1
|
Yan S, Zhang G, Luo W, Xu M, Peng R, Du Z, Liu Y, Bai Z, Xiao X, Qin S. PROTAC technology: From drug development to probe technology for target deconvolution. Eur J Med Chem 2024; 276:116725. [PMID: 39083982 DOI: 10.1016/j.ejmech.2024.116725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/19/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Drug development remains a critical focus within the global pharmaceutical industry. To date, more than 80 % of disease targets are considered difficult to target. The emergence of PROTAC technology has, to some extent, alleviated this challenge. Since introduction, PROTAC technology has evolved through the peptide E3 ligase ligand phase and the small molecule E3 ligase ligand phase. Currently, multiple PROTAC molecules are in the clinical research phase, showing promising potential for addressing drug resistance, disease recurrence, and intractable targets. Target deconvolution is a crucial step in the drug discovery and development process. Due to the exceptional targeting ability and specificity of PROTAC, it is widely used and promoted as an innovative technology for discovering new drug targets, leading to significant breakthroughs. The use of PROTAC probe requires only a catalytic dose and weak interaction with the target protein to achieve target degradation. Thus, it offers substantial advantages over traditional probes, particularly in identifying new targets that are low-abundance or difficult to target. This review provides a comprehensive overview of the advancements made by PROTAC technology in drug development and drug target discovery, while also systematically reviewing the workflow of PROTAC probe. With the ongoing development of PROTAC technology, PROTAC probe is poised to become a key research area in future drug target deconvolution.
Collapse
Affiliation(s)
- Si Yan
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China
| | - Guangshuai Zhang
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China
| | - Wei Luo
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Mengwei Xu
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Rui Peng
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Ziwei Du
- Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Yan Liu
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China
| | - Zhaofang Bai
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China.
| | - Xiaohe Xiao
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China.
| | - Shuanglin Qin
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Research Center for Precision Medication of Chinese Medicine, FuRong Laboratory, Hunan University of Chinese Medicine, Changsha, PR China; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, PR China; Department of Hepatology, China Military Institute of Chinese Materia, The Fifth Medical Center of PLA General Hospital, Beijing, PR China.
| |
Collapse
|
2
|
Wang Z, Che S, Yu Z. PROTAC: Novel degradable approach for different targets to treat breast cancer. Eur J Pharm Sci 2024; 198:106793. [PMID: 38740076 DOI: 10.1016/j.ejps.2024.106793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
The revolutionary Proteolysis Targeting Chimera (PROTACs) have the exciting potential to reshape the pharmaceutical industry landscape by leveraging the ubiquitin-proteasome system for targeted protein degradation. Breast cancer, the most prevalent cancer in women, could be treated using PROTAC therapy. Although substantial work has been conducted, there is not yet a comprehensive overview or progress update on PROTAC therapy for breast cancer. Hence, in this article, we've compiled recent research progress focusing on different breast cancer target proteins, such as estrogen receptor (ER), BET, CDK, HER2, PARP, EZH2, etc. This resource aims to serve as a guide for future PROTAC-based breast cancer treatment design.
Collapse
Affiliation(s)
- Zhenjie Wang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China; Office of Drug Clinical Trials, The People's Hospital of Gaozhou, Maoming, 525200, PR China
| | - Siyao Che
- Hepatological Surgery Department, The People's Hospital of Gaozhou, Maoming, 525200, PR China.
| | - Zhiqiang Yu
- Department of Laboratory Medicine, Dongguan Institute of Clinical Cancer Research, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523018, PR China.
| |
Collapse
|
3
|
Giardina SF, Valdambrini E, Singh PK, Bacolod MD, Babu-Karunakaran G, Peel M, Warren JD, Barany F. Combinatorial Ubiquitination REal-time PROteolysis (CURE-PROs): A Modular Platform for Generating Reversible, Self-Assembling Bifunctional Targeted Degraders. J Med Chem 2024; 67:5473-5501. [PMID: 38554135 DOI: 10.1021/acs.jmedchem.3c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
Proteolysis-Targeting Chimeras (PROTACs) are bifunctional molecules that bring a target protein and an E3 ubiquitin ligase into proximity to append ubiquitin, thus directing target degradation. Although numerous PROTACs have entered clinical trials, their development remains challenging, and their large size can produce poor drug-like properties. To overcome these limitations, we have modified our Coferon platform to generate Combinatorial Ubiquitination REal-time PROteolysis (CURE-PROs). CURE-PROs are small molecule degraders designed to self-assemble through reversible bio-orthogonal linkers to form covalent heterodimers. By modifying known ligands for Cereblon, MDM2, VHL, and BRD with complementary phenylboronic acid and diol/catechol linkers, we have successfully created CURE-PROs that direct degradation of BRD4 both in vitro and in vivo. The combinatorial nature of our platform significantly reduces synthesis time and effort to identify the optimal linker length and E3 ligase partner to each target and is readily amenable to screening for new targets.
Collapse
Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Elena Valdambrini
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Pradeep K Singh
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| | - Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | | | - Michael Peel
- MRP Pharma LLC, Chapel Hill, North Carolina 27514, United States
| | - J David Warren
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| |
Collapse
|
4
|
Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
Collapse
Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| |
Collapse
|
5
|
Ge Y, Zhan Z, Ye M, Jin X. The crosstalk between ubiquitination and endocrine therapy. J Mol Med (Berl) 2023; 101:461-486. [PMID: 36961537 DOI: 10.1007/s00109-023-02300-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/25/2023]
Abstract
Endocrine therapy (ET), also known as hormone therapy, refers to the treatment of tumors by regulating and changing the endocrine environment and hormone levels. Its related mechanism is mainly through reducing hormone levels and blocking the binding of hormones to corresponding receptors, thus blocking the signal transduction pathway to stimulate tumor growth. However, with the application of ET, some patients show resistance to ET, which is attributed to abnormal accumulation of hormone receptors (HRs) and the production of multiple mutants of HRs. The targeted degradation of abnormal accumulation protein mediated by ubiquitination is an important approach that regulates the protein level and function of intracellular proteins in eukaryotes. Here, we provide a brief description of the traditional and novel drugs available for ET in this review. Then, we introduce the link between ubiquitination and ET. In the end, we elaborate the clinical application of ET combined with ubiquitination-related molecules. KEY MESSAGES: • A brief description of the traditional and novel drugs available for endocrine therapy (ET). • The link between ubiquitination and ET. • The clinical application of ET combined with ubiquitination-related molecules.
Collapse
Affiliation(s)
- Yidong Ge
- The Department of Medical Oncology, The First Hospital of Ningbo University, Ningbo University, Ningbo, 315010, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Medical School of Ningbo University, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ziqing Zhan
- The Department of Medical Oncology, The First Hospital of Ningbo University, Ningbo University, Ningbo, 315010, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Medical School of Ningbo University, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Meng Ye
- The Department of Medical Oncology, The First Hospital of Ningbo University, Ningbo University, Ningbo, 315010, China.
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Medical School of Ningbo University, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Xiaofeng Jin
- The Department of Medical Oncology, The First Hospital of Ningbo University, Ningbo University, Ningbo, 315010, China.
