1
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Hara MA, Ramadan M, Abdelhameid MK, Taher ES, Mohamed KO. Pyroptosis and chemical classification of pyroptotic agents. Mol Divers 2024:10.1007/s11030-024-10987-6. [PMID: 39316325 DOI: 10.1007/s11030-024-10987-6] [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: 01/21/2024] [Accepted: 09/03/2024] [Indexed: 09/25/2024]
Abstract
Pyroptosis, as a lytic-inflammatory type of programmed cell death, has garnered considerable attention due to its role in cancer chemotherapy and many inflammatory diseases. This review will discuss the biochemical classification of pyroptotic inducers according to their chemical structure, pyroptotic mechanism, and cancer type of these targets. A structure-activity relationship study on pyroptotic inducers is revealed based on the surveyed pyroptotic inducer chemotherapeutics. The shared features in the chemical structures of current pyroptotic inducer agents were displayed, including an essential cyclic head, a vital linker, and a hydrophilic tail that is significant for π-π interactions and hydrogen bonding. The presented structural features will open the way to design new hybridized classes or scaffolds as potent pyroptotic inducers in the future, which may represent a solution to the apoptotic-resistance dilemma along with synergistic chemotherapeutic advantage.
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Affiliation(s)
- Mohammed A Hara
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al Azhar University (Assiut), Assiut, 71524, Egypt
| | - Mohamed Ramadan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al Azhar University (Assiut), Assiut, 71524, Egypt.
| | - Mohammed K Abdelhameid
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ehab S Taher
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al Azhar University (Assiut), Assiut, 71524, Egypt
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, Jordan
| | - Khaled O Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Sinai University (Arish Branch), ElArich, Egypt
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2
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Li X, Li W, Zhang Y, Xu L, Song Y. Exploiting the potential of the ubiquitin-proteasome system in overcoming tyrosine kinase inhibitor resistance in chronic myeloid leukemia. Genes Dis 2024; 11:101150. [PMID: 38947742 PMCID: PMC11214299 DOI: 10.1016/j.gendis.2023.101150] [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: 01/08/2023] [Revised: 06/15/2023] [Accepted: 09/01/2023] [Indexed: 07/02/2024] Open
Abstract
The advent of tyrosine kinase inhibitors (TKI) targeting BCR-ABL has drastically changed the treatment approach of chronic myeloid leukemia (CML), greatly prolonged the life of CML patients, and improved their prognosis. However, TKI resistance is still a major problem with CML patients, reducing the efficacy of treatment and their quality of life. TKI resistance is mainly divided into BCR-ABL-dependent and BCR-ABL-independent resistance. Now, the main clinical strategy addressing TKI resistance is to switch to newly developed TKIs. However, data have shown that these new drugs may cause serious adverse reactions and intolerance and cannot address all resistance mutations. Therefore, finding new therapeutic targets to overcome TKI resistance is crucial and the ubiquitin-proteasome system (UPS) has emerged as a focus. The UPS mediates the degradation of most proteins in organisms and controls a wide range of physiological processes. In recent years, the study of UPS in hematological malignant tumors has resulted in effective treatments, such as bortezomib in the treatment of multiple myeloma and mantle cell lymphoma. In CML, the components of UPS cooperate or antagonize the efficacy of TKI by directly or indirectly affecting the ubiquitination of BCR-ABL, interfering with CML-related signaling pathways, and negatively or positively affecting leukemia stem cells. Some of these molecules may help overcome TKI resistance and treat CML. In this review, the mechanism of TKI resistance is briefly described, the components of UPS are introduced, existing studies on UPS participating in TKI resistance are listed, and UPS as the therapeutic target and strategies are discussed.
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Affiliation(s)
- Xudong Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, Henan 450008, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Wei Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yanli Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Linping Xu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, Henan 450008, China
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
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3
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Cruz-Rodriguez N, Tang H, Bateman B, Tang W, Deininger M. BCR::ABL1 Proteolysis-targeting chimeras (PROTACs): The new frontier in the treatment of Ph + leukemias? Leukemia 2024; 38:1885-1893. [PMID: 39098922 DOI: 10.1038/s41375-024-02365-w] [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: 05/01/2024] [Revised: 06/19/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
BCR::ABL1 tyrosine kinase inhibitors (TKIs) have turned chronic myeloid leukemia (CML) from a lethal condition into a chronic ailment. With optimal management, the survival of CML patients diagnosed in the chronic phase is approaching that of age-matched controls. However, only one-third of patients can discontinue TKIs and enter a state of functional cure termed treatment-free remission (TFR), while the remainder require life-long TKI therapy to avoid the recurrence of active leukemia. Approximately 10% of patients exhibit primary or acquired TKI resistance and eventually progress to the blast phase. It is thought that recurrence after attempted TFR originates from CML stem cells (LSCs) surviving despite continued suppression of BCR::ABL1 kinase. Although kinase activity is indispensable for induction of overt CML, kinase-independent scaffold functions of BCR::ABL1 are known to contribute to leukemogenesis, raising the intriguing but as yet hypothetical possibility, that degradation of BCR::ABL1 protein may accomplish what TKIs fail to achieve - eliminate residual LSCs to turn functional into real cures. The advent of BCR::ABL1 proteolysis targeting chimeras (PROTACs), heterobifunctional molecules linking a TKI-based warhead to an E3 ligase recruiter, has moved clinical protein degradation into the realm of the possible. Here we examine the molecular rationale as well as pros and cons of degrading BCR::ABL1 protein. We review reported BCR::ABL1 PROTACs, point out limitations of available data and compounds and suggest directions for future research. Ultimately, clinical testing of a potent and specific BCR::ABL1 degrader will be required to determine the efficacy and tolerability of this approach.
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MESH Headings
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/metabolism
- Proteolysis
- Protein Kinase Inhibitors/therapeutic use
- Protein Kinase Inhibitors/pharmacology
- Drug Resistance, Neoplasm
- Proto-Oncogene Proteins c-abl/metabolism
- Animals
- Proteolysis Targeting Chimera
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Affiliation(s)
| | - Hua Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Weiping Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Deininger
- Versiti Blood Research Institute, Milwaukee, WI, USA.
- Medical College of Wisconsin, Milwaukee, WI, USA.
