1
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Kamaraj R, Ghosh S, Das S, Sen S, Kumar P, Majumdar M, Dasgupta R, Mukherjee S, Das S, Ghose I, Pavek P, Raja Karuppiah MP, Chuturgoon AA, Anand K. Targeted Protein Degradation (TPD) for Immunotherapy: Understanding Proteolysis Targeting Chimera-Driven Ubiquitin-Proteasome Interactions. Bioconjug Chem 2024; 35:1089-1115. [PMID: 38990186 PMCID: PMC11342303 DOI: 10.1021/acs.bioconjchem.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Targeted protein degradation or TPD, is rapidly emerging as a treatment that utilizes small molecules to degrade proteins that cause diseases. TPD allows for the selective removal of disease-causing proteins, including proteasome-mediated degradation, lysosome-mediated degradation, and autophagy-mediated degradation. This approach has shown great promise in preclinical studies and is now being translated to treat numerous diseases, including neurodegenerative diseases, infectious diseases, and cancer. This review discusses the latest advances in TPD and its potential as a new chemical modality for immunotherapy, with a special focus on the innovative applications and cutting-edge research of PROTACs (Proteolysis TArgeting Chimeras) and their efficient translation from scientific discovery to technological achievements. Our review also addresses the significant obstacles and potential prospects in this domain, while also offering insights into the future of TPD for immunotherapeutic applications.
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Affiliation(s)
- Rajamanikkam Kamaraj
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Subhrojyoti Ghosh
- Department
of Biotechnology, Indian Institute of Technology
Madras, Chennai 600036, India
| | - Souvadra Das
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Shinjini Sen
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Priyanka Kumar
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Madhurima Majumdar
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Renesa Dasgupta
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Sampurna Mukherjee
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Shrimanti Das
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Indrilla Ghose
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Petr Pavek
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Muruga Poopathi Raja Karuppiah
- Department
of Chemistry, School of Physical Sciences, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod District, Kerala 671320, India
| | - Anil A. Chuturgoon
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Krishnan Anand
- Department
of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State 9300, South Africa
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2
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Gurung HR, Heidersbach AJ, Darwish M, Chan PPF, Li J, Beresini M, Zill OA, Wallace A, Tong AJ, Hascall D, Torres E, Chang A, Lou K'HW, Abdolazimi Y, Hammer C, Xavier-Magalhães A, Marcu A, Vaidya S, Le DD, Akhmetzyanova I, Oh SA, Moore AJ, Uche UN, Laur MB, Notturno RJ, Ebert PJR, Blanchette C, Haley B, Rose CM. Systematic discovery of neoepitope-HLA pairs for neoantigens shared among patients and tumor types. Nat Biotechnol 2024; 42:1107-1117. [PMID: 37857725 PMCID: PMC11251992 DOI: 10.1038/s41587-023-01945-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/14/2023] [Indexed: 10/21/2023]
Abstract
The broad application of precision cancer immunotherapies is limited by the number of validated neoepitopes that are common among patients or tumor types. To expand the known repertoire of shared neoantigen-human leukocyte antigen (HLA) complexes, we developed a high-throughput platform that coupled an in vitro peptide-HLA binding assay with engineered cellular models expressing individual HLA alleles in combination with a concatenated transgene harboring 47 common cancer neoantigens. From more than 24,000 possible neoepitope-HLA combinations, biochemical and computational assessment yielded 844 unique candidates, of which 86 were verified after immunoprecipitation mass spectrometry analyses of engineered, monoallelic cell lines. To evaluate the potential for immunogenicity, we identified T cell receptors that recognized select neoepitope-HLA pairs and elicited a response after introduction into human T cells. These cellular systems and our data on therapeutically relevant neoepitopes in their HLA contexts will aid researchers studying antigen processing as well as neoepitope targeting therapies.