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Medical School of Ningbo University, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
6
|
Abou-Salim MA, Shaaban MA, Abd El Hameid MK, Alanazi MM, Halaweish F, Elshaier YAMM. Utilizing Estra-1,3,5,16-Tetraene Scaffold: Design and Synthesis of Nitric Oxide Donors as Chemotherapeutic Resistance Combating Agents in Liver Cancer. Molecules 2023; 28:molecules28062754. [PMID: 36985726 PMCID: PMC10055446 DOI: 10.3390/molecules28062754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
A new series of nitric oxide-releasing estra-1,3,5,16-tetraene analogs (NO-∆-16-CIEAs) was designed and synthesized as dual inhibitors for EGFR and MRP2 based on our previous findings on estra-1,3,5-triene analog NO-CIEA 17 against both HepG2 and HepG2-R cell lines. Among the target compounds, 14a (R-isomer) and 14b (S-isomer) displayed potent anti-proliferative activity against both HepG2 and HepG2-R cell lines in comparison to the reference drug erlotinib. Remarkably, compound 14a resulted in a prominent reduction in EGFR phosphorylation at a concentration of 1.20 µM with slight activity on the phosphorylation of MEK1/2 and ERK1/2. It also inhibits MRP2 expression in a dose-dependent manner with 24% inhibition and arrested the cells in the S phase of the cell cycle. Interestingly, compound 14a (estratetraene core) exhibited a twofold increase in anti-proliferative activity against both HepG2 and HepG2-R in comparison with the lead estratriene analog, demonstrating the significance of the designed ∆-16 unsaturation. The results shed a light on compound 14a and support further investigations to combat multidrug resistance in chemotherapy of hepatocellular carcinoma patients.
Collapse
Affiliation(s)
- Mahrous A Abou-Salim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Mohamed A Shaaban
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Mohammed K Abd El Hameid
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fathi Halaweish
- Department of Chemistry and Biochemistry, South Dakota State University, Box 2202, Brookings, SD 57007, USA
| | - Yaseen A M M Elshaier
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32958, Egypt
| |
Collapse
|
7
|
Zhao HY, Xin M, Zhang SQ. Progress of small molecules for targeted protein degradation: PROTACs and other technologies. Drug Dev Res 2023; 84:337-394. [PMID: 36606428 DOI: 10.1002/ddr.22026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.
Collapse
Affiliation(s)
- Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| |
Collapse
|
8
|
Li Y, Jia Y, Wang X, Shang H, Tian Y. Protein-Targeted Degradation Agents Based on Natural Products. Pharmaceuticals (Basel) 2022; 16:ph16010046. [PMID: 36678543 PMCID: PMC9865760 DOI: 10.3390/ph16010046] [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: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022] Open
Abstract
Natural products are an important source of drug lead compounds, and natural products with significant biological activity are constantly being discovered and used in clinical practice. At present, natural products play an important role in the targeted therapy of cancer, cardiovascular and cerebrovascular diseases, nervous system diseases, and autoimmune diseases. Meanwhile, in recent years, the rise of protein-targeted degradation technologies, such as proteolysis-targeting chimeras (PROTACs) and molecular glues, has provided a new solution for drug resistance caused by clinical molecular-targeting drugs. It is noteworthy that natural products and their derivatives, as important components of PROTACs and molecular glues, play an important role in the development of protein-targeting drugs. Hence, this review summarized the protein-targeted degradation agents based on natural products, such as PROTACs and molecular glues. More natural products with the potential to be used in the development of PROTACs and molecular glues as targeted protein degradation agents are still being investigated.
Collapse
Affiliation(s)
| | | | | | | | - Yu Tian
- Correspondence: (H.S.); (Y.T.)
| |
Collapse
|
9
|
Liu Z, Hu M, Yang Y, Du C, Zhou H, Liu C, Chen Y, Fan L, Ma H, Gong Y, Xie Y. An overview of PROTACs: a promising drug discovery paradigm. MOLECULAR BIOMEDICINE 2022; 3:46. [PMID: 36536188 PMCID: PMC9763089 DOI: 10.1186/s43556-022-00112-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Proteolysis targeting chimeras (PROTACs) technology has emerged as a novel therapeutic paradigm in recent years. PROTACs are heterobifunctional molecules that degrade target proteins by hijacking the ubiquitin-proteasome system. Currently, about 20-25% of all protein targets are being studied, and most works focus on their enzymatic functions. Unlike small molecules, PROTACs inhibit the whole biological function of the target protein by binding to the target protein and inducing subsequent proteasomal degradation. PROTACs compensate for limitations that transcription factors, nuclear proteins, and other scaffolding proteins are difficult to handle with traditional small-molecule inhibitors. Currently, PROTACs have successfully degraded diverse proteins, such as BTK, BRD4, AR, ER, STAT3, IRAK4, tau, etc. And ARV-110 and ARV-471 exhibited excellent efficacy in clinical II trials. However, what targets are appropriate for PROTAC technology to achieve better benefits than small-molecule inhibitors are not fully understood. And how to rationally design an efficient PROTACs and optimize it to be orally effective poses big challenges for researchers. In this review, we summarize the features of PROTAC technology, analyze the detail of general principles for designing efficient PROTACs, and discuss the typical application of PROTACs targeting different protein categories. In addition, we also introduce the progress of relevant clinical trial results of representative PROTACs and assess the challenges and limitations that PROTACs may face. Collectively, our studies provide references for further application of PROTACs.
Collapse
Affiliation(s)
- Zi Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Mingxing Hu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yu Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Chenghao Du
- grid.42505.360000 0001 2156 6853Department of Biological Sciences, USC Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, 90089 USA
| | - Haoxuan Zhou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Chengyali Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yuanwei Chen
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Lei Fan
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Hongqun Ma
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Youling Gong
- grid.13291.380000 0001 0807 1581Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yongmei Xie
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| |
Collapse
|
10
|
Negi A, Kesari KK, Voisin-Chiret AS. Estrogen Receptor-α Targeting: PROTACs, SNIPERs, Peptide-PROTACs, Antibody Conjugated PROTACs and SNIPERs. Pharmaceutics 2022; 14:pharmaceutics14112523. [PMID: 36432713 PMCID: PMC9699327 DOI: 10.3390/pharmaceutics14112523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Targeting selective estrogen subtype receptors through typical medicinal chemistry approaches is based on occupancy-driven pharmacology. In occupancy-driven pharmacology, molecules are developed in order to inhibit the protein of interest (POI), and their popularity is based on their virtue of faster kinetics. However, such approaches have intrinsic flaws, such as pico-to-nanomolar range binding affinity and continuous dosage after a time interval for sustained inhibition of POI. These shortcomings were addressed by event-driven pharmacology-based approaches, which degrade the POI rather than inhibit it. One such example is PROTACs (Proteolysis targeting chimeras), which has become one of the highly successful strategies of event-driven pharmacology (pharmacology that does the degradation of POI and diminishes its functions). The selective targeting of estrogen receptor subtypes is always challenging for chemical biologists and medicinal chemists. Specifically, estrogen receptor α (ER-α) is expressed in nearly 70% of breast cancer and commonly overexpressed in ovarian, prostate, colon, and endometrial cancer. Therefore, conventional hormonal therapies are most prescribed to patients with ER + cancers. However, on prolonged use, resistance commonly developed against these therapies, which led to selective estrogen receptor degrader (SERD) becoming the first-line drug for metastatic ER + breast cancer. The SERD success shows that removing cellular ER-α is a promising approach to overcoming endocrine resistance. Depending on the mechanism of degradation of ER-α, various types of strategies of developed.
Collapse
Affiliation(s)
- Arvind Negi
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Kavindra Kumar Kesari
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Department of Applied Physics, School of Science, Aalto University, 02150 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Anne Sophie Voisin-Chiret
- CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie), Normandie University UNICAEN, 14000 Caen, France
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| |
Collapse
|
11
|
Li J, Cai Z, Li XW, Zhuang C. Natural Product-Inspired Targeted Protein Degraders: Advances and Perspectives. J Med Chem 2022; 65:13533-13560. [PMID: 36205223 DOI: 10.1021/acs.jmedchem.2c01223] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeted protein degradation (TPD), a promising therapeutic strategy in drug discovery, has great potential to regulate the endogenous degradation of undruggable targets with small molecules. As vital resources that provide diverse structural templates for drug discovery, natural products (NPs) are a rising and robust arsenal for the development of therapeutic TPD. The first proof-of-concept study of proteolysis-targeting chimeras (PROTACs) was a natural polyketide ovalicin-derived degrader; since then, NPs have shown great potential to promote TPD technology. The use of NP-inspired targeted protein degraders has been confirmed to be a promising strategy to treat many human conditions, including cancer, inflammation, and nonalcoholic fatty liver disease. Nevertheless, the development of NP-inspired degraders is challenging, and the field is currently in its infancy. In this review, we summarize the bioactivities and mechanisms of NP-inspired degraders and discuss the associated challenges and future opportunities in this field.