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4
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Li Z, Liu HY, He Z, Chakravarty A, Golden RP, Jiang Z, You I, Yue H, Donovan KA, Du G, Che J, Tse J, Che I, Lu W, Fischer ES, Zhang T, Gray NS, Yang PL. Discovery of Potent Degraders of the Dengue Virus Envelope Protein. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405829. [PMID: 39145423 DOI: 10.1002/advs.202405829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/26/2024] [Indexed: 08/16/2024]
Abstract
Targeted protein degradation has been widely adopted as a new approach to eliminate both established and previously recalcitrant therapeutic targets. Here, it is reported that the development of small molecule degraders of the envelope (E) protein of dengue virus. Two classes of bivalent E-degraders are developed by linking two previously reported E-binding small molecules, GNF-2, and CVM-2-12-2, to a glutarimide-based recruiter of the CRL4CRBN ligase to effect proteosome-mediated degradation of the E protein. ZXH-2-107 (based on GNF-2) is an E-degrader with ABL inhibitory activity while ZXH-8-004 (based on CVM-2-12-2) is a selective and potent E-degrader. These two compounds provide proof of concept that difficult-to-drug targets such as a viral envelope protein can be effectively eliminated using a bivalent degrader and provide starting points for the future development of a new class of direct-acting antiviral drugs.
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Affiliation(s)
- Zhengnian Li
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Han-Yuan Liu
- Department of Microbiology and Immunology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, CA, 94305, USA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Antara Chakravarty
- Department of Microbiology and Immunology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, CA, 94305, USA
| | - Ryan P Golden
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Zixuan Jiang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | | | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
| | - Jason Tse
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Isaac Che
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Wenchao Lu
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Priscilla L Yang
- Department of Microbiology and Immunology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, CA, 94305, USA
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5
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Zhao M, Dai B, Li X, Zhang Y, Qiao C, Qin Y, Li Z, Li Q, Wang S, Yang Y, Chen Y. RAPSYN-mediated neddylation of BCR-ABL alternatively determines the fate of Philadelphia chromosome-positive leukemia. eLife 2024; 12:RP88375. [PMID: 38865175 PMCID: PMC11168747 DOI: 10.7554/elife.88375] [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] [Indexed: 06/13/2024] Open
Abstract
Philadelphia chromosome-positive (Ph+) leukemia is a fatal hematological malignancy. Although standard treatments with tyrosine kinase inhibitors (TKIs) have achieved remarkable success in prolonging patient survival, intolerance, relapse, and TKI resistance remain serious issues for patients with Ph+ leukemia. Here, we report a new leukemogenic process in which RAPSYN and BCR-ABL co-occur in Ph+ leukemia, and RAPSYN mediates the neddylation of BCR-ABL. Consequently, neddylated BCR-ABL enhances the stability by competing its c-CBL-mediated degradation. Furthermore, SRC phosphorylates RAPSYN to activate its NEDD8 E3 ligase activity, promoting BCR-ABL stabilization and disease progression. Moreover, in contrast to in vivo ineffectiveness of PROTAC-based degraders, depletion of RAPSYN expression, or its ligase activity decreased BCR-ABL stability and, in turn, inhibited tumor formation and growth. Collectively, these findings represent an alternative to tyrosine kinase activity for the oncoprotein and leukemogenic cells and generate a rationale of targeting RAPSYN-mediated BCR-ABL neddylation for the treatment of Ph+ leukemia.
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MESH Headings
- Animals
- Humans
- Mice
- Cell Line, Tumor
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- NEDD8 Protein/metabolism
- NEDD8 Protein/genetics
- Ubiquitin-Protein Ligases/metabolism
- Ubiquitin-Protein Ligases/genetics
- Muscle Proteins/metabolism
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Affiliation(s)
- Mengya Zhao
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Beiying Dai
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Xiaodong Li
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Yixin Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Chun Qiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Yaru Qin
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Zhao Li
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Qingmei Li
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Shuzhen Wang
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Yong Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Yijun Chen
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqingChina
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6
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Li Z, Liu HY, He Z, Chakravarty A, Golden RP, Jiang Z, You I, Yue H, Donovan KA, Du G, Che J, Tse J, Che I, Lu W, Fischer ES, Zhang T, Gray NS, Yang PL. Discovery of Potent Degraders of the Dengue Virus Envelope Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596987. [PMID: 38854003 PMCID: PMC11160776 DOI: 10.1101/2024.06.01.596987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Targeted protein degradation has been widely adopted as a new approach to eliminate both established and previously recalcitrant therapeutic targets. Here we report the development of small molecule degraders of the envelope (E) protein of dengue virus. We developed two classes of bivalent E-degraders, linking two previously reported E-binding small molecules, GNF-2 and CVM-2-12-2, to a glutarimide-based recruiter of the CRL4CRBN ligase to effect proteosome-mediated degradation of the E protein. ZXH-2-107 (based on GNF-2) is an E degrader with ABL inhibition while ZXH-8-004 (based on CVM-2-12-2) is a selective and potent E-degrader. These two compounds provide proof-of-concept that difficult-to-drug targets such as a viral envelope protein can be effectively eliminated using a bivalent degrader and provide starting points for the future development of a new class antiviral drugs.
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Affiliation(s)
- Zhengnian Li
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Han-Yuan Liu
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Antara Chakravarty
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Ryan P. Golden
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Zixuan Jiang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Jason Tse
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Isaac Che
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Wenchao Lu
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - 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
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Priscilla L. Yang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
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7
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Vicente ATS, Salvador JAR. PROteolysis-Targeting Chimeras (PROTACs) in leukemia: overview and future perspectives. MedComm (Beijing) 2024; 5:e575. [PMID: 38845697 PMCID: PMC11154823 DOI: 10.1002/mco2.575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/09/2024] Open
Abstract
Leukemia is a heterogeneous group of life-threatening malignant disorders of the hematopoietic system. Immunotherapy, radiotherapy, stem cell transplantation, targeted therapy, and chemotherapy are among the approved leukemia treatments. Unfortunately, therapeutic resistance, side effects, relapses, and long-term sequelae occur in a significant proportion of patients and severely compromise the treatment efficacy. The development of novel approaches to improve outcomes is therefore an unmet need. Recently, novel leukemia drug discovery strategies, including targeted protein degradation, have shown potential to advance the field of personalized medicine for leukemia patients. Specifically, PROteolysis-TArgeting Chimeras (PROTACs) are revolutionary compounds that allow the selective degradation of a protein by the ubiquitin-proteasome system. Developed against a wide range of cancer targets, they show promising potential in overcoming many of the drawbacks associated with conventional therapies. Following the exponential growth of antileukemic PROTACs, this article reviews PROTAC-mediated degradation of leukemia-associated targets. Chemical structures, in vitro and in vivo activities, pharmacokinetics, pharmacodynamics, and clinical trials of PROTACs are critically discussed. Furthermore, advantages, challenges, and future perspectives of PROTACs in leukemia are covered, in order to understand the potential that these novel compounds may have as future drugs for leukemia treatment.
