunctional degraders. By covering syntheses of both established and underexploited E3 ligases, this review can serve as a chemistry blueprint for PROTAC researchers during their future ventures into the complex field of targeted protein degradation.
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Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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3
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Molecular glues modulate protein functions by inducing protein aggregation: A promising therapeutic strategy of small molecules for disease treatment. Acta Pharm Sin B 2022; 12:3548-3566. [PMID: 36176907 PMCID: PMC9513498 DOI: 10.1016/j.apsb.2022.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022] Open
Abstract
Molecular glues can specifically induce aggregation between two or more proteins to modulate biological functions. In recent years, molecular glues have been widely used as protein degraders. In addition, however, molecular glues play a variety of vital roles, such as complex stabilization, interactome modulation and transporter inhibition, enabling challenging therapeutic targets to be druggable and offering an exciting novel approach for drug discovery. Since most molecular glues are identified serendipitously, exploration of their systematic discovery and rational design are important. In this review, representative examples of molecular glues with various physiological functions are divided into those mediating homo-dimerization, homo-polymerization and hetero-dimerization according to their aggregation modes, and we attempt to elucidate their mechanisms of action. In particular, we aim to highlight some biochemical techniques typically exploited within these representative studies and classify them in terms of three stages of molecular glue development: starting point, optimization and identification.
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4
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Gockel LM, Pfeifer V, Baltes F, Bachmaier RD, Wagner KG, Bendas G, Gütschow M, Sosič I, Steinebach C. Design, synthesis, and characterization of PROTACs targeting the androgen receptor in prostate and lung cancer models. Arch Pharm (Weinheim) 2022; 355:e2100467. [PMID: 35128717 DOI: 10.1002/ardp.202100467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
Although the androgen receptor (AR) is a validated target for the treatment of prostate cancer, resistance to antiandrogens necessitates the development of new therapeutic modalities. Exploiting the ubiquitin-proteasome system with proteolysis-targeting chimeras (PROTACs) has become a practical approach to degrade specific proteins and thus to extend the portfolio of small molecules used for the treatment of a broader spectrum of diseases. Herein, we present three subgroups of enzalutamide-based PROTACs in which only the exit vector was modified. By recruiting cereblon, we were able to demonstrate the potent degradation of AR in lung cancer cells. Furthermore, the initial evaluation enabled the design of an optimized PROTAC with a rigid linker that degraded AR with a DC50 value in the nanomolar range. These results provide novel AR-directed PROTACs and a clear rationale for further investigating AR involvement in lung cancer models.
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Affiliation(s)
- Lukas M Gockel
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Vladlena Pfeifer
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Fabian Baltes
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Rafael D Bachmaier
- Department of Pharmaceutical Technology, Pharmaceutical Institute, Bonn, Germany
| | - Karl G Wagner
- Department of Pharmaceutical Technology, Pharmaceutical Institute, Bonn, Germany
| | - Gerd Bendas
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Michael Gütschow
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Izidor Sosič
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Christian Steinebach
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, Bonn, Germany
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5
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Naganuma M, Ohoka N, Tsuji G, Tsujimura H, Matsuno K, Inoue T, Naito M, Demizu Y. Development of Chimeric Molecules That Degrade the Estrogen Receptor Using Decoy Oligonucleotide Ligands. ACS Med Chem Lett 2021; 13:134-139. [PMID: 35059133 PMCID: PMC8762735 DOI: 10.1021/acsmedchemlett.1c00629] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/14/2021] [Indexed: 01/16/2023] Open
Abstract
Targeted protein degradation using chimeric small molecules, such as proteolysis-targeting chimeras (PROTACs) and specific and nongenetic inhibitors of apoptosis protein (IAP)-dependent protein erasers (SNIPERs), has attracted attention as a method for degrading intracellular target proteins via the ubiquitin-proteasome system (UPS). These chimeric molecules target a variety of proteins using small molecules that can bind to the proteins. However, it is difficult to develop such degraders in the absence of suitable small-molecule ligands for the target proteins, such as for transcription factors (TFs). Therefore, we constructed the chimeric molecule LCL-ER(dec), which consists of a decoy oligonucleotide that can bind to estrogen receptor α (ERα) and an IAP ligand, LCL161 (LCL), in a click reaction. LCL-ER(dec) was found to selectively degrade ERα via the UPS. These findings will be applicable to the development of other oligonucleotide-type degraders that target different TFs.
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Affiliation(s)
- Miyako Naganuma
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan,Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan,Department
of Chemistry and Life Science, Kogakuin
University, Tokyo 192-0015, Japan
| | - Nobumichi Ohoka
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa 158-8501, Japan,Tel: +81-44-270-6537.
| | - Genichiro Tsuji
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan
| | - Haruna Tsujimura
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan,Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan
| | - Kenji Matsuno
- Department
of Chemistry and Life Science, Kogakuin
University, Tokyo 192-0015, Japan
| | - Takao Inoue
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa 158-8501, Japan
| | - Mikihiko Naito
- Laboratory
of Targeted Protein Degradation, Graduate School of Pharmaceutical
Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan,Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan,Tel: +81-44-270-6578. Fax: +81-44-270-6578.
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6
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Yokoo H, Ohoka N, Takyo M, Ito T, Tsuchiya K, Kurohara T, Fukuhara K, Inoue T, Naito M, Demizu Y. Peptide Stapling Improves the Sustainability of a Peptide-Based Chimeric Molecule That Induces Targeted Protein Degradation. Int J Mol Sci 2021; 22:ijms22168772. [PMID: 34445478 PMCID: PMC8396023 DOI: 10.3390/ijms22168772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/31/2022] Open
Abstract
Peptide-based target protein degradation inducers called PROTACs/SNIPERs have low cell penetrability and poor intracellular stability as drawbacks. These shortcomings can be overcome by easily modifying these peptides by conjugation with cell penetrating peptides and side-chain stapling. In this study, we succeeded in developing the stapled peptide stPERML-R7, which is based on the estrogen receptor alpha (ERα)-binding peptide PERML and composed of natural amino acids. stPERML-R7, which includes a hepta-arginine motif and a hydrocarbon stapling moiety, showed increased α-helicity and similar binding affinity toward ERα when compared with those of the parent peptide PERML. Furthermore, we used stPERML-R7 to develop a peptide-based degrader LCL-stPERML-R7 targeting ERα by conjugating stPERML-R7 with a small molecule LCL161 (LCL) that recruits the E3 ligase IAPs to induce proteasomal degradation via ubiquitylation. The chimeric peptide LCL-stPERML-R7 induced sustained degradation of ERα and potently inhibited ERα-mediated transcription more effectively than the unstapled chimera LCL-PERML-R7. These results suggest that a stapled structure is effective in maintaining the intracellular activity of peptide-based degraders.
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Affiliation(s)
- Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 606-0823, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (N.O.); (T.I.)
| | - Mami Takyo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Takahito Ito
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
| | - Keisuke Tsuchiya
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Graduate School of Pharmacy, Showa University, Tokyo 142-0064, Japan;
| | - Takashi Kurohara
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
| | - Kiyoshi Fukuhara
- Graduate School of Pharmacy, Showa University, Tokyo 142-0064, Japan;
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (N.O.); (T.I.)
| | - Mikihiko Naito
- Laboratory of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Kanagawa 210-9501, Japan; (H.Y.); (M.T.); (T.I.); (K.T.); (T.K.)
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-44-270-6578
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