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Affiliation(s)
| | | | | | | | - Jenny Li
- Genentech, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ana Marcu
- Genentech, South San Francisco, CA, USA
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3
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Truex N, Mohapatra S, Melo M, Rodriguez J, Li N, Abraham W, Sementa D, Touti F, Keskin DB, Wu CJ, Irvine DJ, Gómez-Bombarelli R, Pentelute BL. Design of Cytotoxic T Cell Epitopes by Machine Learning of Human Degrons. ACS CENTRAL SCIENCE 2024; 10:793-802. [PMID: 38680558 PMCID: PMC11046456 DOI: 10.1021/acscentsci.3c01544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 05/01/2024]
Abstract
Antigen processing is critical for therapeutic vaccines to generate epitopes for priming cytotoxic T cell responses against cancer and pathogens, but insufficient processing often limits the quantity of epitopes released. We address this challenge using machine learning to ascribe a proteasomal degradation score to epitope sequences. Epitopes with varying scores were translocated into cells using nontoxic anthrax proteins. Epitopes with a low score show pronounced immunogenicity due to antigen processing, but epitopes with a high score show limited immunogenicity. This work sheds light on the sequence-activity relationships between proteasomal degradation and epitope immunogenicity. We anticipate that future efforts to incorporate proteasomal degradation signals into vaccine designs will lead to enhanced cytotoxic T cell priming by these vaccines in clinical settings.
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Affiliation(s)
- Nicholas
L. Truex
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Somesh Mohapatra
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Machine
Intelligence and Manufacturing Operations Group, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mariane Melo
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Ragon Institute
of Massachusetts General Hospital, Massachusetts
Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, United States
| | - Jacob Rodriguez
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Na Li
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Wuhbet Abraham
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Deborah Sementa
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Faycal Touti
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Derin B. Keskin
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Harvard
Medical School, Boston, Massachusetts 02115, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Translational
Immunogenomics Laboratory (TIGL), Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Computer Science, Metropolitan College, Boston University, Boston, Massachusetts 02215, United States
- Section
for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Catherine J. Wu
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Harvard
Medical School, Boston, Massachusetts 02115, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Darrell J. Irvine
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Ragon Institute
of Massachusetts General Hospital, Massachusetts
Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, United States
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Rafael Gómez-Bombarelli
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
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Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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5
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [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: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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6
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Li S, Chen T, Liu J, Zhang H, Li J, Wang Z, Shang G. PROTACs: Novel tools for improving immunotherapy in cancer. Cancer Lett 2023; 560:216128. [PMID: 36933781 DOI: 10.1016/j.canlet.2023.216128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Posttranslational modifications (PTMs), such as phosphorylation, methylation, ubiquitination, and acetylation, are important in governing protein expression levels. Proteolysis targeting chimeras (PROTACs) are novel structures designed to target a protein of interest (POI) for ubiquitination and degradation, leading to the selective reduction in the expression levels of the POI. PROTACs have exhibited great promise due to their ability to target undruggable proteins, including several transcription factors. Recently, PROTACs have been characterized to improve anticancer immunotherapy via the regulation of specific proteins. In this review, we describe how the PROTACs target several molecules, including HDAC6, IDO1, EGFR, FoxM1, PD-L1, SHP2, HPK1, BCL-xL, BET proteins, NAMPT, and COX-1/2, to regulate immunotherapy in human cancers. PROTACs may provide potential treatment benefits by enhancing immunotherapy in cancer patients.
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Affiliation(s)
- Shizhe Li
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China.
| | - Ting Chen
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China.
| | - Jinxin Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China.
| | - He Zhang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China.
| | - Jiatong Li
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China.
| | - Zhiwei Wang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China; The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
| | - Guanning Shang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China.