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Affiliation(s)
- André T. S. Vicente
- Laboratory of Pharmaceutical ChemistryFaculty of PharmacyUniversity of CoimbraCoimbraPortugal
- Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical ChemistryFaculty of PharmacyUniversity of CoimbraCoimbraPortugal
- Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
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8
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Alugubelli Y, Xiao J, Khatua K, Kumar S, Sun L, Ma Y, Ma XR, Vulupala VR, Atla S, Blankenship LR, Coleman D, Xie X, Neuman BW, Liu WR, Xu S. Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease. J Med Chem 2024; 67:6495-6507. [PMID: 38608245 PMCID: PMC11056980 DOI: 10.1021/acs.jmedchem.3c02416] [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: 12/22/2023] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
We have witnessed three coronavirus (CoV) outbreaks in the past two decades, including the COVID-19 pandemic caused by SARS-CoV-2. Main protease (MPro), a highly conserved protease among various CoVs, is essential for viral replication and pathogenesis, making it a prime target for antiviral drug development. Here, we leverage proteolysis targeting chimera (PROTAC) technology to develop a new class of small-molecule antivirals that induce the degradation of SARS-CoV-2 MPro. Among them, MPD2 was demonstrated to effectively reduce MPro protein levels in 293T cells, relying on a time-dependent, CRBN-mediated, and proteasome-driven mechanism. Furthermore, MPD2 exhibited remarkable efficacy in diminishing MPro protein levels in SARS-CoV-2-infected A549-ACE2 cells. MPD2 also displayed potent antiviral activity against various SARS-CoV-2 strains and exhibited enhanced potency against nirmatrelvir-resistant viruses. Overall, this proof-of-concept study highlights the potential of targeted protein degradation of MPro as an innovative approach for developing antivirals that could fight against drug-resistant viral variants.
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Affiliation(s)
- Yugendar
R. Alugubelli
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jing Xiao
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kaustav Khatua
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Sathish Kumar
- Department
of Biology, Texas A&M University, College Station, Texas 77843, United States
| | - Long Sun
- Department
of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yuying Ma
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xinyu R. Ma
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Veerabhadra R. Vulupala
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Sandeep Atla
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren R. Blankenship
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Demonta Coleman
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xuping Xie
- Department
of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Benjamin W. Neuman
- Department
of Biology, Texas A&M University, College Station, Texas 77843, United States
- Texas
A&M Global Health Research Complex, Texas A&M University, College
Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, Texas 77843, United States
| | - Shiqing Xu
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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9
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Wang S, He F, Tian C, Sun A. From PROTAC to TPD: Advances and Opportunities in Targeted Protein Degradation. Pharmaceuticals (Basel) 2024; 17:100. [PMID: 38256933 PMCID: PMC10818447 DOI: 10.3390/ph17010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
PROTAC is a rapidly developing engineering technology for targeted protein degradation using the ubiquitin-proteasome system, which has promising applications for inflammatory diseases, neurodegenerative diseases, and malignant tumors. This paper gives a brief overview of the development and design principles of PROTAC, with a special focus on PROTAC-based explorations in recent years aimed at achieving controlled protein degradation and improving the bioavailability of PROTAC, as well as TPD technologies that use other pathways such as autophagy and lysosomes to achieve targeted protein degradation.
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Affiliation(s)
- Siqi Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China; (S.W.); (F.H.)
| | - Fuchu He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China; (S.W.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Chunyan Tian
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China; (S.W.); (F.H.)
| | - Aihua Sun
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China; (S.W.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 100050, China
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10
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Zhang Y, Wu X, Sun X, Yang J, Liu C, Tang G, Lei X, Huang H, Peng J. The Progress of Small Molecule Targeting BCR-ABL in the Treatment of Chronic Myeloid Leukemia. Mini Rev Med Chem 2024; 24:642-663. [PMID: 37855278 DOI: 10.2174/0113895575218335230926070130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/14/2023] [Accepted: 07/14/2023] [Indexed: 10/20/2023]
Abstract
Chronic myelogenous leukemia (CML) is a malignant myeloproliferative disease. According to the American Cancer Society's 2021 cancer data report, new cases of CML account for about 15% of all leukemias. CML is generally divided into three stages: chronic phase, accelerated phase, and blast phase. Nearly 90% of patients are diagnosed as a chronic phase. Allogeneic stem cell transplantation and chemotherapeutic drugs, such as interferon IFN-α were used as the earliest treatments for CML. However, they could generate obvious side effects, and scientists had to seek new treatments for CML. A new era of targeted therapy for CML began with the introduction of imatinib, the first-generation BCR-ABL kinase inhibitor. However, the ensuing drug resistance and mutant strains led by T315I limited the further use of imatinib. With the continuous advancement of research, tyrosine kinase inhibitors (TKI) and BCR-ABL protein degraders with novel structures and therapeutic mechanisms have been discovered. From biological macromolecules to classical target protein inhibitors, a growing number of compounds are being developed to treat chronic myelogenous leukemia. In this review, we focus on summarizing the current situation of a series of candidate small-molecule drugs in CML therapy, including TKIs and BCR-ABL protein degrader. The examples provided herein describe the pharmacology activity of small-molecule drugs. These drugs will provide new enlightenment for future treatment directions.