Collapse
Affiliation(s)
- Jiao Li
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhenyu Cai
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.,Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Chunlin Zhuang
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| |
Collapse
|
12
|
Design and optimization of oestrogen receptor PROTACs based on 4-hydroxytamoxifen. Eur J Med Chem 2022; 243:114770. [PMID: 36148710 DOI: 10.1016/j.ejmech.2022.114770] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 11/20/2022]
Abstract
In the last four decades, treatment of oestrogen receptor positive (ER+) breast cancer (BCa), has focused on targeting the estrogenic receptor signaling pathway. This signaling function is pivotal to sustain cell proliferation. Tamoxifen, a competitive inhibitor of oestrogen, has played a major role in therapeutics. However, primary and acquired resistance to hormone blockade occurs in a large subset of these cancers, and new approaches are urgently needed. Aromatase inhibitors and receptor degraders were approved and alternatively used. Yet, resistance appears in the metastatic setting. Here we report the design and synthesis of a series of proteolysis targeting chimeras (PROTACs) that induce the degradation of estrogen receptor alpha in breast cancer MCF-7 (ER+) cells at nanomolar concentration. Using a warhead based on 4-hydroxytamoxifen, bifunctional degraders recruiting either cereblon or the Von Hippel Lindau E3 ligases were synthesized. Our efforts resulted in the discovery of TVHL-1, a potent ERα degrader (DC50: 4.5 nM) that we envisage as a useful tool for biological study and a platform for potential therapeutics.
Collapse
|
13
|
Design, Synthesis and Biological Characterization of Histone Deacetylase 8 (HDAC8) Proteolysis Targeting Chimeras (PROTACs) with Anti-Neuroblastoma Activity. Int J Mol Sci 2022; 23:ijms23147535. [PMID: 35886887 PMCID: PMC9322761 DOI: 10.3390/ijms23147535] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/07/2023] Open
Abstract
In addition to involvement in epigenetic gene regulation, histone deacetylases (HDACs) regulate multiple cellular processes through mediating the activity of non-histone protein substrates. The knockdown of HDAC8 isozyme is associated with the inhibition of cell proliferation and apoptosis enhancement in several cancer cell lines. As shown in several studies, HDAC8 can be considered a potential target in the treatment of cancer forms such as childhood neuroblastoma. The present work describes the development of proteolysis targeting chimeras (PROTACs) of HDAC8 based on substituted benzhydroxamic acids previously reported as potent and selective HDAC8 inhibitors. Within this study, we investigated the HDAC8-degrading profiles of the synthesized PROTACs and their effect on the proliferation of neuroblastoma cells. The combination of in vitro screening and cellular testing demonstrated selective HDAC8 PROTACs that show anti-neuroblastoma activity in cells.
Collapse
|
14
|
Memon H, Patel BM. PROTACs: Novel approach for cancer breakdown by breaking proteins. Life Sci 2022; 300:120577. [PMID: 35487303 DOI: 10.1016/j.lfs.2022.120577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/21/2021] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
Ubiquitination defects have been reported in various diseases, including neurodegenerative diseases, metabolic disorders and cancer. Balance between degradation and synthesis of the proteins to treat cancer can be managed by designing a chimeric molecule, known as Proteolysis Targeting Chimeric molecule (Lee, Kim et al. 2021). Proteolysis-targeting chimeras (PROTACs) acts as a tool for conducting therapeutic intervention. It eradicates or reduces the proteins that are responsible for causing diseases. Each PROTAC contains a target warhead, an E3 ligand and a linker. E3 ligases are recruited by these bifunctional molecules, and the Ubiquitin (Ub) Proteasome System (UPS) is used to target the degradation of specific proteins. As compared to inhibition, this degradation offers several advantages in the drug resistance, selectivity, and potency. Thus, numerous small molecule PROTACs are identified so far. In this review, the development of PROTACs, historical milestones, the biological mechanism, advantages and recent progress, and role of PROTAC in prostate cancer, breast cancer, non-hodgkin lymphoma, multiple myeloma, and malignant peripheral nerve sheath tumors are summarized.
Collapse
Affiliation(s)
- Humera Memon
- Institute of Pharmacy, Nirma University, Ahmedabad, India
| | | |
Collapse
|
15
|
Targeted Degradation of 53BP1 Using Ubiquitin Variant Induced Proximity. Biomolecules 2022; 12:biom12040479. [PMID: 35454069 PMCID: PMC9029692 DOI: 10.3390/biom12040479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023] Open
Abstract
In recent years, researchers have leveraged the ubiquitin-proteasome system (UPS) to induce selective degradation of proteins by E3 ubiquitin ligases, which has great potential as novel therapeutics for human diseases, including cancer and neurodegenerative disorders. However, despite extensive efforts, only a handful of ~600 human E3 ligases were utilized, and numerous protein–protein interaction surfaces on E3 ligases were not explored. To tackle these problems, we leveraged a structure-based protein engineering technology to develop a multi-domain fusion protein bringing functional E3 ligases to the proximity of a target protein to trigger its proteasomal degradation, which we termed Ubiquitin Variant Induced Proximity (UbVIP). We first generated non-inhibitory synthetic UbV binders for a selected group of human E3 ligases. With these UbVs employed as E3 ligase engagers, we designed a library of UbVIPs targeting a DNA damage response protein 53BP1. We observed that two UbVIPs recruiting RFWD3 and NEDD4L could effectively induce proteasome degradation of 53BP1 in human cell lines. This provides a proof-of-principle that UbVs can act as a means of targeted degradation for nucleus-localized proteins. Our work demonstrated that UbV technology is suitable to develop protein-based molecules for targeted degradation and can help identify novel E3 ligases for future therapeutic development.
Collapse
|
16
|
Yang G, Zhong H, Xia X, Qi Z, Wang C, Li S. Potential application of proteolysis targeting chimera (PROTAC) modification technology in natural products for their targeted protein degradation. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Liu L, Shi L, Wang Z, Zeng J, Wang Y, Xiao H, Zhu Y. Targeting Oncoproteins for Degradation by Small Molecule-Based Proteolysis-Targeting Chimeras (PROTACs) in Sex Hormone-Dependent Cancers. Front Endocrinol (Lausanne) 2022; 13:839857. [PMID: 35370971 PMCID: PMC8971670 DOI: 10.3389/fendo.2022.839857] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
Sex hormone-dependent cancers, including breast, ovary, and prostate cancer, contribute to the high number of cancer-related deaths worldwide. Steroid hormones promote tumor occurrence, development, and metastasis by acting on receptors, such as estrogen receptors (ERs), androgen receptors (ARs), and estrogen-related receptors (ERRs). Therefore, endocrine therapy targeting ERs, ARs, and ERRs represents the potential and pivotal therapeutic strategy in sex hormone-dependent cancers. Proteolysis-targeting chimeras (PROTACs) are a novel strategy that can harness the potential of the endogenous ubiquitin-proteasome system (UPS) to target and degrade specific proteins, rather than simply inhibiting the activity of target proteins. Small molecule PROTACs degrade a variety of proteins in cells, mice, and humans and are an emerging approach for novel drug development. PROTACs targeting ARs, ERs, ERRs, and other proteins in sex hormone-dependent cancers have been reported and may overcome the problem of resistance to existing endocrine therapy and receptor antagonist treatments. This review briefly introduces the PROTAC strategy and summarizes the progress on the development of small molecule PROTACs targeting oncoproteins in sex hormone-dependent cancers, focusing on breast and prostate cancers.