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7
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Wang C, Zhang Y, Deng J, Liang B, Xing D. Developments of PROTACs technology in immune-related diseases. Eur J Med Chem 2023; 249:115127. [PMID: 36724631 DOI: 10.1016/j.ejmech.2023.115127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023]
Abstract
Traditional chemotherapy and immunotherapy are primary disease-treatment strategies. However, they face numerous challenges, including limited therapeutic benefits, off-target effects, serious adverse effects, drug resistance, long half-life time, poor oral bioavailability, and drugging undruggable proteins. Proteolytic targeted chimeras (PROTACs) were suggested to solve these problems. PROTACs are heterogeneous functional molecules linked by a chemical linker and contain a binding ligand for the protein of interest and a recruiting ligand for the E3 ligand. The binding of a PROTAC to a target protein brings the E3 ligand enzyme into proximity, initiating polyubiquitination of the target protein, followed by protease-mediated degradation. To date, PROTACs against dozens of immunological targets have been successfully developed, many of which have been clinically validated drug targets, and several have entered clinical trials for immune-related diseases. This article reviews the role of PROTACs-mediated degradation of critical proteins in immune disorders and cancer immunotherapy. Chemical structures, cellular and in vivo activities, and pharmacodynamics of these PROTACs are summarized. Lastly, we also discuss the prospects and potential limitations that PROTACs face.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Junwen Deng
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China
| | - Bing Liang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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8
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Generation of a live attenuated influenza A vaccine by proteolysis targeting. Nat Biotechnol 2022; 40:1370-1377. [PMID: 35788567 DOI: 10.1038/s41587-022-01381-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/01/2022] [Indexed: 12/19/2022]
Abstract
The usefulness of live attenuated virus vaccines has been limited by suboptimal immunogenicity, safety concerns or cumbersome manufacturing processes and techniques. Here we describe the generation of a live attenuated influenza A virus vaccine using proteolysis-targeting chimeric (PROTAC) technology to degrade viral proteins via the endogenous ubiquitin-proteasome system of host cells. We engineered the genome of influenza A viruses in stable cell lines engineered for virus production to introduce a conditionally removable proteasome-targeting domain, generating fully infective PROTAC viruses that were live attenuated by the host protein degradation machinery upon infection. In mouse and ferret models, PROTAC viruses were highly attenuated and able to elicit robust and broad humoral, mucosal and cellular immunity against homologous and heterologous virus challenges. PROTAC-mediated attenuation of viruses may be broadly applicable for generating live attenuated vaccines.
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9
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Guenette RG, Yang SW, Min J, Pei B, Potts PR. Target and tissue selectivity of PROTAC degraders. Chem Soc Rev 2022; 51:5740-5756. [PMID: 35587208 DOI: 10.1039/d2cs00200k] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Targeted protein degradation (TPD) strategies have revolutionized how scientists tackle challenging protein targets deemed undruggable with traditional small molecule inhibitors. Many promising campaigns to inhibit proteins have failed due to factors surrounding inhibition selectivity and targeting of compounds to specific tissues and cell types. One of the major improvements that PROTAC (proteolysis targeting chimera) and molecular glue technology can exert is highly selective control of target inhibition. Multiple studies have shown that PROTACs can gain selectivity for their protein targets beyond that of their parent ligands via optimization of linker length and stabilization of ternary complexes. Due to the bifunctional nature of PROTACs, the tissue selective nature of E3 ligases can be exploited to uncover novel targeting mechanisms. In this review, we provide critical analysis of the recent progress towards making selective PROTAC molecules and new PROTAC technologies that will continue to push the boundaries of achieving selectivity. These efforts have wide implications in the future of treating disease as they will broaden the possible targets that can be addressed by small molecules, like undruggable proteins or broadly active targets that would benefit from degradation in specific tissue types.
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Affiliation(s)
| | - Seung Wook Yang
- Induced Proximity Platform, Amgen, Thousand Oaks, CA 91320, USA.
| | - Jaeki Min
- Induced Proximity Platform, Amgen, Thousand Oaks, CA 91320, USA.
