1
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Crowe C, Nakasone MA, Chandler S, Craigon C, Sathe G, Tatham MH, Makukhin N, Hay RT, Ciulli A. Mechanism of degrader-targeted protein ubiquitinability. SCIENCE ADVANCES 2024; 10:eado6492. [PMID: 39392888 PMCID: PMC11468923 DOI: 10.1126/sciadv.ado6492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/09/2024] [Indexed: 10/13/2024]
Abstract
Small-molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and potential to tackle previously undrugged targets. Stable and long-lived degrader-mediated ternary complexes drive fast and profound target degradation; however, the mechanisms by which they affect target ubiquitination remain elusive. Here, we show cryo-EM structures of the VHL Cullin 2 RING E3 ligase with the degrader MZ1 directing target protein Brd4BD2 toward UBE2R1-ubiquitin, and Lys456 at optimal positioning for nucleophilic attack. In vitro ubiquitination and mass spectrometry illuminate a patch of favorably ubiquitinable lysines on one face of Brd4BD2, with cellular degradation and ubiquitinomics confirming the importance of Lys456 and nearby Lys368/Lys445, identifying the "ubiquitination zone." Our results demonstrate the proficiency of MZ1 in positioning the substrate for catalysis, the favorability of Brd4BD2 for ubiquitination by UBE2R1, and the flexibility of CRL2 for capturing suboptimal lysines. We propose a model for ubiquitinability of degrader-recruited targets, providing a mechanistic blueprint for further rational drug design.
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Affiliation(s)
- Charlotte Crowe
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Mark A. Nakasone
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Sarah Chandler
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Gajanan Sathe
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Michael H. Tatham
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Ronald T. Hay
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
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2
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Xi M, Zhu J, Zhang F, Shen H, Chen J, Xiao Z, Huangfu Y, Wu C, Sun H, Xia G. Antibody-drug conjugates for targeted cancer therapy: Recent advances in potential payloads. Eur J Med Chem 2024; 276:116709. [PMID: 39068862 DOI: 10.1016/j.ejmech.2024.116709] [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: 07/12/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Antibody-drug conjugates (ADCs) represent a promising cancer therapy modality which specifically delivers highly toxic payloads to cancer cells through antigen-specific monoclonal antibodies (mAbs). To date, 15 ADCs have been approved and more than 100 ADC candidates have advanced to clinical trials for the treatment of various cancers. Among these ADCs, microtubule-targeting and DNA-damaging agents are at the forefront of payload development. However, several challenges including toxicity and drug resistance limit the potential of this modality. To tackle these issues, multiple innovative payloads such as immunomodulators and proteolysis targeting chimeras (PROTACs) are incorporated into ADCs to enable multimodal cancer therapy. In this review, we describe the mechanism of ADCs, highlight the importance of ADC payloads and summarize recent progresses of conventional and unconventional ADC payloads, trying to provide an insight into payload diversification as a key step in future ADC development.
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Affiliation(s)
- Meiyang Xi
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Jingjing Zhu
- NovoCodex Biopharmaceuticals Co. Ltd., Shaoxing, 312090, China
| | - Fengxia Zhang
- NovoCodex Biopharmaceuticals Co. Ltd., Shaoxing, 312090, China
| | - Hualiang Shen
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Jianhui Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Ziyan Xiao
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yanping Huangfu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Chunlei Wu
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing, 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
| | - Gang Xia
- NovoCodex Biopharmaceuticals Co. Ltd., Shaoxing, 312090, China
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3
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Poudel YB, Thakore RR, Chekler EP. The New Frontier: Merging Molecular Glue Degrader and Antibody-Drug Conjugate Modalities To Overcome Strategic Challenges. J Med Chem 2024; 67:15996-16001. [PMID: 39231796 DOI: 10.1021/acs.jmedchem.4c01289] [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: 09/06/2024]
Abstract
Herein, we discuss advancements in the field of a unique class of antibody-drug conjugates (ADCs) named molecular glue-antibody conjugate (MAC). ADCs traditionally employ cytotoxic agents as payloads, and this approach has been used in all approved ADCs to treat cancer. Complementary to this approach, proteolysis targeting chimera (PROTAC) degrader antibody conjugates (DACs) provide a unique opportunity to deliver these bifunctional agents to tumors by using antibodies as a delivery mechanism to overcome the bioavailability issues encountered by PROTAC payloads. Recently, a cereblon binding monovalent degrader called molecular glues has been used in new ADCs that we have coined the term molecular-glue antibody conjugates (MACs). In this article, we intend to review advancements made in the field of targeted delivery of cereblon-based molecular glue degraders.
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Affiliation(s)
- Yam B Poudel
- Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Ruchita R Thakore
- Bristol Myers Squibb, 10300 Campus Point Drive, San Diego, California 92121, United States
| | - Eugene P Chekler
- Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
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4
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Venkatesan J, Murugan D, Lakshminarayanan K, Smith AR, Vasanthakumari Thirumalaiswamy H, Kandhasamy H, Zender B, Zheng G, Rangasamy L. Powering up targeted protein degradation through active and passive tumour-targeting strategies: Current and future scopes. Pharmacol Ther 2024; 263:108725. [PMID: 39322067 DOI: 10.1016/j.pharmthera.2024.108725] [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: 06/01/2024] [Revised: 08/31/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024]
Abstract
Targeted protein degradation (TPD) has emerged as a prominent and vital strategy for therapeutic intervention of cancers and other diseases. One such approach involves the exploration of proteolysis targeting chimeras (PROTACs) for the selective elimination of disease-causing proteins through the innate ubiquitin-proteasome pathway. Due to the unprecedented achievements of various PROTAC molecules in clinical trials, researchers have moved towards other physiological protein degradation approaches for the targeted degradation of abnormal proteins, including lysosome-targeting chimeras (LYTACs), autophagy-targeting chimeras (AUTACs), autophagosome-tethering compounds (ATTECs), molecular glue degraders, and other derivatives for their precise mode of action. Despite numerous advantages, these molecules face challenges in solubility, permeability, bioavailability, and potential off-target or on-target off-tissue effects. Thus, an urgent need arises to direct the action of these degrader molecules specifically against cancer cells, leaving the proteins of non-cancerous cells intact. Recent advancements in TPD have led to innovative delivery methods that ensure the degraders are delivered in a cell- or tissue-specific manner to achieve cell/tissue-selective degradation of target proteins. Such receptor-specific active delivery or nano-based passive delivery of the PROTACs could be achieved by conjugating them with targeting ligands (antibodies, aptamers, peptides, or small molecule ligands) or nano-based carriers. These techniques help to achieve precise delivery of PROTAC payloads to the target sites. Notably, the successful entry of a Degrader Antibody Conjugate (DAC), ORM-5029, into a phase 1 clinical trial underscores the therapeutic potential of these conjugates, including LYTAC-antibody conjugates (LACs) and aptamer-based targeted protein degraders. Further, using bispecific antibody-based degraders (AbTACs) and delivering the PROTAC pre-fused with E3 ligases provides a solution for cell type-specific protein degradation. Here, we highlighted the current advancements and challenges associated with developing new tumour-specific protein degrader approaches and summarized their potential as single agents or combination therapeutics for cancer.
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Affiliation(s)
- Janarthanan Venkatesan
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India; Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Dhanashree Murugan
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India; School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Kalaiarasu Lakshminarayanan
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India; Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Alexis R Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Harashkumar Vasanthakumari Thirumalaiswamy
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India; Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Hariprasath Kandhasamy
- Department of Chemistry, School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Boutheina Zender
- Department of Biomedical Engineering, Bahçeşehir University, Istanbul 34353, Turkey
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
| | - Loganathan Rangasamy
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, India.
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5
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Chen C, Pan Y, Yang X, Li H, Cai X, He S, Wang Q, Yang Y, Zheng R, Li H, Yuan S, Dong X, Samarawickrama PN, Zi M, He Y, Zhang X. Liver-targeting chimeras as a potential modality for the treatment of liver diseases. J Control Release 2024; 374:627-638. [PMID: 39208934 DOI: 10.1016/j.jconrel.2024.08.044] [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: 03/20/2024] [Revised: 07/10/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Liver diseases pose significant challenges to global public health. In the realm of drug discovery and development, overcoming 'on-target off-tissue' effects remains a substantial barrier for various diseases. In this study, we have pioneered a Liver-Targeting Chimera (LIVTAC) approach using a proteolysis-targeting chimera (PROTAC) molecule coupled to the liver-specific asialoglycoprotein receptor (ASGPR) through an innovative linker attachment strategy for the precise induction of target protein degradation within the liver. As a proof-of-concept study, we designed XZ1606, a mammalian bromodomain and extra-terminal domain (BET)-targeting LIVTAC agent, which not only demonstrated enduring tumor suppression (over 2 months) in combination with sorafenib but also an improved safety profile, notably ameliorating the incidence of thrombocytopenia, a common and severe on-target dose-limiting toxic effect associated with conventional BET inhibitors. These encouraging results highlight the potential of LIVTAC as a versatile platform for addressing a broad spectrum of liver diseases.