Collapse
Affiliation(s)
- Li Liu
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lihong Shi
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhaodi Wang
- Department of Gynecology, People’s Hospital of Henan University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Jun Zeng
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yue Wang
- Department of Gynecology, People’s Hospital of Henan University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Hongtao Xiao
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yongxia Zhu
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Yongxia Zhu,
| |
Collapse
|
18
|
Hati S, Zallocchi M, Hazlitt R, Li Y, Vijayakumar S, Min J, Rankovic Z, Lovas S, Zuo J. AZD5438-PROTAC: A selective CDK2 degrader that protects against cisplatin- and noise-induced hearing loss. Eur J Med Chem 2021; 226:113849. [PMID: 34560429 PMCID: PMC8608744 DOI: 10.1016/j.ejmech.2021.113849] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) is a potential therapeutic target for the treatment of hearing loss and cancer. Previously, we identified AZD5438 and AT7519-7 as potent inhibitors of CDK2, however, they also targeted additional kinases, leading to unwanted toxicities. Proteolysis Targeting Chimeras (PROTACs) are a new promising class of small molecules that can effectively direct specific proteins to proteasomal degradation. Herein we report the design, synthesis, and characterization of PROTACs of AT7519-7 and AZD5438 and the identification of PROTAC-8, an AZD5438-PROTAC, that exhibits selective, partial CDK2 degradation. Furthermore, PROTAC-8 protects against cisplatin ototoxicity and kainic acid excitotoxicity in zebrafish. Molecular dynamics simulations reveal the structural requirements for CDK2 degradation. Together, PROTAC-8 is among the first-in-class PROTACs with in vivo therapeutic activities and represents a new lead compound that can be further developed for better efficacy and selectivity for CDK2 degradation against hearing loss and cancer.
Collapse
Affiliation(s)
- Santanu Hati
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Robert Hazlitt
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuju Li
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Sarath Vijayakumar
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Jaeki Min
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sándor Lovas
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Jian Zuo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA.
| |
Collapse
|
19
|
Tecalco-Cruz AC, Zepeda-Cervantes J, Ramírez-Jarquín JO, Rojas-Ochoa A. Proteolysis-targeting chimeras and their implications in breast cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2021; 2:496-510. [PMID: 36046115 PMCID: PMC9400758 DOI: 10.37349/etat.2021.00060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) is a highly heterogeneous neoplasm of the mammary tissue, causing the deaths of a large number of women worldwide. Nearly 70% and 20% of BC cases are estrogen receptor alpha positive (ERα+) and human epidermal growth factor receptor 2-positive (HER2+), respectively; therefore, ER and HER2 targeted therapies have been employed in BC treatment. However, resistance to these therapies has been reported, indicating a need for developing novel therapeutic strategies. Proteolysis-targeting chimeras (PROTACs) are new, promising therapeutic tools designed with a bimodular structure: one module allows specific binding to target proteins, and the other module allows efficient degradation of these target proteins. In this paper, PROTACs and their potential in controlling the progression of ERα and HER2+ BC are discussed.
Collapse
Affiliation(s)
- Angeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), CDMX, Mexico City 03100, Mexico
| | - Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), CDMX, Mexico City 04510, Mexico
| | - Josué O. Ramírez-Jarquín
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), CDMX, Mexico City 04500, Mexico
| | | |
Collapse
|
20
|
Schuler LA, Murdoch FE. Endogenous and Therapeutic Estrogens: Maestro Conductors of the Microenvironment of ER+ Breast Cancers. Cancers (Basel) 2021; 13:cancers13153725. [PMID: 34359625 PMCID: PMC8345134 DOI: 10.3390/cancers13153725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/25/2022] Open
Abstract
Estrogen receptor alpha (ERα) marks heterogeneous breast cancers which display a repertoire of somatic genomic mutations and an immune environment that differs from other breast cancer subtypes. These cancers also exhibit distinct biological behaviors; despite an overall better prognosis than HER2+ or triple negative breast cancers, disseminated dormant cells can lead to disease recurrence decades after the initial diagnosis and treatment. Estrogen is the best studied driver of these cancers, and antagonism or reduction of estrogen activity is the cornerstone of therapeutic approaches. In addition to reducing proliferation of ERα+ cancer cells, these treatments also alter signals to multiple other target cells in the environment, including immune cell subpopulations, cancer-associated fibroblasts, and endothelial cells via several distinct estrogen receptors. In this review, we update progress in our understanding of the stromal cells populating the microenvironments of primary and metastatic ER+ tumors, the effects of estrogen on tumor and stromal cells to modulate immune activity and the extracellular matrix, and net outcomes in experimental and clinical studies. We highlight new approaches that will illuminate the unique biology of these cancers, provide the foundation for developing new treatment and prevention strategies, and reduce mortality of this disease.
Collapse
|
21
|
Mukhamejanova Z, Tong Y, Xiang Q, Xu F, Pang J. Recent Advances in the Design and Development of Anticancer Molecules based on PROTAC Technology. Curr Med Chem 2021; 28:1304-1327. [PMID: 32164504 DOI: 10.2174/0929867327666200312112412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 11/22/2022]
Abstract
PROTAC (Proteolysis Targeting Chimera) degraders based on protein knockdown technology are now suggested as a novel option for the treatment of various diseases. Over the last couple of years, the application of PROTAC technology has spread in a wide range of disorders, and plenty of PROTAC molecules with high potency have been reported. Mostly developing for anticancer therapy, these molecules showed high selectivities to target proteins, the ability to significantly induce degradation of oncoproteins, good in vitro and in vivo results. In this review, we summarized the recent development of PROTAC technology in the anticancer therapy field, including molecular design, types of targeted proteins, in vitro and in vivo results. Additionally, we also discuss the prospects and challenges for the application of candidates based on PROTAC strategy in clinical trials.
Collapse
Affiliation(s)
| | - Yichen Tong
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qi Xiang
- Institute of Biomedicine & Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| |
Collapse
|
22
|
Wang Z, Ma Z, Shen Z. Selective degradation of the estrogen receptor in the treatment of cancers. J Steroid Biochem Mol Biol 2021; 209:105848. [PMID: 33610801 DOI: 10.1016/j.jsbmb.2021.105848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Estrogen receptor subtype α (ERα) plays key roles in breast cancers, and has been a target for endocrine therapy for a long time. Unfortunately, long-term treatment by Aromatase Inhibitors (AIs) or Selective Estrogen Receptor Modulators (SERMs) could cause drug resistance and also would increase the risk for uterine cancer. Therefore, novel anti-breast cancer drugs based on different mechanisms of action have received significant attention, especially through the strategies of selective degradation of ER. In this article, the latest research progress of selective targeting ER for degradation, including Selective ER Downregulators (SERDs), Proteolysis Targeting Chimaeras (PROTACs) and other techniques, was reviewed, and the applications and problems to be solved were prospected.
Collapse
Affiliation(s)
- Zunyuan Wang
- Institute of Materia Medica, Hangzhou Medical College, 310013 Hangzhou, Zhejiang, China
| | - Zhen Ma
- Institute of Materia Medica, Hangzhou Medical College, 310013 Hangzhou, Zhejiang, China
| | - Zhengrong Shen
- Institute of Materia Medica, Hangzhou Medical College, 310013 Hangzhou, Zhejiang, China.
| |
Collapse
|
23
|
Disch JS, Duffy JM, Lee ECY, Gikunju D, Chan B, Levin B, Monteiro MI, Talcott SA, Lau AC, Zhou F, Kozhushnyan A, Westlund NE, Mullins PB, Yu Y, von Rechenberg M, Zhang J, Arnautova YA, Liu Y, Zhang Y, McRiner AJ, Keefe AD, Kohlmann A, Clark MA, Cuozzo JW, Huguet C, Arora S. Bispecific Estrogen Receptor α Degraders Incorporating Novel Binders Identified Using DNA-Encoded Chemical Library Screening. J Med Chem 2021; 64:5049-5066. [PMID: 33844532 DOI: 10.1021/acs.jmedchem.1c00127] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bispecific degraders (PROTACs) of ERα are expected to be advantageous over current inhibitors of ERα signaling (aromatase inhibitors/SERMs/SERDs) used to treat ER+ breast cancer. Information from DNA-encoded chemical library (DECL) screening provides a method to identify novel PROTAC binding features as the linker positioning, and binding elements are determined directly from the screen. After screening ∼120 billion DNA-encoded molecules with ERα WT and 3 gain-of-function (GOF) mutants, with and without estradiol to identify features that enrich ERα competitively, the off-DNA synthesized small molecule exemplar 7 exhibited nanomolar ERα binding, antagonism, and degradation. Click chemistry synthesis on an alkyne E3 ligase engagers panel and an azide variant of 7 rapidly generated bispecific nanomolar degraders of ERα, with PROTACs 18 and 21 inhibiting ER+ MCF7 tumor growth in a mouse xenograft model of breast cancer. This study validates this approach toward identifying novel bispecific degrader leads from DECL screening with minimal optimization.