| | - Baikang Pei
- Genome Analysis Unit, Amgen, Thousand Oaks, CA 91320, USA
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10
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Kim E, Kim YJ, Ji Z, Kang JM, Wirianto M, Paudel KR, Smith JA, Ono K, Kim JA, Eckel-Mahan K, Zhou X, Lee HK, Yoo JY, Yoo SH, Chen Z. ROR activation by Nobiletin enhances antitumor efficacy via suppression of IκB/NF-κB signaling in triple-negative breast cancer. Cell Death Dis 2022; 13:374. [PMID: 35440077 PMCID: PMC9018867 DOI: 10.1038/s41419-022-04826-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/19/2022] [Accepted: 04/04/2022] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease characterized by poor response to standard therapies and therefore unfavorable clinical outcomes. Better understanding of TNBC and new therapeutic strategies are urgently needed. ROR nuclear receptors are multifunctional transcription factors with important roles in circadian pathways and other processes including immunity and tumorigenesis. Nobiletin (NOB) is a natural compound known to display anticancer effects, and our previous studies showed that NOB activates RORs to enhance circadian rhythms and promote physiological fitness in mice. Here, we identified several TNBC cell lines being sensitive to NOB, by itself or in combination. Cell and xenograft experiments showed that NOB significantly inhibited TNBC cell proliferation and motility in vitro and in vivo. ROR loss- and gain-of-function studies showed concordant effects of the NOB–ROR axis on MDA-MB-231 cell growth. Mechanistically, we found that NOB activates ROR binding to the ROR response elements (RRE) of the IκBα promoter, and NOB strongly inhibited p65 nuclear translocation. Consistent with transcriptomic analysis indicating cancer and NF-κB signaling as major pathways altered by NOB, p65-inducible expression abolished NOB effects, illustrating a requisite role of NF-κB suppression mediating the anti-TNBC effect of NOB. Finally, in vivo mouse xenograft studies showed that NOB enhanced the antitumor efficacy in mammary fat pad implanted TNBC, as a single agent or in combination with the chemotherapy agent Docetaxel. Together, our study highlights an anti-TNBC mechanism of ROR-NOB via suppression of NF-κB signaling, suggesting novel preventive and chemotherapeutic strategies against this devastating disease. ![]()
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Affiliation(s)
- Eunju Kim
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Yoon-Jin Kim
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Zhiwei Ji
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Jin Muk Kang
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Marvin Wirianto
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Keshav Raj Paudel
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Joshua A Smith
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Kaori Ono
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Jin-Ah Kim
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kristin Eckel-Mahan
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Hyun Kyoung Lee
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ji Young Yoo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA.
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA.
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11
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Lospinoso Severini L, Bufalieri F, Infante P, Di Marcotullio L. Proteolysis-Targeting Chimera (PROTAC): Is the Technology Looking at the Treatment of Brain Tumors? Front Cell Dev Biol 2022; 10:854352. [PMID: 35242765 PMCID: PMC8886235 DOI: 10.3389/fcell.2022.854352] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Post-translational modifications, such as ubiquitylation, need to be tightly controlled to guarantee the accurate localization and activity of proteins. Ubiquitylation is a dynamic process primarily responsible for proteasome-mediated degradation of substrate proteins and crucial for both normal homeostasis and disease. Alterations in ubiquitylation lead to the upregulation of oncoproteins and/or downregulation of tumor suppressors, thus concurring in tumorigenesis. PROteolysis-TArgeting Chimera (PROTAC) is an innovative strategy that takes advantage by the cell’s own Ubiquitin-Proteasome System (UPS). Each PROTAC molecule is composed by a ligand that recruits the target protein of interest (POI), a ligand specific for an E3 ubiquitin ligase enzyme, and a linker that connects these units. Upon binding to the POI, the PROTAC recruits the E3 inducing ubiquitylation-dependent proteasome degradation of the POI. To date, PROTAC technology has entered in clinical trials for several human cancers. Here, we will discuss the advantages and limitations of PROTACs development and safety considerations for their clinical application. Furthermore, we will review the potential of PROTAC strategy as therapeutic option in brain tumor, focusing on glioblastoma.
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Affiliation(s)
| | - Francesca Bufalieri
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Paola Infante
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, Rome, Italy
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12
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Tumor immunity: a novel dimension for PROTACs to conquer cancer? Acta Pharmacol Sin 2022; 43:2171-2172. [PMID: 34983932 PMCID: PMC9343653 DOI: 10.1038/s41401-021-00829-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/21/2021] [Indexed: 11/08/2022] Open
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13
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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.