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Affiliation(s)
- Chuanjie Chen
- Drug Discovery & Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yongzhang Pan
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China
| | - Xiaoyu Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huiqin Li
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China
| | - Xinhui Cai
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shengyuan He
- Drug Discovery & Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiong Wang
- National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yiwen Yang
- Drug Discovery & Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Runzi Zheng
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Huiwen Li
- Drug Discovery & Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Shengjie Yuan
- University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China
| | - Xin Dong
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China
| | - Priyadarshani Nadeeshika Samarawickrama
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China
| | - Meiting Zi
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China
| | - Yonghan He
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, China.
| | - Xuan Zhang
- Drug Discovery & Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
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6
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Hao Q, Rathinaswamy MK, Klinge KL, Bratkowski M, Mafi A, Baumgartner CK, Hamel KM, Veits GK, Jain R, Catalano C, Fitzgerald M, Hird AW, Park E, Vora HU, Henderson JA, Longenecker K, Hutchins CW, Qiu W, Scapin G, Sun Q, Stoll VS, Sun C, Li P, Eaton D, Stokoe D, Fisher SL, Nasveschuk CG, Paddock M, Kort ME. Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex. Commun Chem 2024; 7:183. [PMID: 39152201 PMCID: PMC11329783 DOI: 10.1038/s42004-024-01263-7] [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: 01/04/2024] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4CRBN, and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.
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Affiliation(s)
- Qi Hao
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
| | | | - Kelly L Klinge
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | | | | | | | - Keith M Hamel
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Gesine K Veits
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | - Rinku Jain
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | | | - Mark Fitzgerald
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | - Alexander W Hird
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | - Eunice Park
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | - Harit U Vora
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | | | | | | | - Wei Qiu
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | | | - Qi Sun
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | | | - Chaohong Sun
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Ping Li
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | - Dan Eaton
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | - David Stokoe
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA
| | - Stewart L Fisher
- C4 Therapeutics Inc., 490 Arsenal Way, Watertown, MA, 02472, USA
| | | | - Marcia Paddock
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
| | - Michael E Kort
- AbbVie, 1 North Waukegan Rd, North Chicago, IL, 60064, USA.
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7
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Rovers E, Schapira M. Benchmarking Methods for PROTAC Ternary Complex Structure Prediction. J Chem Inf Model 2024; 64:6162-6173. [PMID: 39087481 DOI: 10.1021/acs.jcim.4c00426] [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: 08/02/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional compounds that recruit an E3 ligase to a target protein to induce ubiquitination and degradation of the target. Rational optimization of PROTAC requires a structural model of the ternary complex. In the absence of an experimental structure, computational tools have emerged that attempt to predict PROTAC ternary complexes. Here, we systematically benchmark three commonly used tools: PRosettaC, MOE, and ICM. We find that these PROTAC-focused methods produce an array of ternary complex structures, including some that are observed experimentally, but also many that significantly deviate from the crystal structure. Molecular dynamics simulations show that PROTAC complexes may exist in a multiplicity of configurational states and question the use of experimentally observed structures as a reference for accurate predictions. The pioneering computational tools benchmarked here highlight the promises and challenges in the field and may be more valuable when guided by clear structural and biophysical data. The benchmarking data set that we provide may also be valuable for evaluating other and future computational tools for ternary complex modeling.
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Affiliation(s)
- Evianne Rovers
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
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8
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Fan L, Tong W, Wei A, Mu X. Progress of proteolysis-targeting chimeras (PROTACs) delivery system in tumor treatment. Int J Biol Macromol 2024; 275:133680. [PMID: 38971291 DOI: 10.1016/j.ijbiomac.2024.133680] [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: 05/03/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) can use the intrinsic protein degradation system in cells to degrade pathogenic target proteins, and are currently a revolutionary frontier of development strategy for tumor treatment with small molecules. However, the poor water solubility, low cellular permeability, and off-target side effects of most PROTACs have prevented them from passing the preclinical research stage of drug development. This requires the use of appropriate delivery systems to overcome these challenging hurdles and ensure precise delivery of PROTACs towards the tumor site. Therefore, the combination of PROTACs and multifunctional delivery systems will open up new research directions for targeted degradation of tumor proteins. In this review, we systematically reviewed the design principles and the most recent advances of various PROTACs delivery systems. Moreover, the constructive strategies for developing multifunctional PROTACs delivery systems were proposed comprehensively. This review aims to deepen the understanding of PROTACs drugs and promote the further development of PROTACs delivery system.
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Affiliation(s)
- Lianlian Fan
- Department of Pharmacy, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Weifang Tong
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130021, China
| | - Anhui Wei
- Jilin University School of Pharmaceutical Sciences, Changchun 130021, China
| | - Xupeng Mu
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun 130033, China.
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9
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Zou ZF, Yang L, Nie HJ, Gao J, Lei SM, Lai Y, Zhang F, Wagner E, Yu HJ, Chen XH, Xu ZA. Tumor-targeted PROTAC prodrug nanoplatform enables precise protein degradation and combination cancer therapy. Acta Pharmacol Sin 2024; 45:1740-1751. [PMID: 38609561 PMCID: PMC11272941 DOI: 10.1038/s41401-024-01266-z] [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: 12/23/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024] Open
Abstract
Proteolysis targeting chimeras (PROTACs) have emerged as revolutionary anticancer therapeutics that degrade disease-causing proteins. However, the anticancer performance of PROTACs is often impaired by their insufficient bioavailability, unsatisfactory tumor specificity and ability to induce acquired drug resistance. Herein, we propose a polymer-conjugated PROTAC prodrug platform for the tumor-targeted delivery of the most prevalent von Hippel-Lindau (VHL)- and cereblon (CRBN)-based PROTACs, as well as for the precise codelivery of a degrader and conventional small-molecule drugs. The self-assembling PROTAC prodrug nanoparticles (NPs) can specifically target and be activated inside tumor cells to release the free PROTAC for precise protein degradation. The PROTAC prodrug NPs caused more efficient regression of MDA-MB-231 breast tumors in a mouse model by degrading bromodomain-containing protein 4 (BRD4) or cyclin-dependent kinase 9 (CDK9) with decreased systemic toxicity. In addition, we demonstrated that the PROTAC prodrug NPs can serve as a versatile platform for the codelivery of a PROTAC and chemotherapeutics for enhanced anticancer efficiency and combination benefits. This study paves the way for utilizing tumor-targeted protein degradation for precise anticancer therapy and the effective combination treatment of complex diseases.
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Affiliation(s)
- Zhi-Feng Zou
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lei Yang
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Hui-Jun Nie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jing Gao
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Shu-Min Lei
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yi Lai
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Fan Zhang
- Department of Chemistry, Fudan University, Shanghai, 20043, China
| | - Ernst Wagner
- Department of Pharmacy, Ludwig-Maximilians-Universität, 81377, München, Germany
| | - Hai-Jun Yu
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Xiao-Hua Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Zhi-Ai Xu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
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10
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Kanbar K, El Darzi R, Jaalouk DE. Precision oncology revolution: CRISPR-Cas9 and PROTAC technologies unleashed. Front Genet 2024; 15:1434002. [PMID: 39144725 PMCID: PMC11321987 DOI: 10.3389/fgene.2024.1434002] [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: 05/16/2024] [Accepted: 07/02/2024] [Indexed: 08/16/2024] Open
Abstract
Cancer continues to present a substantial global health challenge, with its incidence and mortality rates persistently reflecting its significant impact. The emergence of precision oncology has provided a breakthrough in targeting oncogenic drivers previously deemed "undruggable" by conventional therapeutics and by limiting off-target cytotoxicity. Two groundbreaking technologies that have revolutionized the field of precision oncology are primarily CRISPR-Cas9 gene editing and more recently PROTAC (PROteolysis TArgeting Chimeras) targeted protein degradation technology. CRISPR-Cas9, in particular, has gained widespread recognition and acclaim due to its remarkable ability to modify DNA sequences precisely. Rather than editing the genetic code, PROTACs harness the ubiquitin proteasome degradation machinery to degrade proteins of interest selectively. Even though CRISPR-Cas9 and PROTAC technologies operate on different principles, they share a common goal of advancing precision oncology whereby both approaches have demonstrated remarkable potential in preclinical and promising data in clinical trials. CRISPR-Cas9 has demonstrated its clinical potential in this field due to its ability to modify genes directly and indirectly in a precise, efficient, reversible, adaptable, and tissue-specific manner, and its potential as a diagnostic tool. On the other hand, the ability to administer in low doses orally, broad targeting, tissue specificity, and controllability have reinforced the clinical potential of PROTAC. Thus, in the field of precision oncology, gene editing using CRISPR technology has revolutionized targeted interventions, while the emergence of PROTACs has further expanded the therapeutic landscape by enabling selective protein degradation. Rather than viewing them as mutually exclusive or competing methods in the field of precision oncology, their use is context-dependent (i.e., based on the molecular mechanisms of the disease) and they potentially could be used synergistically complementing the strengths of CRISPR and vice versa. Herein, we review the current status of CRISPR and PROTAC designs and their implications in the field of precision oncology in terms of clinical potential, clinical trial data, limitations, and compare their implications in precision clinical oncology.
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Affiliation(s)
- Karim Kanbar
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Roy El Darzi
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Diana E. Jaalouk
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
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11
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Lynch TL, Marin VL, McClure RA, Phipps C, Ronau JA, Rouhimoghadam M, Adams AM, Kandi S, Wolke ML, Shergalis AG, Potts GK, Nacham O, Richardson P, Kakavas SJ, Chhor G, Jenkins GJ, Woller KR, Warder SE, Vasudevan A, Reitsma JM. Quantitative Measurement of Rate of Targeted Protein Degradation. ACS Chem Biol 2024; 19:1604-1615. [PMID: 38980123 DOI: 10.1021/acschembio.4c00262] [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: 07/10/2024]
Abstract
Targeted protein degradation (TPD) is a therapeutic approach that leverages the cell's natural machinery to degrade targets instead of inhibiting them. This is accomplished by using mono- or bifunctional small molecules designed to induce the proximity of target proteins and E3 ubiquitin ligases, leading to ubiquitination and subsequent proteasome-dependent degradation of the target. One of the most significant attributes of the TPD approach is its proposed catalytic mechanism of action, which permits substoichiometric exposure to achieve the desired pharmacological effects. However, apart from one in vitro study, studies supporting the catalytic mechanism of degraders are largely inferred based on potency. A more comprehensive understanding of the degrader catalytic mechanism of action can help aspects of compound development. To address this knowledge gap, we developed a workflow for the quantitative measurement of the catalytic rate of degraders in cells. Comparing a selective and promiscuous BTK degrader, we demonstrate that both compounds function as efficient catalysts of BTK degradation, with the promiscuous degrader exhibiting faster rates due to its ability to induce more favorable ternary complexes. By leveraging computational modeling, we show that the catalytic rate is highly dynamic as the target is depleted from cells. Further investigation of the promiscuous kinase degrader revealed that the catalytic rate is a better predictor of optimal degrader activity toward a specific target compared to degradation magnitude alone. In summary, we present a versatile method for mapping the catalytic activity of any degrader for TPD in cells.
