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Wells JA, Kumru K. Extracellular targeted protein degradation: an emerging modality for drug discovery. Nat Rev Drug Discov 2024; 23:126-140. [PMID: 38062152 DOI: 10.1038/s41573-023-00833-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2023] [Indexed: 02/08/2024]
Abstract
Targeted protein degradation (TPD) has emerged in the past decade as a major new drug modality to remove intracellular proteins with bispecific small molecules that recruit the protein of interest (POI) to an E3 ligase for degradation in the proteasome. Unlike classic occupancy-based drugs, intracellular TPD (iTPD) eliminates the target and works catalytically, and so can be more effective and sustained, with lower dose requirements. Recently, this approach has been expanded to the extracellular proteome, including both secreted and membrane proteins. Extracellular targeted protein degradation (eTPD) uses bispecific antibodies, conjugates or small molecules to degrade extracellular POIs by trafficking them to the lysosome for degradation. Here, we focus on recent advances in eTPD, covering degrader systems, targets, molecular designs and parameters to advance them. Now almost any protein, intracellular or extracellular, is addressable in principle with TPD.
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Affiliation(s)
- James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| | - Kaan Kumru
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
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2
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Shen F, Dassama LMK. Opportunities and challenges of protein-based targeted protein degradation. Chem Sci 2023; 14:8433-8447. [PMID: 37592990 PMCID: PMC10430753 DOI: 10.1039/d3sc02361c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/02/2023] [Indexed: 08/19/2023] Open
Abstract
In the 20 years since the first report of a proteolysis targeting chimeric (PROTAC) molecule, targeted protein degradation (TPD) technologies have attempted to revolutionize the fields of chemical biology and biomedicine by providing exciting research opportunities and potential therapeutics. However, they primarily focus on the use of small molecules to recruit the ubiquitin proteasome system to mediate target protein degradation. This then limits protein targets to cytosolic domains with accessible and suitable small molecule binding pockets. In recent years, biologics such as proteins and nucleic acids have instead been used as binders for targeting proteins, thereby expanding the scope of TPD platforms to include secreted proteins, transmembrane proteins, and soluble but highly disordered intracellular proteins. This perspective summarizes the recent TPD platforms that utilize nanobodies, antibodies, and other proteins as binding moieties to deplete challenging targets, either through the ubiquitin proteasome system or the lysosomal degradation pathway. Importantly, the perspective also highlights opportunities and remaining challenges of current protein-based TPD technologies.
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Affiliation(s)
- Fangfang Shen
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
| | - Laura M K Dassama
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
- Department of Microbiology & Immunology, Stanford School of Medicine USA
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3
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Qin K, Lan X, Huang P, Saari MS, Khandros E, Keller CA, Giardine B, Abdulmalik O, Shi J, Hardison RC, Blobel GA. Molecular basis of polycomb group protein-mediated fetal hemoglobin repression. Blood 2023; 141:2756-2770. [PMID: 36893455 PMCID: PMC10273169 DOI: 10.1182/blood.2022019578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
The switch from fetal hemoglobin (HbF) to adult hemoglobin (HbA) is a paradigm for developmental gene expression control with relevance to sickle cell disease and β-thalassemia. Polycomb repressive complex (PRC) proteins regulate this switch, and an inhibitor of PRC2 has entered a clinical trial for HbF activation. Yet, how PRC complexes function in this process, their target genes, and relevant subunit composition are unknown. Here, we identified the PRC1 subunit BMI1 as a novel HbF repressor. We uncovered the RNA binding proteins LIN28B, IGF2BP1, and IGF2BP3 genes as direct BMI1 targets, and demonstrate that they account for the entirety of BMI1's effect on HbF regulation. BMI1 functions as part of the canonical PRC1 (cPRC1) subcomplex as revealed by the physical and functional dissection of BMI1 protein partners. Lastly, we demonstrate that BMI1/cPRC1 acts in concert with PRC2 to repress HbF through the same target genes. Our study illuminates how PRC silences HbF, highlighting an epigenetic mechanism involved in hemoglobin switching.