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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,
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14
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Massafra V, Tundo S, Dietzig A, Ducret A, Jost C, Klein C, Kontermann RE, Knoetgen H, Steegmaier M, Romagnani A, Nagel YA. Proteolysis-Targeting Chimeras Enhance T Cell Bispecific Antibody-Driven T Cell Activation and Effector Function through Increased MHC Class I Antigen Presentation in Cancer Cells. THE JOURNAL OF IMMUNOLOGY 2021; 207:493-504. [PMID: 34215653 DOI: 10.4049/jimmunol.2000252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022]
Abstract
The availability of Ags on the surface of tumor cells is crucial for the efficacy of cancer immunotherapeutic approaches using large molecules, such as T cell bispecific Abs (TCBs). Tumor Ags are processed through intracellular proteasomal protein degradation and are displayed as peptides on MHC class I (MHC I). Ag recognition through TCRs on the surface of CD8+ T cells can elicit a tumor-selective immune response. In this article, we show that proteolysis-targeting chimeras (PROTACs) that target bromo- and extraterminal domain proteins increase the abundance of the corresponding target-derived peptide Ags on MHC I in both liquid and solid tumor-derived human cell lines. This increase depends on the engagement of the E3 ligase to bromo- and extraterminal domain protein. Similarly, targeting of a doxycycline-inducible Wilms tumor 1 (WT1)-FKBP12F36V fusion protein, by a mutant-selective FKBP12F36V degrader, increases the presentation of WT1 Ags in human breast cancer cells. T cell-mediated response directed against cancer cells was tested on treatment with a TCR-like TCB, which was able to bridge human T cells to a WT1 peptide displayed on MHC I. FKBP12F36V degrader treatment increased the expression of early and late activation markers (CD69, CD25) in T cells; the secretion of granzyme β, IFN-γ, and TNF-α; and cancer cell killing in a tumor-T cell coculture model. This study supports harnessing targeted protein degradation in tumor cells, for modulation of T cell effector function, by investigating for the first time, to our knowledge, the potential of combining a degrader and a TCB in a cancer immunotherapy setting.
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Affiliation(s)
- Vittoria Massafra
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Sofia Tundo
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Aline Dietzig
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Axel Ducret
- Pharmaceutical Sciences-Biomarkers, Bioinformatics, and Omics, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christian Jost
- Cancer Immunotherapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Zurich, F. Hoffmann-La Roche Ltd., Schlieren, Switzerland
| | - Christian Klein
- Cancer Immunotherapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Zurich, F. Hoffmann-La Roche Ltd., Schlieren, Switzerland
| | - Roland E Kontermann
- Institute of Cell Biology and Immunology, Stuttgart University, Stuttgart, Germany
| | - Hendrik Knoetgen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland; and
| | - Martin Steegmaier
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, F. Hoffmann-La Roche Ltd., Penzberg, Germany
| | - Andrea Romagnani
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Yvonne A Nagel
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland;
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15
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Pollock SB, Rose CM, Darwish M, Bouziat R, Delamarre L, Blanchette C, Lill JR. Sensitive and Quantitative Detection of MHC-I Displayed Neoepitopes Using a Semiautomated Workflow and TOMAHAQ Mass Spectrometry. Mol Cell Proteomics 2021; 20:100108. [PMID: 34129938 PMCID: PMC8255936 DOI: 10.1016/j.mcpro.2021.100108] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/28/2021] [Accepted: 06/04/2021] [Indexed: 12/26/2022] Open
Abstract
Advances in several key technologies, including MHC peptidomics, have helped fuel our understanding of basic immune regulatory mechanisms and the identification of T cell receptor targets for the development of immunotherapeutics. Isolating and accurately quantifying MHC-bound peptides from cells and tissues enables characterization of dynamic changes in the ligandome due to cellular perturbations. However, the current multistep analytical process is challenging, and improvements in throughput and reproducibility would enable rapid characterization of multiple conditions in parallel. Here, we describe a robust and quantitative method whereby peptides derived from MHC-I complexes from a variety of cell lines, including challenging adherent lines such as MC38, can be enriched in a semiautomated fashion on reusable, dry-storage, customized antibody cartridges. Using this method, a researcher, with very little hands-on time and in a single day, can perform up to 96 simultaneous enrichments at a similar level of quality as a manual workflow. TOMAHAQ (Triggered by Offset, Multiplexed, Accurate-mass, High-resolution, and Absolute Quantification), a targeted mass spectrometry technique that combines sample multiplexing and high sensitivity, was employed to characterize neoepitopes displayed on MHC-I by tumor cells and to quantitatively assess the influence of neoantigen expression and induced degradation on neoepitope presentation. This unique combination of robust semiautomated MHC-I peptide isolation and high-throughput multiplexed targeted quantitation allows for both the routine analysis of >4000 unique MHC-I peptides from 250 million cells using nontargeted methods, as well as quantitative sensitivity down to the low amol/μl level using TOMAHAQ targeted MS. Semiautomated peptide immunoprecipitation on reusable antibody cartridges. Application of TOMAHAQ for MHC-I detection and quantitation. Routine analysis of >4000 unique MHC-I peptides from 250 million cells via automation. Quantitative sensitivity down to the low amol/μl level using TOMAHAQ targeted MS.