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Affiliation(s)
- Thomas L Lynch
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Violeta L Marin
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Ryan A McClure
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Colin Phipps
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Judith A Ronau
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Milad Rouhimoghadam
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Ashley M Adams
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Soumya Kandi
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Malerie L Wolke
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Andrea G Shergalis
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Gregory K Potts
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Omprakash Nacham
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Paul Richardson
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Stephan J Kakavas
- Target Enabling Technologies, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Gekleng Chhor
- Target Enabling Technologies, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Gary J Jenkins
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Kevin R Woller
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Scott E Warder
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Justin M Reitsma
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
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12
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Ichikawa S, Payne NC, Xu W, Chang CF, Vallavoju N, Frome S, Flaxman HA, Mazitschek R, Woo CM. The cyclimids: Degron-inspired cereblon binders for targeted protein degradation. Cell Chem Biol 2024; 31:1162-1175.e10. [PMID: 38320555 DOI: 10.1016/j.chembiol.2024.01.003] [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: 05/09/2023] [Revised: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
Cereblon (CRBN) is an E3 ligase substrate adapter widely exploited for targeted protein degradation (TPD) strategies. However, achieving efficient and selective target degradation is a preeminent challenge with ligands that engage CRBN. Here, we report that the cyclimids, ligands derived from the C-terminal cyclic imide degrons of CRBN, exhibit distinct modes of interaction with CRBN and offer a facile approach for developing potent and selective bifunctional degraders. Quantitative TR-FRET-based characterization of 60 cyclimid degraders in binary and ternary complexes across different substrates revealed that ternary complex binding affinities correlated strongly with cellular degradation efficiency. Our studies establish the unique properties of the cyclimids as versatile warheads in TPD and a systematic biochemical approach for quantifying ternary complex formation to predict their cellular degradation activity, which together will accelerate the development of ligands that engage CRBN.
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Affiliation(s)
- Saki Ichikawa
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - N Connor Payne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenqing Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chia-Fu Chang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nandini Vallavoju
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Spencer Frome
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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13
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Diehl CJ, Salerno A, Ciulli A. Ternary Complex-Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo-PROTACs. Angew Chem Int Ed Engl 2024; 63:e202319456. [PMID: 38626385 DOI: 10.1002/anie.202319456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/18/2024]
Abstract
Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof-of-concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL-targeting Homo-PROTACs as model system, and show that the formation of a VHL2 : Homo-PROTAC ternary complex reversibly assembled using thiol-disulfide exchange chemistry leads to amplification of potent VHL Homo-PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo-PROTAC degraders. We anticipate future applications of ternary-complex directed DCC to early PROTAC screenings and expansion to other proximity-inducing modalities beyond PROTACs.
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Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessandra Salerno
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
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14
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Huang X, Wu F, Ye J, Wang L, Wang X, Li X, He G. Expanding the horizons of targeted protein degradation: A non-small molecule perspective. Acta Pharm Sin B 2024; 14:2402-2427. [PMID: 38828146 PMCID: PMC11143490 DOI: 10.1016/j.apsb.2024.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 06/05/2024] Open
Abstract
Targeted protein degradation (TPD) represented by proteolysis targeting chimeras (PROTACs) marks a significant stride in drug discovery. A plethora of innovative technologies inspired by PROTAC have not only revolutionized the landscape of TPD but have the potential to unlock functionalities beyond degradation. Non-small-molecule-based approaches play an irreplaceable role in this field. A wide variety of agents spanning a broad chemical spectrum, including peptides, nucleic acids, antibodies, and even vaccines, which not only prove instrumental in overcoming the constraints of conventional small molecule entities but also provided rapidly renewing paradigms. Herein we summarize the burgeoning non-small molecule technological platforms inspired by PROTACs, including three major trajectories, to provide insights for the design strategies based on novel paradigms.
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Affiliation(s)
- Xiaowei Huang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fengbo Wu
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Ye
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lian Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoyun Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiang Li
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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15
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Wang C, Zhang Y, Chen W, Wu Y, Xing D. New-generation advanced PROTACs as potential therapeutic agents in cancer therapy. Mol Cancer 2024; 23:110. [PMID: 38773495 PMCID: PMC11107062 DOI: 10.1186/s12943-024-02024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) technology has garnered significant attention over the last 10 years, representing a burgeoning therapeutic approach with the potential to address pathogenic proteins that have historically posed challenges for traditional small-molecule inhibitors. PROTACs exploit the endogenous E3 ubiquitin ligases to facilitate degradation of the proteins of interest (POIs) through the ubiquitin-proteasome system (UPS) in a cyclic catalytic manner. Despite recent endeavors to advance the utilization of PROTACs in clinical settings, the majority of PROTACs fail to progress beyond the preclinical phase of drug development. There are multiple factors impeding the market entry of PROTACs, with the insufficiently precise degradation of favorable POIs standing out as one of the most formidable obstacles. Recently, there has been exploration of new-generation advanced PROTACs, including small-molecule PROTAC prodrugs, biomacromolecule-PROTAC conjugates, and nano-PROTACs, to improve the in vivo efficacy of PROTACs. These improved PROTACs possess the capability to mitigate undesirable physicochemical characteristics inherent in traditional PROTACs, thereby enhancing their targetability and reducing off-target side effects. The new-generation of advanced PROTACs will mark a pivotal turning point in the realm of targeted protein degradation. In this comprehensive review, we have meticulously summarized the state-of-the-art advancements achieved by these cutting-edge PROTACs, elucidated their underlying design principles, deliberated upon the prevailing challenges encountered, and provided an insightful outlook on future prospects within this burgeoning field.
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Affiliation(s)
- Chao Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Wujun Chen
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yudong Wu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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16
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Zhang D, Ma B, Dragovich PS, Ma L, Chen S, Chen EC, Ye X, Liu J, Pizzano J, Bortolon E, Chan E, Zhang X, Chen YC, Levy ES, Yauch RL, Khojasteh SC, Hop CECA. Tissue distribution and retention drives efficacy of rapidly clearing VHL-based PROTACs. COMMUNICATIONS MEDICINE 2024; 4:87. [PMID: 38755248 PMCID: PMC11099041 DOI: 10.1038/s43856-024-00505-y] [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: 05/24/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Proteolysis-targeting chimeras (PROTACs) are being developed for therapeutic use. However, they have poor pharmacokinetic profiles and their tissue distribution kinetics are not known. METHODS A typical von Hippel-Lindau tumor suppressor (VHL)-PROTAC 14C-A947 (BRM degrader)-was synthesized and its tissue distribution kinetics was studied by quantitative whole-body autoradiography (QWBA) and tissue excision in rats following IV dosing. Bile duct-cannulated (BDC) rats allowed the elucidation of in vivo clearance pathways. Distribution kinetics was evaluated in the tissues and tumors of mice to support PK-PD correlation. In vitro studies enabled the evaluation of cell uptake mechanisms and cell retention properties. RESULTS Here, we show that A947 quickly distributes into rat tissues after IV dosing, where it accumulates and is retained in tissues such as the lung and liver although it undergoes fast clearance from circulation. Similar uptake/retention kinetics enable tumor growth inhibition over 2-3 weeks in a lung cancer model. A947 quickly excretes in the bile of rats. Solute carrier (SLC) transporters are involved in hepatocyte uptake of PROTACs. Sustained BRM protein degradation is seen after extensive washout that supports prolonged cell retention of A947 in NCI-H1944 cells. A947 tissue exposure and pharmacodynamics are inversely correlated in tumors. CONCLUSIONS Plasma sampling for VHL-PROTAC does not represent the tissue concentrations necessary for efficacy. Understanding of tissue uptake and retention could enable less frequent IV administration to be used for therapeutic dosing.
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Affiliation(s)
- Donglu Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Bin Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Li Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Shu Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eugene C Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xiaofen Ye
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joyce Liu
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Pizzano
- Arvinas; 5 Science Park, 395 Winchester Ave, New Haven, CT, 06511, USA
| | | | - Emily Chan
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xing Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yi-Chen Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Robert L Yauch
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
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17
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Vorderbruggen M, Velázquez-Martínez CA, Natarajan A, Karpf AR. PROTACs in Ovarian Cancer: Current Advancements and Future Perspectives. Int J Mol Sci 2024; 25:5067. [PMID: 38791105 PMCID: PMC11121112 DOI: 10.3390/ijms25105067] [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: 04/04/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy. The majority of patients diagnosed with advanced ovarian cancer will relapse, at which point additional therapies can be administered but, for the most part, these are not curative. As such, a need exists for the development of novel therapeutic options for ovarian cancer patients. Research in the field of targeted protein degradation (TPD) through the use of proteolysis-targeting chimeras (PROTACs) has significantly increased in recent years. The ability of PROTACs to target proteins of interest (POI) for degradation, overcoming limitations such as the incomplete inhibition of POI function and the development of resistance seen with other inhibitors, is of particular interest in cancer research, including ovarian cancer research. This review provides a synopsis of PROTACs tested in ovarian cancer models and highlights PROTACs characterized in other types of cancers with potential high utility in ovarian cancer. Finally, we discuss methods that will help to enable the selective delivery of PROTACs to ovarian cancer and improve the pharmacodynamic properties of these agents.