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Affiliation(s)
- Yuan Zhang
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Xin Wu
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Xueyan Sun
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Jun Yang
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Chang Liu
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Guotao Tang
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Xiaoyong Lei
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Honglin Huang
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Junmei Peng
- Department of Pharmacy, School of Pharmacy, Hengyang Medical School, Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
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11
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Chan K, Sathyamurthi PS, Queisser MA, Mullin M, Shrives H, Coe DM, Burley GA. Antibody-Proteolysis Targeting Chimera Conjugate Enables Selective Degradation of Receptor-Interacting Serine/Threonine-Protein Kinase 2 in HER2+ Cell Lines. Bioconjug Chem 2023; 34:2049-2054. [PMID: 37917829 PMCID: PMC10655034 DOI: 10.1021/acs.bioconjchem.3c00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are a family of heterobifunctional molecules that are now realizing their promise as a therapeutic strategy for targeted protein degradation. However, one limitation of existing designs is the lack of cell-selective targeting of the protein degrading payload. This manuscript reports a cell-targeted approach to degrade receptor-interacting serine/threonine-protein kinase 2 (RIPK2) in HER2+ cell lines. An antibody-PROTAC conjugate is prepared containing a protease-cleavable linkage between the antibody and the corresponding degrader. Potent RIPK2 degradation is observed in HER2+ cell lines, whereas an equivalent anti-IL4 antibody-PROTAC conjugate shows no degradation at therapeutically relevant concentrations. No RIPK2 degradation was observed in HER2- cell lines for both bioconjugates. This work demonstrates the potential for the cell-selective delivery of PROTAC scaffolds by engaging with signature extracellular proteins expressed on the surface of particular cell types.
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Affiliation(s)
- Karina Chan
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Glasgow G1 1XL, United
Kingdom
| | | | - Markus A. Queisser
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Michael Mullin
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Harry Shrives
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Diane M. Coe
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Glenn A. Burley
- Department
of Pure and Applied Chemistry, University
of Strathclyde, Glasgow G1 1XL, United
Kingdom
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12
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Chen S, Zheng Y, Liang B, Yin Y, Yao J, Wang Q, Liu Y, Neamati N. The application of PROTAC in HDAC. Eur J Med Chem 2023; 260:115746. [PMID: 37607440 DOI: 10.1016/j.ejmech.2023.115746] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
Inducing protein degradation by proteolysis targeting chimera (PROTAC) has provided great opportunities for scientific research and industrial applications. Histone deacetylase (HDAC)-PROTAC has been widely developed since the first report of its ability to induce the degradation of SIRT2 in 2017. To date, ten of the eighteen HDACs (HDACs 1-8, HDAC10, and SIRT2) have been successfully targeted and degraded by HDAC-PROTACs. HDAC-PROTACs surpass traditional HDAC inhibitors in many aspects, such as higher selectivity, more potent antiproliferative activity, and the ability to disrupt the enzyme-independent functions of a multifunctional protein and overcome drug resistance. Rationally designing HDAC-PROTACs is a main challenge in development because slight variations in chemical structure can lead to drastic effects on the efficiency and selectivity of the degradation. In the future, HDAC-PROTACs can potentially be involved in clinical research with the support of the increased amount of in vivo data, pharmacokinetic evaluation, and pharmacological studies.
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Affiliation(s)
- Shaoting Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yuxiang Zheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Benji Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yudong Yin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Jian Yao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Quande Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Yanghan Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States.
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13
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Alugubelli YR, Xiao J, Khatua K, Kumar S, Ma Y, Ma XR, Vulupala VR, Atla SR, Blankenship L, Coleman D, Neuman BW, Liu WR, Xu S. Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560163. [PMID: 37808777 PMCID: PMC10557696 DOI: 10.1101/2023.09.29.560163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
We have witnessed three coronavirus (CoV) outbreaks in the past two decades, including the COVID-19 pandemic caused by SARS-CoV-2. Main protease (M Pro ) is a highly conserved and essential protease that plays key roles in viral replication and pathogenesis among various CoVs, representing one of the most attractive drug targets for antiviral drug development. Traditional antiviral drug development strategies focus on the pursuit of high-affinity binding inhibitors against M Pro . However, this approach often suffers from issues such as toxicity, drug resistance, and a lack of broad-spectrum efficacy. Targeted protein degradation represents a promising strategy for developing next-generation antiviral drugs to combat infectious diseases. Here we leverage the proteolysis targeting chimera (PROTAC) technology to develop a new class of small-molecule antivirals that induce the degradation of SARS-CoV-2 M Pro . Our previously developed M Pro inhibitors MPI8 and MPI29 were used as M Pro ligands to conjugate a CRBN E3 ligand, leading to compounds that can both inhibit and degrade SARS-CoV-2 M Pro . Among them, MDP2 was demonstrated to effectively reduce M Pro protein levels in 293T cells (DC 50 = 296 nM), relying on a time-dependent, CRBN-mediated, and proteasome-driven mechanism. Furthermore, MPD2 exhibited remarkable efficacy in diminishing M Pro protein levels in SARS-CoV-2-infected A549-ACE2 cells, concurrently demonstrating potent anti-SARS-CoV-2 activity (EC 50 = 492 nM). This proof-of-concept study highlights the potential of PROTAC-mediated targeted protein degradation of M Pro as an innovative and promising approach for COVID-19 drug discovery.
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14
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Gui W, Giardina SF, Balzarini M, Barany F, Kodadek T. Reversible Assembly of Proteolysis Targeting Chimeras. ACS Chem Biol 2023; 18:1582-1593. [PMID: 37422908 DOI: 10.1021/acschembio.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are of significant current interest for the development of probe molecules and drug leads. However, they suffer from certain limitations. PROTACs are rule-breaking molecules with sub-optimal cellular permeability, solubility, and other drug-like properties. In particular, they exhibit an unusual dose-response curve where high concentrations of the bivalent molecule inhibit degradation activity, a phenomenon known as the hook effect. This will likely complicate their use in vivo. In this study, we explore a novel approach to create PROTACs that do not exhibit a hook effect. This is achieved by equipping the target protein and E3 ubiquitin ligase ligands with functionalities that undergo rapid and reversible covalent assembly in cellulo. We report the development of Self-Assembled Proteolysis Targeting Chimeras that mediate the degradation of the Von Hippel-Lindau E3 ubiquitin ligase and do not evince a hook effect.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Madeline Balzarini
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
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15
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Kelm JM, Pandey DS, Malin E, Kansou H, Arora S, Kumar R, Gavande NS. PROTAC'ing oncoproteins: targeted protein degradation for cancer therapy. Mol Cancer 2023; 22:62. [PMID: 36991452 PMCID: PMC10061819 DOI: 10.1186/s12943-022-01707-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 03/31/2023] Open
Abstract
Molecularly targeted cancer therapies substantially improve patient outcomes, although the durability of their effectiveness can be limited. Resistance to these therapies is often related to adaptive changes in the target oncoprotein which reduce binding affinity. The arsenal of targeted cancer therapies, moreover, lacks coverage of several notorious oncoproteins with challenging features for inhibitor development. Degraders are a relatively new therapeutic modality which deplete the target protein by hijacking the cellular protein destruction machinery. Degraders offer several advantages for cancer therapy including resiliency to acquired mutations in the target protein, enhanced selectivity, lower dosing requirements, and the potential to abrogate oncogenic transcription factors and scaffolding proteins. Herein, we review the development of proteolysis targeting chimeras (PROTACs) for selected cancer therapy targets and their reported biological activities. The medicinal chemistry of PROTAC design has been a challenging area of active research, but the recent advances in the field will usher in an era of rational degrader design.