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Affiliation(s)
- Kunhua Qin
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Xianjiang Lan
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Huang
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Megan S. Saari
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Eugene Khandros
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Osheiza Abdulmalik
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Gerd A. Blobel
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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4
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Emerging Strategies in Proteolysis-Targeting Chimeras (PROTACs): Highlights from 2022. Int J Mol Sci 2023; 24:ijms24065190. [PMID: 36982263 PMCID: PMC10049114 DOI: 10.3390/ijms24065190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Targeted protein degradation (TPD) is a promising therapeutic modality that has garnered attention in academic, industrial, and pharmaceutical research for treating diseases such as cancer, neurodegenerative disorders, inflammation, and viral infections. In this context, proteolysis-targeting chimeras (PROTACs) present a reliable technology for degrading disease-causing proteins. PROTACs complement small-molecule inhibitors, which primarily rely on direct protein regulation. From concept-to-clinic, PROTACs have evolved from cell impermeable peptide molecules to orally bioavailable drugs. Despite their potential in medicinal chemistry, certain aspects regarding PROTACs remain unclear. The clinical significance of PROTACs is primarily limited owing to their lack of selectivity and drug-like properties. This review focused on recently reported PROTAC strategies, particularly in 2022. It aimed to address and overcome the challenges posed by classical PROTACs by correlating them with emerging approaches with improved selectivity and controllability, cell permeability, linker flexibility, druggability, and PROTAC-based approaches, developed in 2022. Furthermore, recently reported PROTAC-based approaches are discussed, highlighting each of their advantages and limitations. We predict that several improved PROTAC molecules will be accessible for treating patients exhibiting various conditions, including cancer, neurodegenerative disorders, inflammation, and viral infections.
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Shen F, Zheng G, Setegne M, Tenglin K, Izadi M, Xie H, Zhai L, Orkin SH, Dassama LMK. A Cell-Permeant Nanobody-Based Degrader That Induces Fetal Hemoglobin. ACS CENTRAL SCIENCE 2022; 8:1695-1703. [PMID: 36589886 PMCID: PMC9801508 DOI: 10.1021/acscentsci.2c00998] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 06/13/2023]
Abstract
Proximity-based strategies to degrade proteins have enormous therapeutic potential in medicine, but the technologies are limited to proteins for which small molecule ligands exist. The identification of such ligands for therapeutically relevant but "undruggable" proteins remains challenging. Herein, we employed yeast surface display of synthetic nanobodies to identify a protein ligand selective for BCL11A, a critical repressor of fetal globin gene transcription. Fusion of the nanobody to a cell-permeant miniature protein and an E3 adaptor creates a degrader that depletes cellular BCL11A in differentiated primary erythroid precursor cells, thereby inducing the expression of fetal hemoglobin, a modifier of clinical severity of sickle cell disease and β-thalassemia. Our strategy provides a means of fetal hemoglobin induction through reversible, temporal modulation of BCL11A. Additionally, it establishes a new paradigm for the targeted degradation of previously intractable proteins.
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Affiliation(s)
- Fangfang Shen
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Ge Zheng
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mekedlawit Setegne
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Karin Tenglin
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Manizheh Izadi
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
| | - Henry Xie
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Liting Zhai
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Stuart H. Orkin
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura M. K. Dassama
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
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Mehta S, Buyanbat A, Kai Y, Karayel O, Goldman SR, Seruggia D, Zhang K, Fujiwara Y, Donovan KA, Zhu Q, Yang H, Nabet B, Gray NS, Mann M, Fischer ES, Adelman K, Orkin SH. Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells. Cell Chem Biol 2022; 29:1273-1287.e8. [PMID: 35839780 PMCID: PMC9391307 DOI: 10.1016/j.chembiol.2022.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/01/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022]
Abstract
Reactivation of fetal hemoglobin expression by the downregulation of BCL11A is a promising treatment for β-hemoglobinopathies. A detailed understanding of BCL11A-mediated repression of γ-globin gene (HBG1/2) transcription is lacking, as studies to date used perturbations by shRNA or CRISPR-Cas9 gene editing. We leveraged the dTAG PROTAC degradation platform to acutely deplete BCL11A protein in erythroid cells and examined consequences by nascent transcriptomics, proteomics, chromatin accessibility, and histone profiling. Among 31 genes repressed by BCL11A, HBG1/2 and HBZ show the most abundant and progressive changes in transcription and chromatin accessibility upon BCL11A loss. Transcriptional changes at HBG1/2 were detected in <2 h. Robust HBG1/2 reactivation upon acute BCL11A depletion occurred without the loss of promoter 5-methylcytosine (5mC). Using targeted protein degradation, we establish a hierarchy of gene reactivation at BCL11A targets, in which nascent transcription is followed by increased chromatin accessibility, and both are uncoupled from promoter DNA methylation at the HBG1/2 loci.
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Affiliation(s)
- Stuti Mehta
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Altantsetseg Buyanbat
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Yan Kai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Planegg, Germany
| | - Seth Raphael Goldman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Davide Seruggia
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kevin Zhang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Yuko Fujiwara
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Qian Zhu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Huan Yang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Planegg, Germany
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Howard Hughes Medical Institute and Harvard Medical School, Boston, MA 02115, USA.