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Affiliation(s)
- Makenzie Vorderbruggen
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | | | - Amarnath Natarajan
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Adam R. Karpf
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
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18
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Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [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: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
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Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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19
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Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, Rodriguez MS. Breaking Bad Proteins-Discovery Approaches and the Road to Clinic for Degraders. Cells 2024; 13:578. [PMID: 38607017 PMCID: PMC11011670 DOI: 10.3390/cells13070578] [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: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD), with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focuses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.
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Affiliation(s)
- Corentin Bouvier
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
| | - Rachel Lawrence
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Francesca Cavallo
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - Allan Jordan
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Roland Hjerpe
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Manuel S. Rodriguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
- Pharmadev, UMR 152, Université de Toulouse, IRD, UT3, 31400 Toulouse, France
- B Molecular, Centre Pierre Potier, Canceropôle, 31106 Toulouse, France
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20
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Guo Y, Li X, Xie Y, Wang Y. What influences the activity of Degrader-Antibody conjugates (DACs). Eur J Med Chem 2024; 268:116216. [PMID: 38387330 DOI: 10.1016/j.ejmech.2024.116216] [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: 12/12/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
The targeted protein degradation (TPD) technology employing proteolysis-targeting chimeras (PROTACs) has been widely applied in drug chemistry and chemical biology for the treatment of cancer and other diseases. PROTACs have demonstrated significant advantages in targeting undruggable targets and overcoming drug resistance. However, despite the efficient degradation of targeted proteins achieved by PROTACs, they still face challenges related to selectivity between normal and cancer cells, as well as issues with poor membrane permeability due to their substantial molecular weight. Additionally, the noteworthy toxicity resulting from off-target effects also needs to be addressed. To solve these issues, Degrader-Antibody Conjugates (DACs) have been developed, leveraging the targeting and internalization capabilities of antibodies. In this review, we elucidates the characteristics and distinctions between DACs, and traditional Antibody-drug conjugates (ADCs). Meanwhile, we emphasizes the significance of DACs in facilitating the delivery of PROTACs and delves into the impact of various components on DAC activity. These components include antibody targets, drug-antibody ratio (DAR), linker types, PROTACs targets, PROTACs connections, and E3 ligase ligands. The review also explores the suitability of different targets (antibody targets or PROTACs targets) for DACs, providing insights to guide the design of PROTACs better suited for antibody conjugation.
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Affiliation(s)
- Yaolin Guo
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Xiaoxue Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Xie
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
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21
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Tsuchikama K, Anami Y, Ha SYY, Yamazaki CM. Exploring the next generation of antibody-drug conjugates. Nat Rev Clin Oncol 2024; 21:203-223. [PMID: 38191923 DOI: 10.1038/s41571-023-00850-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/10/2024]
Abstract
Antibody-drug conjugates (ADCs) are a promising cancer treatment modality that enables the selective delivery of highly cytotoxic payloads to tumours. However, realizing the full potential of this platform necessitates innovative molecular designs to tackle several clinical challenges such as drug resistance, tumour heterogeneity and treatment-related adverse effects. Several emerging ADC formats exist, including bispecific ADCs, conditionally active ADCs (also known as probody-drug conjugates), immune-stimulating ADCs, protein-degrader ADCs and dual-drug ADCs, and each offers unique capabilities for tackling these various challenges. For example, probody-drug conjugates can enhance tumour specificity, whereas bispecific ADCs and dual-drug ADCs can address resistance and heterogeneity with enhanced activity. The incorporation of immune-stimulating and protein-degrader ADCs, which have distinct mechanisms of action, into existing treatment strategies could enable multimodal cancer treatment. Despite the promising outlook, the importance of patient stratification and biomarker identification cannot be overstated for these emerging ADCs, as these factors are crucial to identify patients who are most likely to derive benefit. As we continue to deepen our understanding of tumour biology and refine ADC design, we will edge closer to developing truly effective and safe ADCs for patients with treatment-refractory cancers. In this Review, we highlight advances in each ADC component (the monoclonal antibody, payload, linker and conjugation chemistry) and provide more-detailed discussions on selected examples of emerging novel ADCs of each format, enabled by engineering of one or more of these components.
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Affiliation(s)
- Kyoji Tsuchikama
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Yasuaki Anami
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Summer Y Y Ha
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Chisato M Yamazaki
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
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22
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Wang C, Zhang Y, Yu W, Xu J, Xing D. PROTAC-biomacromolecule conjugates for precise protein degradation in cancer therapy: A review. Int J Biol Macromol 2024; 261:129864. [PMID: 38302015 DOI: 10.1016/j.ijbiomac.2024.129864] [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: 12/06/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Proteolysis targeting chimera (PROTAC) technology is a promising new mode of targeted protein degradation with significant transformative implications for the clinical treatment of different diseases. Nevertheless, while this technology offers numerous advantages, on-target off-tumour toxicity in healthy cells remains a major challenge for clinical application in cancer therapy. Strategies are presently being explored to optimize degradation activity with cellular selectivity to minimize undesirable side effects. PROTAC-antibody conjugates and PROTAC-aptamer conjugates are unique innovations that combine PROTACs and biomacromolecules. These novel PROTAC-biomacromolecule conjugates (PBCs) can enhance the targetability of PROTACs and reduce their off-target side-effects. The combination of potent PROTACs and highly safe biomacromolecules will pioneer an emerging trend in targeted protein degradation. In our review, we have summarized recent advances in PBCs, discussed current challenges, and outlooked opportunities for future research in the field.
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Affiliation(s)
- Chao Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China.
| | - Wanpeng Yu
- Qingdao Medical College, Qingdao University, Qingdao 266071, China.
| | - Jiazhen Xu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China.
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
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23
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Zhang A, Seiss K, Laborde L, Palacio-Ramirez S, Guthy D, Lanter M, Lorber J, Vulpetti A, Arista L, Zoller T, Radimerski T, Thoma C, Hebach C, Tschantz WR, Karpov A, Hollingworth GJ, D'Alessio JA, Ferretti S, Burger MT. Design, Synthesis, and In Vitro and In Vivo Evaluation of Cereblon Binding Bruton's Tyrosine Kinase (BTK) Degrader CD79b Targeted Antibody-Drug Conjugates. Bioconjug Chem 2024; 35:140-146. [PMID: 38265691 DOI: 10.1021/acs.bioconjchem.3c00535] [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: 01/25/2024]
Abstract
Antibody-drug conjugates (ADCs) are an established modality that allow for targeted delivery of a potent molecule, or payload, to a desired site of action. ADCs, wherein the payload is a targeted protein degrader, are an emerging area in the field. Herein we describe our efforts of delivering a Bruton's tyrosine kinase (BTK) bifunctional degrader 1 via a CD79b mAb (monoclonal antibody) where the degrader is linked at the ligase binding portion of the payload via a cleavable linker to the mAb. The resulting CD79b ADCs, 3 and 4, exhibit in vitro degradation and cytotoxicity comparable with that of 1, and ADC 3 can achieve more sustained in vivo degradation than intravenously administered 1 with markedly reduced systemic exposure of the payload.
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Affiliation(s)
- Alan Zhang
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139 United States
| | - Katherine Seiss
- Oncology Biotherapeutics, Novartis Biomedical Research, Cambridge, Massachusetts 02139 United States
| | - Laurent Laborde
- Oncology, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Sebastian Palacio-Ramirez
- Novartis Biologics Center, Novartis Biomedical Research, Cambridge, Massachusetts 02139 United States
| | - Daniel Guthy
- Oncology, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Mylene Lanter
- Oncology, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Julien Lorber
- Global Discovery Chemistry, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Luca Arista
- Global Discovery Chemistry, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Thomas Zoller
- Global Discovery Chemistry, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | - Claudio Thoma
- Oncology, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Christina Hebach
- Oncology, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - William R Tschantz
- Novartis Biologics Center, Novartis Biomedical Research, Cambridge, Massachusetts 02139 United States
| | - Alexei Karpov
- Global Discovery Chemistry, Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | - Joseph A D'Alessio
- Oncology Biotherapeutics, Novartis Biomedical Research, Cambridge, Massachusetts 02139 United States
| | | | - Matthew T Burger
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139 United States
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24
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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.
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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.
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25
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Yang N, Kong B, Zhu Z, Huang F, Zhang L, Lu T, Chen Y, Zhang Y, Jiang Y. Recent advances in targeted protein degraders as potential therapeutic agents. Mol Divers 2024; 28:309-333. [PMID: 36790583 PMCID: PMC9930057 DOI: 10.1007/s11030-023-10606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/12/2023] [Indexed: 02/16/2023]
Abstract
Targeted protein degradation (TPD) technology has gradually become widespread in the past 20 years, which greatly boosts the development of disease treatment. Contrary to small inhibitors that act on protein kinases, transcription factors, ion channels, and other targets they can bind to, targeted protein degraders could target "undruggable targets" and overcome drug resistance through ubiquitin-proteasome pathway (UPP) and lysosome pathway. Nowadays, some bivalent degraders such as proteolysis-targeting chimeras (PROTACs) have aroused great interest in drug discovery, and some of them have successfully advanced into clinical trials. In this review, to better understand the mechanism of degraders, we elucidate the targeted protein degraders according to their action process, relying on the ubiquitin-proteasome system or lysosome pathway. Then, we briefly summarize the study of PROTACs employing different E3 ligases. Subsequently, the effect of protein of interest (POI) ligands, linker, and E3 ligands on PROTAC degradation activity is also discussed in detail. Other novel technologies based on UPP and lysosome pathway have been discussed in this paper such as in-cell click-formed proteolysis-targeting chimeras (CLIPTACs), molecular glues, Antibody-PROTACs (Ab-PROTACs), autophagy-targeting chimeras, and lysosome-targeting chimeras. Based on the introduction of these degradation technologies, we can clearly understand the action process and degradation mechanism of these approaches. From this perspective, it will be convenient to obtain the development status of these drugs, choose appropriate degradation methods to achieve better disease treatment and provide basis for future research and simultaneously distinguish the direction of future research efforts.