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Affiliation(s)
- Jeremy M Kelm
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Deepti S Pandey
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Evan Malin
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Hussein Kansou
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA.
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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16
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Cho N, Naito M. Synthesis of SNIPERs against BCR-ABL with kinase inhibitors and a method to evaluate their growth inhibitory activity derived from BCR-ABL degradation. Methods Enzymol 2023; 681:41-60. [PMID: 36764763 DOI: 10.1016/bs.mie.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Specific and nongenetic IAP-dependent Protein Erasers (SNIPERs) are a kind of PROTACs recruiting IAP ubiquitin ligases to induce degradation of target proteins. We have developed a series of SNIPERs against BCR-ABL oncogenic kinases by employing kinase inhibitors as target ligands. Some of these SNIPERs show potent activities to degrade BCR-ABL protein and inhibit CML cell growth. However, since SNIPERs also inhibit kinase activity, it takes some ingenuity to show that degradation of BCR-ABL plays a significant role on growth inhibitory activity. Here we describe protocols for synthesizing SNIPERs against BCR-ABL oncogenic kinase that contain kinase inhibitors as target ligands, and methods for evaluating the growth inhibitory activity against cancer cells, especially focusing on a method to discriminate the significance of protein degradation from that of kinase inhibition.
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Affiliation(s)
- Nobuo Cho
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Mikihiko Naito
- Social Cooperation Program of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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17
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Wang YW, Lan L, Wang M, Zhang JY, Gao YH, Shi L, Sun LP. PROTACS: A technology with a gold rush-like atmosphere. Eur J Med Chem 2023; 247:115037. [PMID: 36566716 DOI: 10.1016/j.ejmech.2022.115037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Abnormally expressed or malfunctioning proteins may affect or even damage cells, leading to the onset of diseases. Proteolysis targeting chimera (PROTAC) technology has been proven to be a fresh therapeutic strategy, superior to conventional small molecule inhibitors for the treatment of diseases caused by pathogenic proteins. Unlike conventional small molecule inhibitors that are occupancy-driven, PROTACs are heterobifunctional small molecules with catalytic properties. They combine with E3 ligases and target proteins to form a ternary complex, rendering the target protein ubiquitous and subsequently degraded by the proteasome. This paper focuses first on significant events in the development of PROTAC technology from 2001 to 2022, followed by a brief overview of various PROTACs categorized by target proteins. In addition, the applications of PROTACs in the treatment of diseases and fundamental biology are also under discussion.
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Affiliation(s)
- Yu-Wei Wang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Li Lan
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Min Wang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jin-Yang Zhang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yu-Hui Gao
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Lei Shi
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Li-Ping Sun
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China.
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18
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Zhao HY, Xin M, Zhang SQ. Progress of small molecules for targeted protein degradation: PROTACs and other technologies. Drug Dev Res 2023; 84:337-394. [PMID: 36606428 DOI: 10.1002/ddr.22026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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19
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Chatterjee DR, Kapoor S, Jain M, Das R, Chowdhury MG, Shard A. PROTACting the kinome with covalent warheads. Drug Discov Today 2023; 28:103417. [PMID: 36306996 DOI: 10.1016/j.drudis.2022.103417] [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: 07/10/2022] [Revised: 09/19/2022] [Accepted: 10/19/2022] [Indexed: 02/02/2023]
Abstract
The dawn of targeted degradation using proteolysis-targeting chimeras (PROTACs) against recalcitrant proteins has prompted numerous efforts to develop complementary drugs. Although many of these are specifically directed against undruggable proteins, there is increasing interest in small molecule-based PROTACs that target intracellular pathways, and some have recently entered clinical trials. Concurrently, small molecule-based PROTACs that target protumorigenic pathways in cancer cells, the tumor microenvironment (TME), and angiogenesis have been found to have potent effects that synergize with the action of antibodies. This has led to the augmentation of PROTACs with variable substitution patterns. Several combinations with small molecules targeting undruggable proteins are now under clinical investigation. In this review, we discuss the recent milestones achieved as well as challenges encountered in this area of drug development, as well as our opinion on the best path forward.
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Affiliation(s)
- Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Meenakshi Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India.