Collapse
Affiliation(s)
- Jeremy S Disch
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Jennifer M Duffy
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Esther C Y Lee
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Diana Gikunju
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Benjamin Levin
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Michael I Monteiro
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Sarah A Talcott
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Anthony C Lau
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Fei Zhou
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Anton Kozhushnyan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Neil E Westlund
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Patrick B Mullins
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Yan Yu
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | | | - Junyi Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Yelena A Arnautova
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Yanbin Liu
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Andrew J McRiner
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Anthony D Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Anna Kohlmann
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Matthew A Clark
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Christelle Huguet
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Shilpi Arora
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| |
Collapse
|
24
|
Bai N, Miller SA, Andrianov GV, Yates M, Kirubakaran P, Karanicolas J. Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta. J Chem Inf Model 2021; 61:1368-1382. [PMID: 33625214 DOI: 10.1021/acs.jcim.0c01451] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteolysis-targeting chimaeras (PROTACs) are molecules that combine a target-binding warhead with an E3 ligase-recruiting moiety; by drawing the target protein into a ternary complex with the E3 ligase, PROTACs induce target protein degradation. While PROTACs hold exciting potential as chemical probes and as therapeutic agents, development of a PROTAC typically requires synthesis of numerous analogs to thoroughly explore variations on the chemical linker; without extensive trial and error, it is unclear how to link the two protein-recruiting moieties to promote formation of a productive ternary complex. Here, we describe a structure-based computational method for evaluating the suitability of a given linker for ternary complex formation. Our method uses Rosetta to dock the protein components and then builds the PROTAC from its component fragments into each binding mode; complete models of the ternary complex are then refined. We apply this approach to retrospectively evaluate multiple PROTACs from the literature, spanning diverse target proteins. We find that modeling ternary complex formation is sufficient to explain both activity and selectivity reported for these PROTACs, implying that other cellular factors are not key determinants of activity in these cases. We further find that interpreting PROTAC activity is best approached using an ensemble of structures of the ternary complex rather than a single static conformation and that members of a structurally conserved protein family can be recruited by the same PROTAC through vastly different binding modes. To encourage adoption of these methods and promote further analyses, we disseminate both the computational methods and the models of ternary complexes.
Collapse
Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Sven A Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - Grigorii V Andrianov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Max Yates
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - Palani Kirubakaran
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| |
Collapse
|
25
|
Chen X, Shen H, Shao Y, Ma Q, Niu Y, Shang Z. A narrative review of proteolytic targeting chimeras (PROTACs): future perspective for prostate cancer therapy. Transl Androl Urol 2021; 10:954-962. [PMID: 33718095 PMCID: PMC7947434 DOI: 10.21037/tau-20-1357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Proteolysis-TArgeting Chimeras (PROTACs) technology, as a strategy to chemically knock down transcription factors at the protein levels, can hijack the ubiquitin-proteasome degradation system to initiate the intracellular ubiquitin-proteasome hydrolysis process to degrade proteins. In the past, the development of drugs that target transcription factors has been greatly restricted, and even historically transcription factors have been regarded as “undruggable targets”. PROTAC technology breaks through this limitation with its unique targeting design. With several generations of technical innovation, PROTACs have become more mature and continue to make breakthroughs in the field of targeted therapy including prostate cancer (PCa), with a new strategy for the development of anti-tumor targeted drugs. PROTACs have all the advantages of existing small molecule inhibitors, are easy to administer orally, have good cell permeability, and have wider targeting profiles compared to conventional inhibitors. The disadvantage of PROTACs is the noncancer specificity, off-target and sustained-release control, due to its catalytic role. Some androgen receptor (AR) and CDK4/6 degraders have advanced the field of PCa treatment, which is being further modified given the effects of these degraders in preclinical and clinical studies. This review summarizes in detail the technological progress and challenges that have been faced with PROTACs, the progress of research on PCa, and the prospective future of PROTACs development.
Collapse
Affiliation(s)
- Xuanrong Chen
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Haishan Shen
- Urology Development, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Yi Shao
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Qianwang Ma
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuanjie Niu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhiqun Shang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| |
Collapse
|
26
|
The Potential of Proteolytic Chimeras as Pharmacological Tools and Therapeutic Agents. Molecules 2020; 25:molecules25245956. [PMID: 33339292 PMCID: PMC7766482 DOI: 10.3390/molecules25245956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
The induction of protein degradation in a highly selective and efficient way by means of druggable molecules is known as targeted protein degradation (TPD). TPD emerged in the literature as a revolutionary idea: a heterobifunctional chimera with the capacity of creating an interaction between a protein of interest (POI) and a E3 ubiquitin ligase will induce a process of events in the POI, including ubiquitination, targeting to the proteasome, proteolysis and functional silencing, acting as a sort of degradative knockdown. With this programmed protein degradation, toxic and disease-causing proteins could be depleted from cells with potentially effective low drug doses. The proof-of-principle validation of this hypothesis in many studies has made the TPD strategy become a new attractive paradigm for the development of therapies for the treatment of multiple unmet diseases. Indeed, since the initial protacs (Proteolysis targeting chimeras) were posited in the 2000s, the TPD field has expanded extraordinarily, developing innovative chemistry and exploiting multiple degradation approaches. In this article, we review the breakthroughs and recent novel concepts in this highly active discipline.
Collapse
|
27
|
Discovery of novel anti-angiogenesis agents. Part 11: Development of PROTACs based on active molecules with potency of promoting vascular normalization. Eur J Med Chem 2020; 205:112654. [DOI: 10.1016/j.ejmech.2020.112654] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 12/22/2022]
|
28
|
Zaidman D, Prilusky J, London N. PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes. J Chem Inf Model 2020; 60:4894-4903. [PMID: 32976709 PMCID: PMC7592117 DOI: 10.1021/acs.jcim.0c00589] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 12/22/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs), which induce degradation by recruitment of an E3 ligase to a target protein, are gaining much interest as a new pharmacological modality. However, designing PROTACs is challenging. Formation of a ternary complex between the protein target, the PROTAC, and the recruited E3 ligase is considered paramount for successful degradation. A structural model of this ternary complex could in principle inform rational PROTAC design. Unfortunately, only a handful of structures are available for such complexes, necessitating tools for their modeling. We developed a combined protocol for the modeling of a ternary complex induced by a given PROTAC. Our protocol alternates between sampling of the protein-protein interaction space and the PROTAC molecule conformational space. Application of this protocol-PRosettaC-to a benchmark of known PROTAC ternary complexes results in near-native predictions, with often atomic accuracy prediction of the protein chains, as well as the PROTAC binding moieties. It allowed the modeling of a CRBN/BTK complex that recapitulated experimental results for a series of PROTACs. PRosettaC generated models may be used to design PROTACs for new targets, as well as improve PROTACs for existing targets, potentially cutting down time and synthesis efforts. To enable wide access to this protocol, we have made it available through a web server (https://prosettac.weizmann.ac.il/).