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Affiliation(s)
- Na Yang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Bo Kong
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Zhaohong Zhu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Fei Huang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Liliang Zhang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Tao Lu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, People's Republic of China
| | - Yadong Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China.
| | - Yanmin Zhang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China.
| | - Yulei Jiang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China.
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26
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Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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27
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Berlin M, Cantley J, Bookbinder M, Bortolon E, Broccatelli F, Cadelina G, Chan EW, Chen H, Chen X, Cheng Y, Cheung TK, Davenport K, DiNicola D, Gordon D, Hamman BD, Harbin A, Haskell R, He M, Hole AJ, Januario T, Kerry PS, Koenig SG, Li L, Merchant M, Pérez-Dorado I, Pizzano J, Quinn C, Rose CM, Rousseau E, Soto L, Staben LR, Sun H, Tian Q, Wang J, Wang W, Ye CS, Ye X, Zhang P, Zhou Y, Yauch R, Dragovich PS. PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. J Med Chem 2024; 67:1262-1313. [PMID: 38180485 DOI: 10.1021/acs.jmedchem.3c01781] [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: 01/06/2024]
Abstract
The identification of VHL-binding proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) in SW1573 cell-based experiments is described. These molecules exhibit between 10- and 100-fold degradation selectivity for BRM over the closely related paralog protein BRG1 (SMARCA4). They also selectively impair the proliferation of the H1944 "BRG1-mutant" NSCLC cell line, which lacks functional BRG1 protein and is thus highly dependent on BRM for growth, relative to the wild-type Calu6 line. In vivo experiments performed with a subset of compounds identified PROTACs that potently and selectively degraded BRM in the Calu6 and/or the HCC2302 BRG1 mutant NSCLC xenograft models and also afforded antitumor efficacy in the latter system. Subsequent PK/PD analysis established a need to achieve strong BRM degradation (>95%) in order to trigger meaningful antitumor activity in vivo. Intratumor quantitation of mRNA associated with two genes whose transcription was controlled by BRM (PLAU and KRT80) also supported this conclusion.
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Affiliation(s)
- Michael Berlin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Jennifer Cantley
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mark Bookbinder
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Elizabeth Bortolon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Fabio Broccatelli
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Greg Cadelina
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Emily W Chan
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Huifen Chen
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xin Chen
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Yunxing Cheng
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Tommy K Cheung
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kim Davenport
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Dean DiNicola
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Debbie Gordon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Brian D Hamman
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Alicia Harbin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Roy Haskell
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mingtao He
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Alison J Hole
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Thomas Januario
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Philip S Kerry
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Stefan G Koenig
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Limei Li
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Mark Merchant
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Jennifer Pizzano
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Connor Quinn
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Christopher M Rose
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Emma Rousseau
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leofal Soto
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leanna R Staben
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hongming Sun
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Qingping Tian
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Wang
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Weifeng Wang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Crystal S Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xiaofen Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Penghong Zhang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Yuhui Zhou
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Yauch
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter S Dragovich
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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28
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Amirian R, Azadi Badrbani M, Izadi Z, Samadian H, Bahrami G, Sarvari S, Abdolmaleki S, Nabavi SM, Derakhshankhah H, Jaymand M. Targeted protein modification as a paradigm shift in drug discovery. Eur J Med Chem 2023; 260:115765. [PMID: 37659194 DOI: 10.1016/j.ejmech.2023.115765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Targeted Protein Modification (TPM) is an umbrella term encompassing numerous tools and approaches that use bifunctional agents to induce a desired modification over the POI. The most well-known TPM mechanism is PROTAC-directed protein ubiquitination. PROTAC-based targeted degradation offers several advantages over conventional small-molecule inhibitors, has shifted the drug discovery paradigm, and is acquiring increasing interest as over ten PROTACs have entered clinical trials in the past few years. Targeting the protein of interest for proteasomal degradation by PROTACS was the pioneer of various toolboxes for selective protein degradation. Nowadays, the ever-increasing number of tools and strategies for modulating and modifying the POI has expanded far beyond protein degradation, which phosphorylation and de-phosphorylation of the protein of interest, targeted acetylation, and selective modification of protein O-GlcNAcylation are among them. These novel strategies have opened new avenues for achieving more precise outcomes while remaining feasible and minimizing side effects. This field, however, is still in its infancy and has a long way to precede widespread use and translation into clinical practice. Herein, we investigate the pros and cons of these novel strategies by exploring the latest advancements in this field. Ultimately, we briefly discuss the emerging potential applications of these innovations in cancer therapy, neurodegeneration, viral infections, and autoimmune and inflammatory diseases.
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Affiliation(s)
- Roshanak Amirian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Azadi Badrbani
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hadi Samadian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Gholamreza Bahrami
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sajad Sarvari
- Department of Pharmaceutical Science, School of Pharmacy, West Virginia University, Morgantown, WV, USA.
| | - Sara Abdolmaleki
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Seyed Mohammad Nabavi
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy.
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Zhang C, He Y, Sun X, Wei W, Liu Y, Rao Y. PROTACs Targeting Epigenetic Proteins. ACTA MATERIA MEDICA 2023; 2:409-429. [PMID: 39221114 PMCID: PMC11364368 DOI: 10.15212/amm-2023-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Epigenetics, a field that investigates alterations in gene function that can be inherited without changes in DNA sequence, encompasses molecular pathways such as histone variants, posttranslational modifications of amino acids, and covalent modifications of DNA bases. These pathways modulate the transformation of genotypes into specific phenotypes. Epigenetics plays a substantial role in cell growth, development, and differentiation by dynamically regulating gene transcription and ensuring genomic stability. This regulation is carried out by three key players: writers, readers, and erasers. In recent years, epigenetic proteins have played a crucial role in epigenetic regulation and have gradually become important targets in drug research and development. Targeted therapy is an essential strategy; however, the effectiveness of targeted drugs is often limited by drug resistance, posing a significant dilemma in clinical practice. Targeted protein degradation technologies, including proteolysis-targeting chimeras (PROTACs), have great potential in overcoming drug resistance and targeting undruggable targets. These areas of research are gaining increasing attention to various epigenetic related disease. In this review, we have provided a summary of the recently developed degraders targeting epigenetic readers, writers, and erasers. Additionally, we have outlined new applications for epigenetic protein degraders. Finally, we have addressed several unresolved challenges within the PROTAC field and offered potential solutions from our perspective. As the field continues to advance, the integration of these innovative methodologies holds great promise for addressing the challenges associated with PROTAC development.
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Affiliation(s)
- Chao Zhang
- Changping Laboratory, Beijing 102206, China
| | - Yuna He
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuyun Sun
- Changping Laboratory, Beijing 102206, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yu Rao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
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30
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Hassan MM, Li YD, Ma MW, Teng M, Byun WS, Puvar K, Lumpkin R, Sandoval B, Rutter JC, Jin CY, Wang MY, Xu S, Schmoker AM, Cheong H, Groendyke BJ, Qi J, Fischer ES, Ebert BL, Gray NS. Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.07.561308. [PMID: 37873358 PMCID: PMC10592706 DOI: 10.1101/2023.10.07.561308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4CRBN ligase, have been mostly discovered serendipitously. We recently reported a trans-labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 trans-labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4CRBN glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michelle W. Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cyrus Y. Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna M. Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Hakyung Cheong
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | | | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
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31
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Alameddine R, Mallea P, Shahab F, Zakharia Y. Antibody Drug Conjugates in Bladder Cancer: Current Milestones and Future Perspectives. Curr Treat Options Oncol 2023; 24:1167-1182. [PMID: 37403009 DOI: 10.1007/s11864-023-01114-y] [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] [Accepted: 05/24/2023] [Indexed: 07/06/2023]
Abstract
OPINION STATEMENT Over the last several years, the treatment landscape of urothelial carcinoma has witnessed an unprecedented expansion of therapeutic options including checkpoint inhibitors, tyrosine kinase inhibitors, and antibody drug conjugates (ADC). Early trial data has shown that ADCs are safer and potentially effective treatment options in advanced bladder cancer as well as in the early disease. In particular, enfortumab-vedotin (EV) has shown promising results with a recent cohort of a clinical trial demonstrating that EV is effective as neoadjuvant monotherapy as well as in combination with pembrolizumab in metastatic setting. Similar promising results have been shown by other classes of ADC in other trials including sacituzumab-govitecan (SG) and oportuzumab monatox (OM). ADCs are likely to become a mainstay treatment option in the urothelial carcinoma playbook as either a monotherapy or combination therapy. The cost of the drug presents a real challenge, but further trial data may justify the use of the drug as mainstay treatment.