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20
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Liu H, Mi Q, Ding X, Lin C, Liu L, Ren C, Shen S, Shao Y, Chen J, Zhou Y, Ji L, Zhang H, Bai F, Yang X, Yin Q, Jiang B. Discovery and characterization of novel potent BCR-ABL degraders by conjugating allosteric inhibitor. Eur J Med Chem 2022; 244:114810. [DOI: 10.1016/j.ejmech.2022.114810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022]
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21
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Negi A, Kesari KK, Voisin-Chiret AS. Estrogen Receptor-α Targeting: PROTACs, SNIPERs, Peptide-PROTACs, Antibody Conjugated PROTACs and SNIPERs. Pharmaceutics 2022; 14:pharmaceutics14112523. [PMID: 36432713 PMCID: PMC9699327 DOI: 10.3390/pharmaceutics14112523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Targeting selective estrogen subtype receptors through typical medicinal chemistry approaches is based on occupancy-driven pharmacology. In occupancy-driven pharmacology, molecules are developed in order to inhibit the protein of interest (POI), and their popularity is based on their virtue of faster kinetics. However, such approaches have intrinsic flaws, such as pico-to-nanomolar range binding affinity and continuous dosage after a time interval for sustained inhibition of POI. These shortcomings were addressed by event-driven pharmacology-based approaches, which degrade the POI rather than inhibit it. One such example is PROTACs (Proteolysis targeting chimeras), which has become one of the highly successful strategies of event-driven pharmacology (pharmacology that does the degradation of POI and diminishes its functions). The selective targeting of estrogen receptor subtypes is always challenging for chemical biologists and medicinal chemists. Specifically, estrogen receptor α (ER-α) is expressed in nearly 70% of breast cancer and commonly overexpressed in ovarian, prostate, colon, and endometrial cancer. Therefore, conventional hormonal therapies are most prescribed to patients with ER + cancers. However, on prolonged use, resistance commonly developed against these therapies, which led to selective estrogen receptor degrader (SERD) becoming the first-line drug for metastatic ER + breast cancer. The SERD success shows that removing cellular ER-α is a promising approach to overcoming endocrine resistance. Depending on the mechanism of degradation of ER-α, various types of strategies of developed.
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Affiliation(s)
- Arvind Negi
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Kavindra Kumar Kesari
- Department of Bioproduct and Biosystems, Aalto University, 00076 Espoo, Finland
- Department of Applied Physics, School of Science, Aalto University, 02150 Espoo, Finland
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
| | - Anne Sophie Voisin-Chiret
- CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie), Normandie University UNICAEN, 14000 Caen, France
- Correspondence: or (A.N.); or (K.K.K.); (A.S.V.-C.)
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22
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Liu J, Peng Y, Inuzuka H, Wei W. Targeting micro-environmental pathways by PROTACs as a therapeutic strategy. Semin Cancer Biol 2022; 86:269-279. [PMID: 35798235 PMCID: PMC11000491 DOI: 10.1016/j.semcancer.2022.07.001] [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: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 10/31/2022]
Abstract
Tumor microenvironment (TME) composes of multiple cell types and non-cellular components, which supports the proliferation, metastasis and immune surveillance evasion of tumor cells, as well as accounts for the resistance to therapies. Therefore, therapeutic strategies using small molecule inhibitors (SMIs) and antibodies to block potential targets in TME are practical for cancer treatment. Targeted protein degradation using PROteolysis-TArgeting Chimera (PROTAC) technic has several advantages over traditional SMIs and antibodies, including overcoming drug resistance. Thus many PROTACs are currently under development for cancer treatment. In this review, we summarize the recent progress of PROTAC development that target TME pathways and propose the potential direction of future PROTAC technique to advance as novel cancer treatment options.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States.
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23
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Lee J, Lee Y, Jung YM, Park JH, Yoo HS, Park J. Discovery of E3 Ligase Ligands for Target Protein Degradation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196515. [PMID: 36235052 PMCID: PMC9573645 DOI: 10.3390/molecules27196515] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022]
Abstract
Target protein degradation has emerged as a promising strategy for the discovery of novel therapeutics during the last decade. Proteolysis-targeting chimera (PROTAC) harnesses a cellular ubiquitin-dependent proteolysis system for the efficient degradation of a protein of interest. PROTAC consists of a target protein ligand and an E3 ligase ligand so that it enables the target protein degradation owing to the induced proximity with ubiquitin ligases. Although a great number of PROTACs has been developed so far using previously reported ligands of proteins for their degradation, E3 ligase ligands have been mostly limited to either CRBN or VHL ligands. Those PROTACs showed their limitation due to the cell type specific expression of E3 ligases and recently reported resistance toward PROTACs with CRBN ligands or VHL ligands. To overcome these hurdles, the discovery of various E3 ligase ligands has been spotlighted to improve the current PROTAC technology. This review focuses on currently reported E3 ligase ligands and their application in the development of PROTACs.
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Affiliation(s)
- Jaeseok Lee
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Youngjun Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Young Mee Jung
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
| | - Ju Hyun Park
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Hyuk Sang Yoo
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: ; Tel.: +82-33-250-8482
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24
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Kamaraj R, Drastik M, Maixnerova J, Pavek P. Allosteric Antagonism of the Pregnane X Receptor (PXR): Current-State-of-the-Art and Prediction of Novel Allosteric Sites. Cells 2022; 11:2974. [PMID: 36230936 PMCID: PMC9563780 DOI: 10.3390/cells11192974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
The pregnane X receptor (PXR, NR1I2) is a xenobiotic-activated transcription factor with high levels of expression in the liver. It not only plays a key role in drug metabolism and elimination, but also promotes tumor growth, drug resistance, and metabolic diseases. It has been proposed as a therapeutic target for type II diabetes, metabolic syndrome, and inflammatory bowel disease, and PXR antagonists have recently been considered as a therapy for colon cancer. There are currently no PXR antagonists that can be used in a clinical setting. Nevertheless, due to the large and complex ligand-binding pocket (LBP) of the PXR, it is challenging to discover PXR antagonists at the orthosteric site. Alternative ligand binding sites of the PXR have also been proposed and are currently being studied. Recently, the AF-2 allosteric binding site of the PXR has been identified, with several compounds modulating the site discovered. Herein, we aimed to summarize our current knowledge of allosteric modulation of the PXR as well as our attempt to unlock novel allosteric sites. We describe the novel binding function 3 (BF-3) site of PXR, which is also common for other nuclear receptors. In addition, we also mention a novel allosteric site III based on in silico prediction. The identified allosteric sites of the PXR provide new insights into the development of safe and efficient allosteric modulators of the PXR receptor. We therefore propose that novel PXR allosteric sites might be promising targets for treating chronic metabolic diseases and some cancers.