Collapse
Affiliation(s)
- Daniel Zaidman
- Department
of Organic Chemistry, The Weizmann Institute
of Science, 76100, Rehovot, Israel
| | - Jaime Prilusky
- Life
Sciences Core Facilities, Weizmann Institute
of Science, 76100, Rehovot, Israel
| | - Nir London
- Department
of Organic Chemistry, The Weizmann Institute
of Science, 76100, Rehovot, Israel
| |
Collapse
|
29
|
Troup RI, Fallan C, Baud MGJ. Current strategies for the design of PROTAC linkers: a critical review. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:273-312. [PMID: 36046485 PMCID: PMC9400730 DOI: 10.37349/etat.2020.00018] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules consisting of two ligands; an “anchor” to bind to an E3 ubiquitin ligase and a “warhead” to bind to a protein of interest, connected by a chemical linker. Targeted protein degradation by PROTACs has emerged as a new modality for the knock down of a range of proteins, with the first agents now reaching clinical evaluation. It has become increasingly clear that the length and composition of the linker play critical roles on the physicochemical properties and bioactivity of PROTACs. While linker design has historically received limited attention, the PROTAC field is evolving rapidly and currently undergoing an important shift from synthetically tractable alkyl and polyethylene glycol to more sophisticated functional linkers. This promises to unlock a wealth of novel PROTAC agents with enhanced bioactivity for therapeutic intervention. Here, the authors provide a timely overview of the diverse linker classes in the published literature, along with their underlying design principles and overall influence on the properties and bioactivity of the associated PROTACs. Finally, the authors provide a critical analysis of current strategies for PROTAC assembly. The authors highlight important limitations associated with the traditional “trial and error” approach around linker design and selection, and suggest potential future avenues to further inform rational linker design and accelerate the identification of optimised PROTACs. In particular, the authors believe that advances in computational and structural methods will play an essential role to gain a better understanding of the structure and dynamics of PROTAC ternary complexes, and will be essential to address the current gaps in knowledge associated with PROTAC design.
Collapse
Affiliation(s)
- Robert I. Troup
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, UK
| | - Charlene Fallan
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Milton Road, CB4 0WG Cambridge, UK
| | - Matthias G. J. Baud
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, UK
| |
Collapse
|
30
|
Jin J, Wu Y, Chen J, Shen Y, Zhang L, Zhang H, Chen L, Yuan H, Chen H, Zhang W, Luan X. The peptide PROTAC modality: a novel strategy for targeted protein ubiquitination. Theranostics 2020; 10:10141-10153. [PMID: 32929339 PMCID: PMC7481416 DOI: 10.7150/thno.46985] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023] Open
Abstract
Despite dramatic advances in drug discovery over the decades, effective therapeutic strategies for cancers treatment are still in urgent demands. PROteolysis TArgeting Chimera (PROTAC), a novel therapeutic modality, has been vigorously promoted in preclinical and clinical applications. Unlike small molecule PROTAC, peptide PROTAC (p-PROTAC) with advantages of high specificity and low toxicity, while avoiding the limitations of shallow binding pockets through large interacting surfaces, provides promising substitutions for E3 ubiquitin ligase complex-mediated ubiquitination of "undruggable proteins". It is worth noting that successful applications of p-PROTAC still have some obstacles, including low stability and poor membrane permeability. Hence, we highlight that p-PROTAC combined with cell-penetrating peptides, constrained conformation technique, and targeted delivery systems could be the future efforts for potential translational research.
Collapse
Affiliation(s)
- Jinmei Jin
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ye Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jinjiao Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yiwen Shen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lijun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hebao Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109 US
| | - Hongzhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacology and Chemical Biology, Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| |
Collapse
|
31
|
Lin X, Xiang H, Luo G. Targeting estrogen receptor α for degradation with PROTACs: A promising approach to overcome endocrine resistance. Eur J Med Chem 2020; 206:112689. [PMID: 32829249 DOI: 10.1016/j.ejmech.2020.112689] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
Estrogen receptor alfa (ERα) is expressed in approximate 70% of breast cancer (BC) which is the most common malignancy in women worldwide. To date, the foremost intervention in the treatment of ER positive (ER+) BC is still the endocrine therapy. However, resistance to endocrine therapies remains a major hurdle in the long-term management of ER + BC. Although the mechanisms underlying endocrine resistance are complex, cumulative evidence revealed that ERα still plays a critical role in driving BC tumor cells to grow in resistance state. Fulvestrant, a selective estrogen receptor degrader (SERD), has moved to first line therapy for metastatic ER + BC, suggesting that removing ERα would be a useful strategy to overcome endocrine resistance. Proteolysis-Targeting Chimera (PROTAC) technology, an emerging paradigm for protein degradation, has the potential to eliminate both wild type and mutant ERα in breast cancer cells. Excitingly, ARV-471, an ERα-targeted PROTAC developed by Arvinas, has been in phase 1 clinical trials. In this review, we will summarize recent progress of ER-targeting PROTACs from publications and patents along with their therapeutic opportunities for the treatment of endocrine-resistant BC.
Collapse
Affiliation(s)
- Xin Lin
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Hua Xiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
32
|
Zhou X, Dong R, Zhang JY, Zheng X, Sun LP. PROTAC: A promising technology for cancer treatment. Eur J Med Chem 2020; 203:112539. [PMID: 32698111 DOI: 10.1016/j.ejmech.2020.112539] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
Proteolysis-targeting chimeric molecules (PROTACs), which attract much more attention today, may be a potential way to treat cancer. PROTACs are made up of ligands of target proteins, E3 ligase recruiting elements and linkers. PROTACs can hijack the intracellular inherent ubiquitin proteasome system in cells to degrade different target proteins. PROTACs targeting different cancer-related proteins have been successfully developed and outperform small inhibitors, the traditional way of treating cancer. In this review, we focus on PROTACs targeting cancer-related proteins and their superiority over inhibitors.
Collapse
Affiliation(s)
- Xin Zhou
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ru Dong
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jin-Yang Zhang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Xin Zheng
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Li-Ping Sun
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China.
| |
Collapse
|
33
|
Burslem GM, Bondeson DP, Crews CM. Scaffold hopping enables direct access to more potent PROTACs with in vivo activity. Chem Commun (Camb) 2020; 56:6890-6892. [PMID: 32519703 PMCID: PMC7404552 DOI: 10.1039/d0cc02201b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein we employ a scaffold hopping approach to enhance the activity of a previously reported BCR-Abl PROTAC. This represents a significant advance in the PROTAC field since it can abrogate the need to optimize the linker to access a more potent degrader. The new PROTAC demonstrates a >10 fold increase in ability to induce degradation and demonstrates in vivo activity.
Collapse
Affiliation(s)
- George M Burslem
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
| | - Daniel P Bondeson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA. and Departments of Chemistry and Pharmacology, Yale University, New Haven, CT, USA
| |
Collapse
|
34
|
Bafna D, Ban F, Rennie PS, Singh K, Cherkasov A. Computer-Aided Ligand Discovery for Estrogen Receptor Alpha. Int J Mol Sci 2020; 21:E4193. [PMID: 32545494 PMCID: PMC7352601 DOI: 10.3390/ijms21124193] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 02/08/2023] Open
Abstract
Breast cancer (BCa) is one of the most predominantly diagnosed cancers in women. Notably, 70% of BCa diagnoses are Estrogen Receptor α positive (ERα+) making it a critical therapeutic target. With that, the two subtypes of ER, ERα and ERβ, have contrasting effects on BCa cells. While ERα promotes cancerous activities, ERβ isoform exhibits inhibitory effects on the same. ER-directed small molecule drug discovery for BCa has provided the FDA approved drugs tamoxifen, toremifene, raloxifene and fulvestrant that all bind to the estrogen binding site of the receptor. These ER-directed inhibitors are non-selective in nature and may eventually induce resistance in BCa cells as well as increase the risk of endometrial cancer development. Thus, there is an urgent need to develop novel drugs with alternative ERα targeting mechanisms that can overcome the limitations of conventional anti-ERα therapies. Several functional sites on ERα, such as Activation Function-2 (AF2), DNA binding domain (DBD), and F-domain, have been recently considered as potential targets in the context of drug research and discovery. In this review, we summarize methods of computer-aided drug design (CADD) that have been employed to analyze and explore potential targetable sites on ERα, discuss recent advancement of ERα inhibitor development, and highlight the potential opportunities and challenges of future ERα-directed drug discovery.