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Affiliation(s)
- Raafat Alameddine
- Division of Hematology Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Patrick Mallea
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Farhan Shahab
- Department of Emergency Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Yousef Zakharia
- Division of Hematology Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
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32
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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Zhao C, Wang H, Zhan W, Lv X, Ma X. Exploitation of Proximity-Mediated Effects in Drug Discovery: An Update of Recent Research Highlights in Perturbing Pathogenic Proteins and Correlated Issues. J Med Chem 2023; 66:10122-10149. [PMID: 37489834 DOI: 10.1021/acs.jmedchem.3c00079] [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: 07/26/2023]
Abstract
The utilization of proximity-mediated effects to perturb pathogenic proteins of interest (POIs) has emerged as a powerful strategic alternative to conventional drug design approaches based on target occupancy. Over the past three years, the burgeoning field of targeted protein degradation (TPD) has witnessed the expansion of degradable POIs to membrane-associated, extracellular, proteasome-resistant, and even microbial proteins. Beyond TPD, researchers have achieved the proximity-mediated targeted protein stabilization, the recruitment of intracellular immunophilins to disturb undruggable targets, and the nonphysiological post-translational modifications of POIs. All of these strides provide new avenues for innovative drug discovery aimed at battling human malignancies and other major diseases. This perspective presents recent research highlights and discusses correlated issues in developing therapeutic modalities that exploit proximity-mediated effects to modulate pathogenic proteins, thereby guiding future academic and industrial efforts in this field.
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Affiliation(s)
- Can Zhao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Henian Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Wenhu Zhan
- iCarbonX (Shenzhen) Co., Ltd., Shenzhen, 518000, China
| | - Xiaoqing Lv
- College of Medicine, Jiaxing University, Jiaxing 314001, China
| | - Xiaodong Ma
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
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34
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Wang W, Zhu C, Zhang B, Feng Y, Zhang Y, Li J. Self-Assembled Nano-PROTAC Enables Near-Infrared Photodynamic Proteolysis for Cancer Therapy. J Am Chem Soc 2023; 145:16642-16649. [PMID: 37477624 DOI: 10.1021/jacs.3c04109] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Confining the protein degradation activity of proteolysis-targeting chimera (PROTAC) to cancer lesions ensures precision treatment. However, it still remains challenging to precisely control PROTAC function in tumor regions in vivo. We herein describe a near-infrared (NIR) photoactivatable nano-PROTAC (NAP) for remote-controllable proteolysis in tumor-bearing mice. NAP is formed by molecular self-assembly from an amphiphilic conjugate of PROTAC linked with an NIR photosensitizer through a singlet oxygen (1O2)-cleavable linker. The activity of PROTAC is initially silenced but can be remotely switched on upon NIR photoirradiation to generate 1O2 by the photosensitizer. We demonstrated that NAP enabled tumor-specific degradation of bromodomain-containing protein 4 (BRD4) in an NIR light-instructed manner. This in combination with photodynamic therapy (PDT) elicited an effective suppression of tumor growth. This work thus presents a novel approach for spatiotemporal control over targeted protein degradation by PROTAC.
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Affiliation(s)
- Weishan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Chenghong Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Bin Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yi Feng
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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Dumontet C, Reichert JM, Senter PD, Lambert JM, Beck A. Antibody-drug conjugates come of age in oncology. Nat Rev Drug Discov 2023; 22:641-661. [PMID: 37308581 DOI: 10.1038/s41573-023-00709-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 159.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Antibody-drug conjugates (ADCs) combine the specificity of monoclonal antibodies with the potency of highly cytotoxic agents, potentially reducing the severity of side effects by preferentially targeting their payload to the tumour site. ADCs are being increasingly used in combination with other agents, including as first-line cancer therapies. As the technology to produce these complex therapeutics has matured, many more ADCs have been approved or are in late-phase clinical trials. The diversification of antigenic targets as well as bioactive payloads is rapidly broadening the scope of tumour indications for ADCs. Moreover, novel vector protein formats as well as warheads targeting the tumour microenvironment are expected to improve the intratumour distribution or activation of ADCs, and consequently their anticancer activity for difficult-to-treat tumour types. However, toxicity remains a key issue in the development of these agents, and better understanding and management of ADC-related toxicities will be essential for further optimization. This Review provides a broad overview of the recent advances and challenges in ADC development for cancer treatment.
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Affiliation(s)
- Charles Dumontet
- CRCL INSERM 1052/CNRS 5286, University of Lyon, Hospices Civils de Lyon, Lyon, France.
| | | | | | | | - Alain Beck
- Institut de Recherche Pierre Fabre, CIPF, Saint-Julien-en-Genevois, France
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Wang H, Zhou R, Xu F, Yang K, Zheng L, Zhao P, Shi G, Dai L, Xu C, Yu L, Li Z, Wang J, Wang J. Beyond canonical PROTAC: biological targeted protein degradation (bioTPD). Biomater Res 2023; 27:72. [PMID: 37480049 PMCID: PMC10362593 DOI: 10.1186/s40824-023-00385-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/21/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy with the potential to modulate disease-associated proteins that have previously been considered undruggable, by employing the host destruction machinery. The exploration and discovery of cellular degradation pathways, including but not limited to proteasomes and lysosome pathways as well as their degraders, is an area of active research. Since the concept of proteolysis-targeting chimeras (PROTACs) was introduced in 2001, the paradigm of TPD has been greatly expanded and moved from academia to industry for clinical translation, with small-molecule TPD being particularly represented. As an indispensable part of TPD, biological TPD (bioTPD) technologies including peptide-, fusion protein-, antibody-, nucleic acid-based bioTPD and others have also emerged and undergone significant advancement in recent years, demonstrating unique and promising activities beyond those of conventional small-molecule TPD. In this review, we provide an overview of recent advances in bioTPD technologies, summarize their compositional features and potential applications, and briefly discuss their drawbacks. Moreover, we present some strategies to improve the delivery efficacy of bioTPD, addressing their challenges in further clinical development.
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Affiliation(s)
- Huifang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Runhua Zhou
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Fushan Xu
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Kongjun Yang
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Liuhai Zheng
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Pan Zhao
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Guangwei Shi
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Lingyun Dai
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Chengchao Xu
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Le Yu
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
| | - Zhijie Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jianhong Wang
- Shenzhen Mental Health Center, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jigang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China.
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Chang M, Gao F, Pontigon D, Gnawali G, Xu H, Wang W. Bioorthogonal PROTAC Prodrugs Enabled by On-Target Activation. J Am Chem Soc 2023; 145:14155-14163. [PMID: 37327395 PMCID: PMC11249063 DOI: 10.1021/jacs.3c05159] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although proteolysis targeting chimeras (PROTACs) have become promising therapeutic modalities, important concerns exist about the potential toxicity of the approach owing to uncontrolled degradation of proteins and undesirable ligase-mediated off-target effects. Precision manipulation of degradation activity of PROTACs could minimize potential toxicity and side effects. As a result, extensive efforts have been devoted to developing cancer biomarker activating prodrugs of PROTACs. In this investigation, we developed a bioorthogonal on-demand prodrug strategy (termed click-release "crPROTACs") that enables on-target activation of PROTAC prodrugs and release of PROTACs in cancer cells selectively. Inactive PROTAC prodrugs TCO-ARV-771 and TCO-DT2216 are rationally designed by conjugating a bioorthogonal trans-cyclooctenes (TCO) group into the ligand of the VHL E3 ubiquitin ligase. The tetrazine (Tz)-modified RGD peptide, c(RGDyK)-Tz, which targets integrin αvβ3 biomarker in cancer cells, serves as the activation component for click-release of the PROTAC prodrugs to achieve targeted degradation of proteins of interest (POIs) in cancer cells versus noncancerous normal cells. The results of studies accessing the viability of this strategy show that the PROTAC prodrugs are selectively activated in an integrin αvβ3-dependent manner to produce PROTACs, which degrade POIs in cancer cells. The crPROTAC strategy might be a general, abiotic approach to induce selective cancer cell death through the ubiquitin-proteasome pathway.
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Affiliation(s)
- Mengyang Chang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Feng Gao
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Devin Pontigon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giri Gnawali
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Hang Xu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85721, United States
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38
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Tashima T. Proteolysis-Targeting Chimera (PROTAC) Delivery into the Brain across the Blood-Brain Barrier. Antibodies (Basel) 2023; 12:43. [PMID: 37489365 PMCID: PMC10366925 DOI: 10.3390/antib12030043] [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: 04/22/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 07/26/2023] Open
Abstract
Drug development for neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease has challenging difficulties due to the pharmacokinetic impermeability based on the blood-brain barrier (BBB) as well as the blurriness of pharmacodynamic targets based on their unclarified pathogenesis and complicated progression mechanisms. Thus, in order to produce innovative central nervous system (CNS) agents for patients suffering from CNS diseases, effective, selective delivery of CNS agents into the brain across the BBB should be developed. Currently, proteolysis-targeting chimeras (PROTACs) attract rising attention as a new modality to degrade arbitrary intracellular proteins by the ubiquitin-proteasome system. The internalizations of peptide-based PROTACs by cell-penetrating peptides and that of small molecule-based PROTACs through passive diffusion lack cell selectivity. Therefore, these approaches may bring off-target side effects due to wrong distribution. Furthermore, efflux transporters such as multiple drug resistance 1 (MDR1) expressed at the BBB might interrupt the entry of small molecule-based PROTACs into the brain. Nonetheless, intelligent delivery using machinery systems to absorb the nutrition into the brain for homeostasis, such as carrier-mediated transport (CMT) or receptor-mediated transcytosis (RMT), can be established. PROTACs with N-containing groups that are recognized by the proton-coupled organic cation antiporter might cross the BBB through CMT. PROTAC-antibody conjugates (PACs) might cross the BBB through RMT. Subsequently, such small molecule-based PROTACs released in the brain interstitial fluid would be transported into cells such as neurons through passive diffusion and then demonstrate arbitrary protein degradation. In this review, I introduce the potential and advantages of PROTAC delivery into the brain across the BBB through CMT or RMT using PACs in a non-invasive way.