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Affiliation(s)
- Rajamanikkam Kamaraj
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Martin Drastik
- Department of Physical Chemistry and Biophysics, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Jana Maixnerova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
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25
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MDM2-Based Proteolysis-Targeting Chimeras (PROTACs): An Innovative Drug Strategy for Cancer Treatment. Int J Mol Sci 2022; 23:ijms231911068. [PMID: 36232374 PMCID: PMC9570454 DOI: 10.3390/ijms231911068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) are molecules that selectively degrade a protein of interest (POI). The incorporation of ligands that recruit mouse double minute 2 (MDM2) into PROTACs, forming the so-called MDM2-based PROTACs, has shown promise in cancer treatment due to its dual mechanism of action: a PROTAC that recruits MDM2 prevents its binding to p53, resulting not only in the degradation of POI but also in the increase of intracellular levels of the p53 suppressor, with the activation of a whole set of biological processes, such as cell cycle arrest or apoptosis. In addition, these PROTACs, in certain cases, allow for the degradation of the target, with nanomolar potency, in a rapid and sustained manner over time, with less susceptibility to the development of resistance and tolerance, without causing changes in protein expression, and with selectivity to the target, including the respective isoforms or mutations, and to the cell type, overcoming some limitations associated with the use of inhibitors for the same therapeutic target. Therefore, the aim of this review is to analyze and discuss the characteristics of MDM2-based PROTACs developed for the degradation of oncogenic proteins and to understand what potential they have as future anticancer drugs.
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26
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Anwar Z, Ali MS, Galvano A, Perez A, La Mantia M, Bukhari I, Swiatczak B. PROTACs: The Future of Leukemia Therapeutics. Front Cell Dev Biol 2022; 10:851087. [PMID: 36120561 PMCID: PMC9479449 DOI: 10.3389/fcell.2022.851087] [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: 01/09/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
The fight to find effective, long-lasting treatments for cancer has led many researchers to consider protein degrading entities. Recent developments in PROteolysis TArgeting Chimeras (PROTACs) have signified their potential as possible cancer therapies. PROTACs are small molecule, protein degraders that function by hijacking the built-in Ubiquitin-Proteasome pathway. This review mainly focuses on the general design and functioning of PROTACs as well as current advancements in the development of PROTACs as anticancer therapies. Particular emphasis is given to PROTACs designed against various types of Leukemia/Blood malignancies.
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Affiliation(s)
- Zubair Anwar
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
- *Correspondence: Zubair Anwar, ; Bartlomiej Swiatczak,
| | - Muhammad Shahzad Ali
- Department of Clinical and Biological Sciences, University of Turin, San Luigi Hospital, Turin, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
| | - Alessandro Perez
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
| | - Maria La Mantia
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
| | - Ihtisham Bukhari
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, Hefei, China
- *Correspondence: Zubair Anwar, ; Bartlomiej Swiatczak,
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27
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Cao C, He M, Wang L, He Y, Rao Y. Chemistries of bifunctional PROTAC degraders. Chem Soc Rev 2022; 51:7066-7114. [PMID: 35916511 DOI: 10.1039/d2cs00220e] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) technology is a novel and promising therapeutic strategy using small molecules to induce ubiquitin-dependent degradation of proteins. It has received extensive attention from both academia and industry as it can potentially access previously inaccessible targets. However, the design and optimization of PROTACs present big challenges for researchers, and the general strategy for its development and optimization is a lot of trial and error based on experience. This review highlights the important advances in this rapidly growing field and critical limitations of the traditional trial-and-error approach to developing PROTACs by analyzing numerous representative examples of PROTACs development. We summarize and analyze the general principles and strategies for PROTACs design and optimization from the perspective of chemical structure design, and propose potential future pathways to facilitate the development of PROTACs.
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Affiliation(s)
- Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China. .,Tsinghua-Peking Center for Life Sciences, Beijing 100084, P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Liguo Wang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
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28
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Aguti R, Gardini E, Bertazzo M, Decherchi S, Cavalli A. Probabilistic Pocket Druggability Prediction via One-Class Learning. Front Pharmacol 2022; 13:870479. [PMID: 35847005 PMCID: PMC9278401 DOI: 10.3389/fphar.2022.870479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/24/2022] [Indexed: 12/31/2022] Open
Abstract
The choice of target pocket is a key step in a drug discovery campaign. This step can be supported by in silico druggability prediction. In the literature, druggability prediction is often approached as a two-class classification task that distinguishes between druggable and non-druggable (or less druggable) pockets (or voxels). Apart from obvious cases, however, the non-druggable class is conceptually ambiguous. This is because any pocket (or target) is only non-druggable until a drug is found for it. It is therefore more appropriate to adopt a one-class approach, which uses only unambiguous information, namely, druggable pockets. Here, we propose using the import vector domain description (IVDD) algorithm to support this task. IVDD is a one-class probabilistic kernel machine that we previously introduced. To feed the algorithm, we use customized DrugPred descriptors computed via NanoShaper. Our results demonstrate the feasibility and effectiveness of the approach. In particular, we can remove or mitigate biases chiefly due to the labeling.
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Affiliation(s)
- Riccardo Aguti
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Erika Gardini
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Martina Bertazzo
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Sergio Decherchi
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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29
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Luo H, Wu L, He Y, Qin C, Tang X. Major Advances in Emerging Degrader Technologies. Front Cell Dev Biol 2022; 10:921958. [PMID: 35813205 PMCID: PMC9257139 DOI: 10.3389/fcell.2022.921958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/03/2022] [Indexed: 12/11/2022] Open
Abstract
Recently, degrader technologies have attracted increasing interest in the academic field and the pharmaceuticals industry. As one of the degrader technologies, proteolysis-targeting chimeras (PROTACs) have emerged as an attractive pharmaceutical development approach due to their catalytic ability to degrade numerous undruggable disease-causing proteins. Despite the remarkable progress, many aspects of traditional PROTACs still remain elusive. Its expansion could lead to PROTACs with new paradigm. Currently, many reviews focused on the design and optimization strategies through summarizing classical PROTACs, application in diseases and prospect of PROTACs. In this review, we categorize various emerging PROTACs ranging from simply modified classical PROTACs to atypical PROTACs such as nucleic acid-based PROTACs, and we put more emphasis on molecular design of PROTACs with different strategies. Furthermore, we summarize alternatives of PROTACs as lysosome-targeting chimeras (LYTACs) and macroautophagy degradation targeting chimeras (MADTACs) based on different degradation mechanism despite of lysosomal pathway. Beyond these protein degraders, targeting RNA degradation with the potential for cancer and virus therapeutics has been discussed. In doing so, we provide our perspective on the potential development or concerns of each degrader technology. Overall, we hope this review will offer a better mechanistic understanding of emerging degraders and prove as useful guide for the development of the coming degrader technologies.