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Affiliation(s)
- Samuel B Pollock
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, California, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, California, USA
| | - Martine Darwish
- Department of Protein Chemistry, Genentech, South San Francisco, California, USA
| | - Romain Bouziat
- Department of Cancer Immunology, Genentech, South San Francisco, California, USA
| | - Lélia Delamarre
- Department of Cancer Immunology, Genentech, South San Francisco, California, USA
| | - Craig Blanchette
- Department of Protein Chemistry, Genentech, South San Francisco, California, USA
| | - Jennie R Lill
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, California, USA.
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16
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Wang K, Zhou H. Proteolysis targeting chimera (PROTAC) for epidermal growth factor receptor enhances anti-tumor immunity in non-small cell lung cancer. Drug Dev Res 2021; 82:422-429. [PMID: 33231319 DOI: 10.1002/ddr.21765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022]
Abstract
While immunotherapy has dramatically revolutionized the treatment of non-small cell lung cancer (NSCLC), it still faces challenges such as low therapeutic efficacy and immune-related adverse events, indicating that safe and effective approaches to enhance NSCLC immunotherapy are still highly demanded. Epidermal growth factor receptor (EGFR) is an established target for molecularly targeted therapy of NSCLC. Overexpression and activating mutations of EGFR can promote the resistance of NSCLC to immunotherapy via upregulating inhibitory immune checkpoints such as programmed death receptor ligand 1 (PD-L1) and indoleamine-2,3-dioxygenase-1 (IDO1). Thus, therapeutic inhibition of EGFR also holds promise in modulating the immune microenvironment to advance NSCLC immunotherapy. In this study, we employed a proteolysis targeting chimera (PROTAC) that degrades EGFRL858R to investigate its potential in dually inhibiting PD-L1 and IDO1 to potentiate the anti-tumor immunity in NSCLC. We demonstrated that PROTAC significantly downregulated the protein levels of both PD-L1 and IDO1 in NSCLC H3255 cell and tumor. We also confirmed that PROTAC significantly suppressed the H3255 tumor growth and enhanced the anti-tumor immune response in H3255 tumor. Overall, our study provides a novel strategy for future NSCLC therapy.
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Affiliation(s)
- Kai Wang
- Oncology Department, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Hongping Zhou
- Oncology Department, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
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17
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Nabet B. Charting a New Path Towards Degrading Every Protein. Chembiochem 2020; 22:483-484. [PMID: 33103843 DOI: 10.1002/cbic.202000531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/16/2020] [Indexed: 11/07/2022]
Abstract
Strategies to directly alter protein abundance such as small-molecule-induced targeted protein degradation (TPD) are innovative pharmacological modalities with promising clinical potential. Herein, I describe my experience with the development of the degradation tag (dTAG) system, which is a chemical biology strategy to induce rapid and precise degradation of any target protein. Open-source collaborative discovery has been critical for advancing the versatility and accessibility of the dTAG system and will be necessary to understand the benefits and limits of TPD-based strategies in the clinic.
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Affiliation(s)
- Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02215, USA
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18
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Nabet B, Ferguson FM, Seong BKA, Kuljanin M, Leggett AL, Mohardt ML, Robichaud A, Conway AS, Buckley DL, Mancias JD, Bradner JE, Stegmaier K, Gray NS. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat Commun 2020; 11:4687. [PMID: 32948771 PMCID: PMC7501296 DOI: 10.1038/s41467-020-18377-w] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Chemical biology strategies for directly perturbing protein homeostasis including the degradation tag (dTAG) system provide temporal advantages over genetic approaches and improved selectivity over small molecule inhibitors. We describe dTAGV-1, an exclusively selective VHL-recruiting dTAG molecule, to rapidly degrade FKBP12F36V-tagged proteins. dTAGV-1 overcomes a limitation of previously reported CRBN-recruiting dTAG molecules to degrade recalcitrant oncogenes, supports combination degrader studies and facilitates investigations of protein function in cells and mice.