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Affiliation(s)
- Toshihiko Tashima
- Tashima Laboratories of Arts and Sciences, 1239-5 Toriyama-cho, Kohoku-ku, Yokohama 222-0035, Japan
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Liang J, Wu Y, Lan K, Dong C, Wu S, Li S, Zhou HB. Antiviral PROTACs: Opportunity borne with challenge. CELL INSIGHT 2023; 2:100092. [PMID: 37398636 PMCID: PMC10308200 DOI: 10.1016/j.cellin.2023.100092] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 07/04/2023]
Abstract
Proteolysis targeting chimera (PROTAC) degradation of pathogenic proteins by hijacking of the ubiquitin-proteasome-system has become a promising strategy in drug design. The overwhelming advantages of PROTAC technology have ensured a rapid and wide usage, and multiple PROTACs have entered clinical trials. Several antiviral PROTACs have been developed with promising bioactivities against various pathogenic viruses. However, the number of reported antiviral PROTACs is far less than that of other diseases, e.g., cancers, immune disorders, and neurodegenerative diseases, possibly because of the common deficiencies of PROTAC technology (e.g., limited available ligands and poor membrane permeability) plus the complex mechanism involved and the high tendency of viral mutation during transmission and replication, which may challenge the successful development of effective antiviral PROTACs. This review highlights the important advances in this rapidly growing field and critical limitations encountered in developing antiviral PROTACs by analyzing the current status and representative examples of antiviral PROTACs and other PROTAC-like antiviral agents. We also summarize and analyze the general principles and strategies for antiviral PROTAC design and optimization with the intent of indicating the potential strategic directions for future progress.
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Affiliation(s)
- Jinsen Liang
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Yihe Wu
- Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chune Dong
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shu Li
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Hai-Bing Zhou
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
- Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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Gao J, Yang L, Lei S, Zhou F, Nie H, Peng B, Xu T, Chen X, Yang X, Sheng C, Rao Y, Pu K, Jin J, Xu Z, Yu H. Stimuli-activatable PROTACs for precise protein degradation and cancer therapy. Sci Bull (Beijing) 2023; 68:1069-1085. [PMID: 37169612 DOI: 10.1016/j.scib.2023.04.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
The proteolysis targeting chimeras (PROTACs) approach has attracted extensive attention in the past decade, which represents an emerging therapeutic modality with the potential to tackle disease-causing proteins that are historically challengeable for conventional small molecular inhibitors. PROTAC harnesses the endogenic E3 ubiquitin ligase to degrade protein of interest (POI) via ubiquitin-proteasome system in a cycle-catalytic manner. The event-driven pharmacology of PROTAC is poised to pursue those targets that are conventionally undruggable, which enormously extends the space of drug development. Furthermore, PROTAC has the potential to address drug resistance of small molecular inhibitors by degrading the whole POI. Nevertheless, PROTACs display high-efficiency and always-on properties to degrade POI, they may cause severe side effects due to an "on-target but off-tissue" protein degradation profile at the undesirable tissues and cells. Given that, the stimuli-activatable PROTAC prodrugs have been recently exploited to confine precise protein degradation of the favorable targets, which may conquer the adverse effects of PROTAC due to uncontrollable protein degradation. Herein, we summarized the cutting-edge advances of the stimuli-activatable PROTAC prodrugs. We also overviewed the progress of PROTAC prodrug-based nanomedicine to improve PROTAC delivery to the tumors and precise POI degradation in the targeted cells.
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Affiliation(s)
- Jing Gao
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lei Yang
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shumin Lei
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feng Zhou
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huijun Nie
- Center of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bo Peng
- Information Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tianfeng Xu
- Center of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaohua Chen
- Center of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiaobao Yang
- Gluetacs Therapeutics (Shanghai) Co., Ltd. Shanghai 201306, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Yu Rao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York NY 10029, USA
| | - Zhiai Xu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Haijun Yu
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Qian L, Lin X, Gao X, Khan RU, Liao JY, Du S, Ge J, Zeng S, Yao SQ. The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics. Chem Rev 2023. [PMID: 37186942 DOI: 10.1021/acs.chemrev.2c00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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Lahnif H, Grus T, Salvanou EA, Deligianni E, Stellas D, Bouziotis P, Rösch F. Old Drug, New Delivery Strategy: MMAE Repackaged. Int J Mol Sci 2023; 24:ijms24108543. [PMID: 37239890 DOI: 10.3390/ijms24108543] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Targeting therapy is a concept that has gained significant importance in recent years, especially in oncology. The severe dose-limiting side effects of chemotherapy necessitate the development of novel, efficient and tolerable therapy approaches. In this regard, the prostate specific membrane antigene (PSMA) has been well established as a molecular target for diagnosis of, as well as therapy for, prostate cancer. Although most PSMA-targeting ligands are radiopharmaceuticals used in imaging or radioligand therapy, this article evaluates a PSMA-targeting small molecule-drug conjugate, and, thus, addresses a hitherto little-explored field. PSMA binding affinity and cytotoxicity were determined in vitro using cell-based assays. Enzyme-specific cleavage of the active drug was quantified via an enzyme-based assay. Efficacy and tolerability in vivo were assessed using an LNCaP xenograft model. Histopathological characterization of the tumor in terms of apoptotic status and proliferation rate was carried out using caspase-3 and Ki67 staining. The binding affinity of the Monomethyl auristatin E (MMAE) conjugate was moderate, compared to the drug-free PSMA ligand. Cytotoxicity in vitro was in the nanomolar range. Both binding and cytotoxicity were found to be PSMA-specific. Additionally, complete MMAE release could be reached after incubation with cathepsin B. In vivo, the MMAE conjugate displayed good tolerability and dose-dependent inhibition of tumor growth. Immunohistochemical and histological studies revealed the antitumor effect of MMAE.VC.SA.617, resulting in the inhibition of proliferation and the enhancement of apoptosis. The developed MMAE conjugate showed good properties in vitro, as well as in vivo, and should, therefore, be considered a promising candidate for a translational approach.
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Affiliation(s)
- Hanane Lahnif
- Department of Chemistry-TRIGA Site, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Tilmann Grus
- Department of Chemistry-TRIGA Site, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Evangelia-Alexandra Salvanou
- Radiochemical Studies Laboratory, INRASTES, National Center for Scientific Research "Demokritos", Ag. Paraskevi, 15341 Athens, Greece
| | - Elisavet Deligianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Dimitris Stellas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Penelope Bouziotis
- Radiochemical Studies Laboratory, INRASTES, National Center for Scientific Research "Demokritos", Ag. Paraskevi, 15341 Athens, Greece
| | - Frank Rösch
- Department of Chemistry-TRIGA Site, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
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Yan Z, Lyu X, Lin D, Wu G, Gong Y, Ren X, Xiao J, Lou J, Huang H, Chen Y, Zhao Y. Selective degradation of cellular BRD3 and BRD4-L promoted by PROTAC molecules in six cancer cell lines. Eur J Med Chem 2023; 254:115381. [PMID: 37084596 DOI: 10.1016/j.ejmech.2023.115381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Targeted degradation of BET family proteins BRD2/3/4 or only BRD4 with PROTAC molecules has been a promising strategy for the treatment of human cancer. Meanwhile, selective degradation of cellular BRD3 and BRD4-L remains a challenging task. We report herein a novel PROTAC molecule 24 that promoted selective degradation of cellular BRD3 and BRD4-L, but not BRD2 or BRD4-S, in a panel of six cancer cell lines. The observed target selectivity was partially attributed to differences in protein degradation kinetics and in types of cell lines. In a MM.1S mouse xenograft model, an optimized lead compound 28 promoted selective degradation of BRD3 and BRD4-L in vivo and exhibited robust antitumor activity. In summary, we have demonstrated that selective degradation of BRD3 and BRD4-L over BRD2 and BRD4-S is a feasible and robust approach in multiple cancer cell lines and an animal model, which could be helpful for further investigations on BRD3 and BRD4-L that ultimately benefitting cancer research and therapeutics.
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Affiliation(s)
- Ziqin Yan
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Dongze Lin
- Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Gaoxing Wu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yang Gong
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, China
| | - Xuelian Ren
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Jian Xiao
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Jianfeng Lou
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - He Huang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Yi Chen
- Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China.
| | - Yujun Zhao
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan, 250101, China.
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Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc 2023; 145:7123-7135. [PMID: 36961978 PMCID: PMC10240388 DOI: 10.1021/jacs.2c09387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The design of PROteolysis-TArgeting Chimeras (PROTACs) requires bringing an E3 ligase into proximity with a target protein to modulate the concentration of the latter through its ubiquitination and degradation. Here, we present a method for generating high-accuracy structural models of E3 ligase-PROTAC-target protein ternary complexes. The method is dependent on two computational innovations: adding a "silent" convolution term to an efficient protein-protein docking program to eliminate protein poses that do not have acceptable linker conformations and clustering models of multiple PROTACs that use the same E3 ligase and target the same protein. Results show that the largest consensus clusters always have high predictive accuracy and that the ensemble of models can be used to predict the dissociation rate and cooperativity of the ternary complex that relate to the degrading activity of the PROTAC. The method is demonstrated by applications to known PROTAC structures and a blind test involving PROTACs against BRAF mutant V600E. The results confirm that PROTACs function by stabilizing a favorable interaction between the E3 ligase and the target protein but do not necessarily exploit the most energetically favorable geometry for interaction between the proteins.