Collapse
Affiliation(s)
| | | | | | | | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.B.); (F.B.); (P.S.R.); (K.S.)
| |
Collapse
|
35
|
Gerry CJ, Schreiber SL. Unifying principles of bifunctional, proximity-inducing small molecules. Nat Chem Biol 2020; 16:369-378. [PMID: 32198490 PMCID: PMC7312755 DOI: 10.1038/s41589-020-0469-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/07/2020] [Indexed: 01/14/2023]
Abstract
Nature uses a variety of tools to mediate the flow of information in cells, many of which control distances between key biomacromolecules. Researchers have thus generated compounds whose activities stem from interactions with two (or more) proteins simultaneously. In this Perspective, we describe how these 'bifunctional' small molecules facilitate the study of an increasingly wide range of complex biological phenomena and enable the drugging of otherwise challenging therapeutic targets and processes. Despite their structural and functional differences, all bifunctional molecules employ Nature's strategy of altering interactomes and inducing proximity to modulate biology. They therefore exhibit a shared set of chemical and biophysical principles that have not yet been appreciated fully. By highlighting these commonalities-and their wide-ranging consequences-we hope to chip away at the artificial barriers that threaten to constrain this interdisciplinary field. Doing so promises to yield remarkable benefits for biological research and therapeutics discovery.
Collapse
Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
| |
Collapse
|
36
|
Liu J, Ma J, Liu Y, Xia J, Li Y, Wang ZP, Wei W. PROTACs: A novel strategy for cancer therapy. Semin Cancer Biol 2020; 67:171-179. [PMID: 32058059 DOI: 10.1016/j.semcancer.2020.02.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/08/2020] [Accepted: 02/09/2020] [Indexed: 12/29/2022]
Abstract
Chemotherapeutic strategy has been widely used for treating malignance by targeting irregular expressed or mutant proteins with small molecular inhibitors (SMIs) or monoclonal antibodies (mAbs). However, most intracellular proteins lack of active sites or antigens where SMIs or mAbs bind with, and are called as non-druggable targets for a long time. From the first year of this century, PROteolysis-TArgeting Chimeras (PROTACs) has emerged to be a promising approach for proteins, including those non-druggable ones, such as transcriptional factors and scaffold proteins. The first generation of peptide-based PROTACs adopts β-TrCP and VHL as E3 ligases, but the cellular permeability and chemical stability issues restrict their clinical application. The second generation of small molecule-based PROTACs adopts MDM2, VHL, IAPs and Cereblon as E3 ligases have been tensely studied. To date, the targets of PROTACs including those overexpressed oncogenic proteins such as ER, AR and BRDs, disease-relevant fusion proteins such as NPM/EML4-ALK and BCR-ABL, cancer-driven mutant proteins such as EGFR, kinases such as CDKs and RTKs. The major disadvantage of PROTACs is the noncancer specificity and relative higher toxicity, due to its catalytic role. To overcome this, we and other have recently developed several similar light-controllable PROTACs, termed as the third generation controllable PROTACs. The degradation of targets by those PROTACs can be triggered by UVA or visible light, providing a tool box for further PROTACs design. Here in this review, we introduce the historical milestones and prospective for further PROTACs development in clinical use.
Collapse
Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jia Ma
- Department of Biochemistry and Molecular Biology, Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Yi Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Jun Xia
- Department of Biochemistry and Molecular Biology, Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Yuyun Li
- Department of Clinical Laboratory Diagnostics, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Z Peter Wang
- Department of Biochemistry and Molecular Biology, Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
37
|
Wang B, Wu S, Liu J, Yang K, Xie H, Tang W. Development of selective small molecule MDM2 degraders based on nutlin. Eur J Med Chem 2019; 176:476-491. [DOI: 10.1016/j.ejmech.2019.05.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 01/22/2023]
|
38
|
Li Y, Zhang S, Zhang J, Hu Z, Xiao Y, Huang J, Dong C, Huang S, Zhou HB. Exploring the PROTAC degron candidates: OBHSA with different side chains as novel selective estrogen receptor degraders (SERDs). Eur J Med Chem 2019; 172:48-61. [DOI: 10.1016/j.ejmech.2019.03.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/23/2019] [Accepted: 03/24/2019] [Indexed: 12/23/2022]
|
39
|
Drummond ML, Williams CI. In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application. J Chem Inf Model 2019; 59:1634-1644. [DOI: 10.1021/acs.jcim.8b00872] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
40
|
Hu W, Zhao J, Hua W, Gou S. A study on platinum(iv) species containing an estrogen receptor modulator to reverse tamoxifen resistance of breast cancer. Metallomics 2019; 10:346-359. [PMID: 29349448 DOI: 10.1039/c7mt00289k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Several dual-action Tam-Pt(iv) complexes derived from tamoxifen (Tam) and platinum(ii) drugs were designed and synthesized for targeting estrogen receptors (ERs) and DNA. These novel compounds not only exhibited potent cytotoxicity against breast cancer cells, but also reversed the tamoxifen resistance of TamR-MCF-7 cancer cells. Computational docking assays together with cellular uptake data demonstrated that the ER ligand portion of these conjugates plays a targeting role in ER-positive tumor cells and promotes the uptake of platinum via an estrogen receptor-mediated pathway. A study on the preliminary mechanism of the typical conjugate, complex 1, revealed that the Tam-Pt(iv) complex induced apoptosis via the mitochondrial-dependent apoptosis pathway mediated through the activation of caspase 3 and PARP proteins. These results suggested that the conjugation of estrogen receptor modulators with the platinum moiety could facilitate a selective enrichment of platinum in estrogen-positive tumors and possibly broaden the scope of ER ligand clinical use to resistant breast tumors.
Collapse
Affiliation(s)
- Weiwei Hu
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | | | | | | |
Collapse
|
41
|
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.
Collapse
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.
| |
Collapse
|
42
|
Zoppi V, Hughes SJ, Maniaci C, Testa A, Gmaschitz T, Wieshofer C, Koegl M, Riching KM, Daniels DL, Spallarossa A, Ciulli A. Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel-Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7. J Med Chem 2018; 62:699-726. [PMID: 30540463 PMCID: PMC6348446 DOI: 10.1021/acs.jmedchem.8b01413] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Developing
PROTACs to redirect the ubiquitination activity of E3
ligases and potently degrade a target protein within cells can be
a lengthy and unpredictable process, and it remains unclear whether
any combination of E3 and target might be productive for degradation.
We describe a probe-quality degrader for a ligase–target pair
deemed unsuitable: the von Hippel–Lindau (VHL) and BRD9, a
bromodomain-containing subunit of the SWI/SNF chromatin remodeling
complex BAF. VHL-based degraders could be optimized from suboptimal
compounds in two rounds by systematically varying conjugation patterns
and linkers and monitoring cellular degradation activities, kinetic
profiles, and ubiquitination, as well as ternary complex formation
thermodynamics. The emerged structure–activity relationships
guided the discovery of VZ185, a potent, fast, and selective degrader
of BRD9 and of its close homolog BRD7. Our findings qualify a new
chemical tool for BRD7/9 knockdown and provide a roadmap for PROTAC
development against seemingly incompatible target–ligase combinations.