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Affiliation(s)
- Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan L Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy S Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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19
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Khan S, He Y, Zhang X, Yuan Y, Pu S, Kong Q, Zheng G, Zhou D. PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics. Oncogene 2020; 39:4909-4924. [PMID: 32475992 PMCID: PMC7319888 DOI: 10.1038/s41388-020-1336-y] [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: 04/10/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/21/2022]
Abstract
Using PROteolysis TArgeting Chimeras (PROTACs) to degrade proteins that are important for tumorigenesis has emerged as a potential therapeutic strategy for cancer. PROTACs are heterobifunctional molecules consisting of one ligand for binding to a protein of interest (POI) and another to an E3 ubiquitin (E3) ligase, connected via a linker. PROTACs recruit the E3 ligase to the POI and cause proximity-induced ubiquitination and degradation of the POI by the ubiquitin proteasome system (UPS). PROTACs have been developed to degrade a variety of cancer targets with unprecedented efficacy against a multitude of tumor types. To date, most of the PROTACs developed have utilized ligands to recruit E3 ligases that are ubiquitously expressed in both tumor and normal tissues. These PROTACs can cause on-target toxicities if the POIs are not tumor-specific. Therefore, identifying and recruiting the E3 ligases that are enriched in tumors with minimal expression in normal tissues holds the potential to develop tumor-specific/selective PROTACs. In this review, we will discuss the potential of PROTACs to become anticancer therapeutics, chemical and bioinformatics approaches for PROTAC design, and safety concerns with a special focus on the development of tumor-specific/selective PROTACs. In addition, the identification of tumor types in terms of solid versus hematological malignancies that can be best targeted with PROTAC approach will be briefly discussed.
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Affiliation(s)
- Sajid Khan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yonghan He
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Shaoyan Pu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Qingpeng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
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20
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Jensen SM, Potts GK, Ready DB, Patterson MJ. Specific MHC-I Peptides Are Induced Using PROTACs. Front Immunol 2018; 9:2697. [PMID: 30524438 PMCID: PMC6262898 DOI: 10.3389/fimmu.2018.02697] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/01/2018] [Indexed: 01/10/2023] Open
Abstract
Peptides presented by the class-I major histocompatibility complex (MHC-I) are important targets for immunotherapy. The identification of these peptide targets greatly facilitates the generation of T-cell-based therapeutics. Herein, we report the capability of proteolysis targeting chimera (PROTAC) compounds to induce the presentation of specific MHC class-I peptides derived from endogenous cellular proteins. Using LC-MS/MS, we identified several BET-derived MHC-I peptides induced by treatment with three BET-directed PROTAC compounds. To understand our ability to tune this process, we measured the relative rate of presentation of these peptides under varying treatment conditions using label-free mass spectrometry quantification. We found that the rate of peptide presentation reflected the rate of protein degradation, indicating a direct relationship between PROTAC treatment and peptide presentation. We additionally analyzed the effect of PROTAC treatment on the entire immunopeptidome and found many new peptides that were displayed in a PROTAC-specific fashion: we determined that these identifications map to the BET pathway, as well as, potential off-target or unique-to-PROTAC pathways. This work represents the first evidence of the use of PROTAC compounds to induce the presentation of MHC-I peptides from endogenous cellular proteins, highlighting the capability of PROTAC compounds for the discovery and generation of new targets for immunotherapy.
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Affiliation(s)
- Stephanie M Jensen
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
| | - Gregory K Potts
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
| | - Damien B Ready
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
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21
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Pemovska T, Bigenzahn JW, Superti-Furga G. Recent advances in combinatorial drug screening and synergy scoring. Curr Opin Pharmacol 2018; 42:102-110. [PMID: 30193150 PMCID: PMC6219891 DOI: 10.1016/j.coph.2018.07.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022]
Abstract
Treatment of complex diseases such as cancer, cardiovascular disease, diabetes or neurological disorders frequently warrants the utilization of drug combinations for therapeutic intervention. In fact, the most successful example is the current standard of care for HIV patients. However, identification of successful drug cocktails is not a simple task and is hampered by lack of standardization in terminology, experimental protocols and models as well as data analysis. Here we discuss the most recent developments in combinatorial drug screening by covering technological advancements in screening strategies, cellular model systems as well as novel drug classes. We believe the research progress being made provides promising basis to build on and identify, develop and optimize efficacious clinically relevant combinatorial drug treatments.
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Affiliation(s)
- Tea Pemovska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17A, 1090 Vienna, Austria.
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