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Affiliation(s)
- Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Akhil Jindal
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Acpharis Inc., Holliston, Massachusetts 01746, USA
| | - Ganna Posternak
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Xiaojing Tang
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Pierre Maisonneuve
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario L4K-M9W, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario L4K-M9W, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
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Xue Y, Bolinger AA, Zhou J. Novel approaches to targeted protein degradation technologies in drug discovery. Expert Opin Drug Discov 2023; 18:467-483. [PMID: 36895136 PMCID: PMC11089573 DOI: 10.1080/17460441.2023.2187777] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
INTRODUCTION Target protein degradation (TPD) provides a novel therapeutic modality, other than inhibition, through the direct depletion of target proteins. Two primary human protein homeostasis mechanisms are exploited: the ubiquitin-proteasome system (UPS) and the lysosomal system. TPD technologies based on these two systems are progressing at an impressive pace. AREAS COVERED This review focuses on the TPD strategies based on UPS and lysosomal system, mainly classified into three types: Molecular Glue (MG), PROteolysis Targeting Chimera (PROTAC), and lysosome-mediated TPD. Starting with a brief background introduction of each strategy, exciting examples and perspectives on these novel approaches are provided. EXPERT OPINION MGs and PROTACs are two major UPS-based TPD strategies that have been extensively investigated in the past decade. Despite some clinical trials, several critical issues remain, among which is emphasized by the limitation of targets. Recently developed lysosomal system-based approaches provide alternative solutions for TPD beyond UPS' capability. The newly emerging novel approaches may partially address issues that have long plagued researchers, such as low potency, poor cell permeability, on-/off-target toxicity, and delivery efficiency. Comprehensive considerations for the rational design of protein degraders and continuous efforts to seek effective solutions are imperative to advance these strategies into clinical medications.
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Affiliation(s)
- Yu Xue
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
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Jin Y, Fan J, Wang R, Wang X, Li N, You Q, Jiang Z. Ligation to Scavenging Strategy Enables On-Demand Termination of Targeted Protein Degradation. J Am Chem Soc 2023; 145:7218-7229. [PMID: 36971523 DOI: 10.1021/jacs.2c12809] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Event-driven bifunctional molecules, typified by proteolysis targeting chimera (PROTAC) technology, have been successfully applied in degrading many proteins of interest (POI). Due to the unique catalytic mechanism, PROTACs will induce multiple cycles of degradation until the elimination of the target protein. Here, we propose a versatile "Ligation to scavenging" approach to terminate event-driven degradation for the first time. Ligation to the scavenging system consists of a TCO-modified dendrimer (PAMAM-G5-TCO) and tetrazine-modified PROTACs (Tz-PROTACs). PAMAM-G5-TCO can rapidly scavenge intracellular free PROTACs via an inverse electron demand Diels-Alder reaction and terminate the degradation of certain proteins in living cells. Thus, this work proposes a flexible chemical knockdown approach to adjust the levels of POI on-demand in living cells, which paves the way for controlled target protein degradation.
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Zhu H, Wang J, Zhang Q, Pan X, Zhang J. Novel strategies and promising opportunities for targeted protein degradation: An innovative therapeutic approach to overcome cancer resistance. Pharmacol Ther 2023; 244:108371. [PMID: 36871783 DOI: 10.1016/j.pharmthera.2023.108371] [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: 12/31/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Targeted Protein Degradation is an emerging and rapidly developing technique for designing and treating new drugs. With the emergence of a promising class of pharmaceutical molecules, Heterobifunctional Proteolysis-targeting chimeras (PROTACs), TPD has become a powerful tool to completely tackle pathogenic proteins with traditional small molecule inhibitors. However, the conventional PROTACs have gradually exposed potential disadvantages of poor oral bioavailability and pharmacokinetic (PK) and absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics due to their larger molecular weight and more complex structure than the conventional small-molecule inhibitors. Therefore, 20 years after the concept of PROTAC was proposed, more and more scientists are committed to developing new TPD technology to overcome its defects. And several new technologies and means have been explored based on "PROTAC" to target "undruggable proteins". Here, we aim to comprehensively summarize and profoundly analyze the research progress of targeted protein degradation based on PROTAC targeting the degradation of "undruggable" targets. In order to clarify the significance of emerging and highly effective strategies based PROTACs in the treatment of various diseases especially in overcoming drug resistance in cancer, we will focus on the molecular structure, action mechanism, design concepts, development advantages and challenges of these emerging methods(e.g., aptamer-PROTAC conjugates, antibody-PROTACs and folate-PROTACs).
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Affiliation(s)
- Huanjie Zhu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jin Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qingqing Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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O'Brien Laramy MN, Luthra S, Brown MF, Bartlett DW. Delivering on the promise of protein degraders. Nat Rev Drug Discov 2023; 22:410-427. [PMID: 36810917 DOI: 10.1038/s41573-023-00652-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/23/2023]
Abstract
Over the past 3 years, the first bivalent protein degraders intentionally designed for targeted protein degradation (TPD) have advanced to clinical trials, with an initial focus on established targets. Most of these clinical candidates are designed for oral administration, and many discovery efforts appear to be similarly focused. As we look towards the future, we propose that an oral-centric discovery paradigm will overly constrain the chemical designs that are considered and limit the potential to drug novel targets. In this Perspective, we summarize the current state of the bivalent degrader modality and propose three categories of degrader designs, based on their likely route of administration and requirement for drug delivery technologies. We then describe a vision for how parenteral drug delivery, implemented early in research and supported by pharmacokinetic-pharmacodynamic modelling, can enable exploration of a broader drug design space, expand the scope of accessible targets and deliver on the promise of protein degraders as a therapeutic modality.
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Affiliation(s)
| | - Suman Luthra
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, MA, USA
| | - Matthew F Brown
- Discovery Sciences, Worldwide Research, Development, and Medical, Pfizer Inc., Groton, CT, USA
| | - Derek W Bartlett
- Pharmacokinetics, Dynamics, & Metabolism, Worldwide Research, Development, and Medical, Pfizer Inc., San Diego, CA, USA
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Park D, Izaguirre J, Coffey R, Xu H. Modeling the Effect of Cooperativity in Ternary Complex Formation and Targeted Protein Degradation Mediated by Heterobifunctional Degraders. ACS BIO & MED CHEM AU 2023; 3:74-86. [PMID: 37101604 PMCID: PMC10125322 DOI: 10.1021/acsbiomedchemau.2c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Chemically induced proximity between certain endogenous enzymes and a protein of interest (POI) inside cells may cause post-translational modifications to the POI with biological consequences and potential therapeutic effects. Heterobifunctional (HBF) molecules that bind with one functional part to a target POI and with the other to an E3 ligase induce the formation of a target-HBF-E3 ternary complex, which can lead to ubiquitination and proteasomal degradation of the POI. Targeted protein degradation (TPD) by HBFs offers a promising approach to modulate disease-associated proteins, especially those that are intractable using other therapeutic approaches, such as enzymatic inhibition. The three-way interactions among the HBF, the target POI, and the ligase-including the protein-protein interaction between the POI and the ligase-contribute to the stability of the ternary complex, manifested as positive or negative binding cooperativity in its formation. How such cooperativity affects HBF-mediated degradation is an open question. In this work, we develop a pharmacodynamic model that describes the kinetics of the key reactions in the TPD process, and we use this model to investigate the role of cooperativity in the ternary complex formation and in the target POI degradation. Our model establishes the quantitative connection between the ternary complex stability and the degradation efficiency through the former's effect on the rate of catalytic turnover. We also develop a statistical inference model for determining cooperativity in intracellular ternary complex formation from cellular assay data and demonstrate it by quantifying the change in cooperativity due to site-directed mutagenesis at the POI-ligase interface of the SMARCA2-ACBI1-VHL ternary complex. Our pharmacodynamic model provides a quantitative framework to dissect the complex HBF-mediated TPD process and may inform the rational design of effective HBF degraders.
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Affiliation(s)
- Daniel Park
- Roivant Discovery, New York, New York10036, United States
| | | | - Rory Coffey
- Roivant Discovery, New York, New York10036, United States
| | - Huafeng Xu
- Roivant Discovery, New York, New York10036, United States
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Holz E, Darwish M, Tesar DB, Shatz-Binder W. A Review of Protein- and Peptide-Based Chemical Conjugates: Past, Present, and Future. Pharmaceutics 2023; 15:600. [PMID: 36839922 PMCID: PMC9959917 DOI: 10.3390/pharmaceutics15020600] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Over the past few decades, the complexity of molecular entities being advanced for therapeutic purposes has continued to evolve. A main propellent fueling innovation is the perpetual mandate within the pharmaceutical industry to meet the needs of novel disease areas and/or delivery challenges. As new mechanisms of action are uncovered, and as our understanding of existing mechanisms grows, the properties that are required and/or leveraged to enable therapeutic development continue to expand. One rapidly evolving area of interest is that of chemically enhanced peptide and protein therapeutics. While a variety of conjugate molecules such as antibody-drug conjugates, peptide/protein-PEG conjugates, and protein conjugate vaccines are already well established, others, such as antibody-oligonucleotide conjugates and peptide/protein conjugates using non-PEG polymers, are newer to clinical development. This review will evaluate the current development landscape of protein-based chemical conjugates with special attention to considerations such as modulation of pharmacokinetics, safety/tolerability, and entry into difficult to access targets, as well as bioavailability. Furthermore, for the purpose of this review, the types of molecules discussed are divided into two categories: (1) therapeutics that are enhanced by protein or peptide bioconjugation, and (2) protein and peptide therapeutics that require chemical modifications. Overall, the breadth of novel peptide- or protein-based therapeutics moving through the pipeline each year supports a path forward for the pursuit of even more complex therapeutic strategies.
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Affiliation(s)
- Emily Holz
- Department of Pharmaceutical Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Martine Darwish
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Devin B. Tesar
- Department of Pharmaceutical Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Whitney Shatz-Binder
- Department of Pharmaceutical Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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