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Tesarik J, Mendoza-Tesarik R. Patient-tailored reproductive health care. FRONTIERS IN REPRODUCTIVE HEALTH 2022; 4:917159. [PMID: 36303620 PMCID: PMC9580787 DOI: 10.3389/frph.2022.917159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022] Open
Abstract
Patient-tailored reproductive health care represents an important challenge for the current practice of infertility prevention, diagnosis and treatment. This approach is based on the concept of precision medicine, taking into account genetic, epigenetic, metabolic and lifestyle characteristics of each individual patient. Even though this goal is still far from being wholly achieved, some aspects can already be put into practice nowadays. Personalization can be based on a comprehensive analysis and synthesis of the patients' personal and familial history, taking into account outcomes of previous assisted reproduction technique (ART) attempts, if available, and confronting these data with the past and the latest clinical and laboratory examination outcomes. As to the male fertility status, there is an urgent need for the inclusion of an accurate diagnostic workup of infertile men leading to the choice of the most adequate follow-up for each particular pathological condition. The follow-up of women who have become pregnant as a result of the ART attempt has also to be personalized. This should be done taking into account both the basic data extracted from the patient's file and those derived from the experience gathered during the latest attempt. Last but not least, the individual condition of each couple has to be taken into account when counseling the patients as to the urgency of the actions to be taken to resolve their fertility problem.
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Steinberg MH. World Sickle Cell Day 2022: Progress & prospects. Indian J Med Res 2022; 156:10-13. [PMID: 35946231 PMCID: PMC9903380 DOI: 10.4103/ijmr.ijmr_1049_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Martin H. Steinberg
- Department of Medicine, Division of Hematology & Medical Oncology, Center of Excellence for Sickle Cell Disease, Boston University School of Medicine & Boston Medical Center, Boston, MA, USA
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Abstract
INTRODUCTION Sickle cell disease and β thalassemia are the principal β hemoglobinopathies. The complex pathophysiology of sickle cell disease is initiated by sickle hemoglobin polymerization. In β thalassemia, insufficient β-globin synthesis results in excessive free α globin, ineffective erythropoiesis and severe anemia. Fetal hemoglobin (HbF) prevents sickle hemoglobin polymerization; in β thalassemia HbF compensates for the deficit of normal hemoglobin. When HbF constitutes about a third of total cell hemoglobin, the complications of sickle cell disease are nearly totally prevented. Similarly, sufficient HbF in β thalassemia diminishes or prevents ineffective erythropoiesis and hemolysis. AREAS COVERED This article examines the pathophysiology of β hemoglobinopathies, the physiology of HbF, intracellular distribution and the regulation of HbF expression. Inducing high levels of HbF by targeting its regulatory pathways pharmacologically or with cell-based therapeutics provides major clinical benefit and perhaps a "cure." EXPERT OPINION Erythrocytes must contain about 10 pg of HbF to "cure" sickle cell disease. If HbF is the only hemoglobin present, much higher levels are needed to "cure" β thalassemia. These levels of HbF can be obtained by different iterations of gene therapy. Small molecule drugs that can achieve even modest pancellular HbF concentrations are a major unmet need.
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Affiliation(s)
- Martin H Steinberg
- Professor of Medicine, Pediatrics, Pathology and Laboratory Medicine, Boston University School of Medicine.,Department of Medicine, Division of Hematology/Oncology, Center of Excellence for Sickle Cell Disease, Boston University School of Medicine, 72 East Concord St., Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 72 E. Concord St. Boston, MA 02118. ., Tel
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Salinas Cisneros G, Thein SL. Research in Sickle Cell Disease: From Bedside to Bench to Bedside. Hemasphere 2021; 5:e584. [PMID: 34095767 PMCID: PMC8171370 DOI: 10.1097/hs9.0000000000000584] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 01/25/2023] Open
Abstract
Sickle cell disease (SCD) is an exemplar of bidirectional translational research, starting with a remarkable astute observation of the abnormally shaped red blood cells that motivated decades of bench research that have now translated into new drugs and genetic therapies. Introduction of hydroxyurea (HU) therapy, the only SCD-modifying treatment for >30 years and now standard care, was initiated through another clinical observation by a pediatrician. While the clinical efficacy of HU is primarily due to its fetal hemoglobin (HbF) induction, the exact mechanism of how it increases HbF remains not fully understood. Unraveling of the molecular mechanism of how HU increases HbF has provided insights on the development of new HbF-reactivating agents in the pipeline. HU has other salutary effects, reduction of cellular adhesion to the vascular endothelium and inflammation, and dissecting these mechanisms has informed bench-both cellular and animal-research for development of the 3 recently approved agents: endari, voxelotor, and crizanlizumab; truly, a bidirectional bench to bedside translation. Decades of research to understand the mechanisms of fetal to adult hemoglobin have also culminated in promising anti-sickling genetic therapies and the first-in-human studies of reactivating an endogenous (γ-globin) gene HBG utilizing innovative genomic approaches.
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Affiliation(s)
- Gabriel Salinas Cisneros
- Sickle Cell Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
- Division of Hematology and Oncology, Children’s National Medical Center, Washington, District of Columbia, USA
| | - Swee Lay Thein
- Sickle Cell Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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