Collapse
Affiliation(s)
- Vittoria Zoppi
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom.,Dipartimento di Farmacia, Sezione di Chimica del Farmaco e del Prodotto Cosmetico , Università degli Studi di Genova , Viale Benedetto XV 3 , 16132 Genova , Italy
| | - Scott J Hughes
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom.,Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| | | | | | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co. KG , 1221 Vienna , Austria
| | - Kristin M Riching
- Promega Corporation , 2800 Woods Hollow Road , Madison , Wisconsin 53711 , United States
| | - Danette L Daniels
- Promega Corporation , 2800 Woods Hollow Road , Madison , Wisconsin 53711 , United States
| | - Andrea Spallarossa
- Dipartimento di Farmacia, Sezione di Chimica del Farmaco e del Prodotto Cosmetico , Università degli Studi di Genova , Viale Benedetto XV 3 , 16132 Genova , Italy
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| |
Collapse
|
43
|
Yesbolatova A, Tominari Y, Kanemaki MT. Ligand-induced genetic degradation as a tool for target validation. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 31:91-98. [PMID: 31200864 DOI: 10.1016/j.ddtec.2018.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/02/2023]
Abstract
Targeted protein degraders, known as proteolysis targeting chimeras (PROTACs), are drawing more attention as next-generation drugs to target currently undruggable proteins. As drug discovery of functional degraders involves time- and cost-consuming laborious processes, we propose employing a ligand-induced genetic degradation system to validate candidate proteins before degrader development. Genetic degradation mimics degrader treatment by depleting a degron-fused protein in the presence of a defined ligand. All genetic systems use a combination of a degron and defined ligand that enables a protein of interest fused with the degron to be recruited to an E3 ubiquitin ligase for ubiquitylation and subsequent degradation by the proteasome. However, these events are based on different principles and have different features. We review the dTAG, HaloTag-based, auxin-inducible degron (AID), and destabilizing domain (DD) systems and discuss a strategy for degrader discovery against novel target proteins.
Collapse
Affiliation(s)
- Aisha Yesbolatova
- National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yusuke Tominari
- FIMECS, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Masato T Kanemaki
- National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan.
| |
Collapse
|
44
|
Qin C, Hu Y, Zhou B, Fernandez-Salas E, Yang CY, Liu L, McEachern D, Przybranowski S, Wang M, Stuckey J, Meagher J, Bai L, Chen Z, Lin M, Yang J, Xu F, Hu J, Xing W, Huang L, Li S, Wen B, Sun D, Wang S, Wang S. Discovery of QCA570 as an Exceptionally Potent and Efficacious Proteolysis Targeting Chimera (PROTAC) Degrader of the Bromodomain and Extra-Terminal (BET) Proteins Capable of Inducing Complete and Durable Tumor Regression. J Med Chem 2018; 61:6685-6704. [PMID: 30019901 PMCID: PMC6545111 DOI: 10.1021/acs.jmedchem.8b00506] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proteins of the bromodomain and extra-terminal (BET) family are epigenetics "readers" and promising therapeutic targets for cancer and other human diseases. We describe herein a structure-guided design of [1,4]oxazepines as a new class of BET inhibitors and our subsequent design, synthesis, and evaluation of proteolysis-targeting chimeric (PROTAC) small-molecule BET degraders. Our efforts have led to the discovery of extremely potent BET degraders, exemplified by QCA570, which effectively induces degradation of BET proteins and inhibits cell growth in human acute leukemia cell lines even at low picomolar concentrations. QCA570 achieves complete and durable tumor regression in leukemia xenograft models in mice at well-tolerated dose-schedules. QCA570 is the most potent and efficacious BET degrader reported to date.
Collapse
Affiliation(s)
- Chong Qin
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yang Hu
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Bing Zhou
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Ester Fernandez-Salas
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Sally Przybranowski
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Mi Wang
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Meagher
- Life Sciences Institute, University of Michigan, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Zhuo Chen
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Mei Lin
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Jiuling Yang
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Fuming Xu
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Jiantao Hu
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Weiguo Xing
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Liyue Huang
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Siwei Li
- Pharmacokinetics Core, College of Pharmacy, University of Michigan, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Pharmacokinetics Core, College of Pharmacy, University of Michigan, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Pharmacokinetics Core, College of Pharmacy, University of Michigan, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- The Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Department of Medicinal Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States,Corresponding Author: Professor Shaomeng Wang at
| | | |
Collapse
|
45
|
Targeted protein degradation and the enzymology of degraders. Curr Opin Chem Biol 2018; 44:47-55. [DOI: 10.1016/j.cbpa.2018.05.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
|
46
|
Marchal E, Figliola C, Thompson A. Prodigiosenes conjugated to tamoxifen and estradiol. Org Biomol Chem 2018. [PMID: 28628182 DOI: 10.1039/c7ob00943g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the synthesis of the first click-appended prodigiosene conjugates. Four prodigiosene conjugates of estradiol functionalised at the 7α-position were prepared, as were three prodigiosene conjugates of tamoxifen. The coupling between a prodigiosene and an 11-hydroxy estradiol derivative via an ether linkage was investigated, as was the 11- and 7-functionalisation of the estradiol core. The robustness of estradiol protecting groups was severely challenged by reactions typically used to equip such frameworks for 11- and 7-functionalisation. Specifically, and important to synthesis involving estradiol, TBS, TMS and THP are not useful protecting groups for the functionalisation of this core. When the chemical features of the therapeutic agent limit the choice of protecting group (in this case, prodigiosenes bearing aryl, NH, alkenyl and ester groups), click chemistry becomes an attractive synthetic strategy. The anti-cancer activity of the seven click prodigiosene conjugates was evaluated.
Collapse
Affiliation(s)
- Estelle Marchal
- Department of Chemistry, Dalhousie University, PO BOX 15000, Halifax, NS B3H 4R2, Canada.
| | | | | |
Collapse
|
47
|
Shagufta, Ahmad I. Tamoxifen a pioneering drug: An update on the therapeutic potential of tamoxifen derivatives. Eur J Med Chem 2018; 143:515-531. [DOI: 10.1016/j.ejmech.2017.11.056] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/25/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
|
48
|
Amako Y. Development and Advances of PROTACs: Induced Protein Degradation by Hijacking Ubiquitin Ligase. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University
| |
Collapse
|
49
|
Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders. Essays Biochem 2017; 61:505-516. [PMID: 29118097 PMCID: PMC5869862 DOI: 10.1042/ebc20170041] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 12/27/2022]
Abstract
Molecular glues and bivalent inducers of protein degradation (also known as PROTACs) represent a fascinating new modality in pharmacotherapeutics: the potential to knockdown previously thought 'undruggable' targets at sub-stoichiometric concentrations in ways not possible using conventional inhibitors. Mounting evidence suggests these chemical agents, in concert with their target proteins, can be modelled as three-body binding equilibria that can exhibit significant cooperativity as a result of specific ligand-induced molecular recognition. Despite this, many existing drug design and optimization regimens still fixate on binary target engagement, in part due to limited structural data on ternary complexes. Recent crystal structures of protein complexes mediated by degrader molecules, including the first PROTAC ternary complex, underscore the importance of protein-protein interactions and intramolecular contacts to the mode of action of this class of compounds. These discoveries have opened the door to a new paradigm for structure-guided drug design: borrowing surface area and molecular recognition from nature to elicit cellular signalling.
Collapse
|
50
|
Targeting the cancer epigenome: synergistic therapy with bromodomain inhibitors. Drug Discov Today 2017; 23:76-89. [PMID: 28943305 DOI: 10.1016/j.drudis.2017.09.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 08/21/2017] [Accepted: 09/14/2017] [Indexed: 11/21/2022]
Abstract
Epigenetic and genomic alterations regulate the transcriptional landscape of cells during cancer onset and progression. Recent clinical studies targeting the epigenetic 'readers' (bromodomains) for cancer therapy have established the effectiveness of bromodomain (BRD) and extraterminal (BET) inhibitors in treating several types of cancer. In this review, we discuss key mechanisms of BET inhibition and synergistic combinations of BET inhibitors with histone deacetylase inhibitors (HDACi), histone methyltransferase inhibitors (HMTi), DNA methyltransferase inhibitors (DNMTi), kinase, B-cell lymphoma 2 (Bcl-2) and proteosome inhibitors, and immunomodulatory drugs for cancer therapy. We also highlight the potential of such combinations to overcome drug resistance, and the evolving approaches to developing novel BET inhibitors.
Collapse
|