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Affiliation(s)
- Hang Luo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chong Qin
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
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30
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Wang C, Zhang Y, Shi L, Yang S, Chang J, Zhong Y, Li Q, Xing D. Recent advances in IAP-based PROTACs (SNIPERs) as potential therapeutic agents. J Enzyme Inhib Med Chem 2022; 37:1437-1453. [PMID: 35589670 PMCID: PMC9122363 DOI: 10.1080/14756366.2022.2074414] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteolytic targeting chimaeras (PROTACs) have been developed as an effective technology for targeted protein degradation. PROTACs are heterobifunctional molecules that can trigger the polyubiquitination of proteins of interest (POIs) by recruiting the ubiquitin-proteasome system, thereby inhibiting the intracellular level of POIs. To date, a variety of small-molecule PROTACs (CRBN, VHL, IAP, and MDM2-based PROTACs) have been developed. IAP-based PROTACs, also known as specific and nongenetic IAP-dependent protein erasers (SNIPERs), are used to degrade the target proteins closely related to diseases. Their structures consist of three parts, including target protein ligand, E3 ligase ligand, and the linker between them. So far, many SNIPERs have been extensively studied worldwide and have performed well in multiple diseases, especially cancer. In this review, we will present the most relevant advances in the field of SNIPERs and provide our perspective on the opportunities and challenges for SNIPERs to become therapeutic agents.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Lingyu Shi
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Shanbo Yang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Jing Chang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Yingjie Zhong
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Qian Li
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China.,School of Life Sciences, Tsinghua University, Beijing, China
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31
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Pan YL, Zeng SX, Hao RR, Liang MH, Shen ZR, Huang WH. The progress of small-molecules and degraders against BCR-ABL for the treatment of CML. Eur J Med Chem 2022; 238:114442. [PMID: 35551036 DOI: 10.1016/j.ejmech.2022.114442] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/04/2022]
Abstract
Chronic myeloid leukemia (CML) is a malignant disease of the hematopoietic system with crucial pathogenic protein named BCR-ABL, which endangers the life of patients severely. As a milestone of targeted drug, Imatinib has achieved great success in the treatment of CML. Nevertheless, inevitable drug resistance of Imatinib has occurred frequently in clinical due to the several mutations in the BCR-ABL kinase. Subsequently, the second-generation of tyrosine kinase inhibitors (TKIs) against BCR-ABL was developed to address the mutants of Imatinib resistance, except T315I. To date, the third-generation of TKIs targeting T315I has been developed for improving the selectivity and safety. Notably, the first allosteric inhibitor has been in market which could overcome the mutations in ATP binding site effectively. Meanwhile, some advanced technology, such as proteolysis-targeting chimeras (PROTAC) based on different E3 ligand, are highly expected to overcome the drug resistance by selectively degrading the targeted proteins. In this review, we summarized the current research progress of inhibitors and degraders targeting BCR-ABL for the treatment of CML.
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Affiliation(s)
- You-Lu Pan
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Shen-Xin Zeng
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Rong-Rong Hao
- Hangzhou Chinese Academy of Sciences-Hangzhou Medical College Advanced Medical Technology Institute, Zhejiang, China
| | - Mei-Hao Liang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zheng-Rong Shen
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Wen-Hai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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32
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Chen L, Wan X, Shan X, Zha W, Fan R. Smart PROTACs Enable Controllable Protein Degradation for Precision Cancer Therapy. Mol Diagn Ther 2022; 26:283-291. [PMID: 35471699 DOI: 10.1007/s40291-022-00586-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional chemicals that degrade proteins at the post-translational level, which represent an emerging therapeutic modality to fight cancer and other diseases. Although several PROTACs have now entered clinical trials, potential off-tissue side effects have resulted from nonspecific accumulation at non-cancerous sites after systemic administration, and this remains a major challenge. To this end, in the past 3 years, activatable PROTACs whose activity can only be launched on demand have gained tremendous momentum. In this review, we provide an overview of these new smart activatable PROTACs, which exert protein degradation action only in response to internal or external stimuli. We categorize these activatable PROTACs according to their activation mechanism contributed by different stimuli, including reduction-activatable, hypoxia-activatable, and enzyme-activatable PROTACs and photo-caged or photo-switchable PROTACs. The use of stimuli-responsive chemical blocks in these activatable PROTACs allows local activation of the antitumor effects while reducing the incidence of off-site side effects for precision cancer therapy. The design principle and category of smart PROTACs are introduced along with an overview of their therapeutic prospects and challenges.
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Affiliation(s)
- Lixia Chen
- Medical College of Nantong University, Nantong, China
| | - Xinqiang Wan
- Department of Gynaecology and Obstetrics, The Fourth Affiliated Hospital of Nantong University, The First People's Hospital of Yancheng, Yancheng, China
| | - Xiangxiang Shan
- Department of Geraeology, Yancheng City No. 1 People's Hospital, Yancheng, China
| | - Wenzhang Zha
- Department of General Surgery, The Fourth Affiliated Hospital of Nantong University, The First People's Hospital of Yancheng, 166 Yulong Road, Yancheng, 224001, China
| | - Rengen Fan
- Department of General Surgery, The Fourth Affiliated Hospital of Nantong University, The First People's Hospital of Yancheng, 166 Yulong Road, Yancheng, 224001, China.
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33
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Burke MR, Smith AR, Zheng G. Overcoming Cancer Drug Resistance Utilizing PROTAC Technology. Front Cell Dev Biol 2022; 10:872729. [PMID: 35547806 PMCID: PMC9083012 DOI: 10.3389/fcell.2022.872729] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer drug resistance presents a major barrier to continued successful treatment of malignancies. Current therapies inhibiting proteins indicated in cancer progression are consistently found to lose efficacy as a result of acquired drug resistance, often caused by mutated or overexpressed protein targets. By hijacking the cellular ubiquitin-proteasome protein degradation machinery, proteolysis-targeting chimeras (PROTACs) offer an alternative therapeutic modality to cancer treatments with various potential advantages. PROTACs specific for a number of known cancer targets have been developed in the last 5 years, which present new options for remission in patients with previously untreatable malignancies and provide a foundation for future-generation compounds. One notable advantage of PROTACs, supported by evidence from a number of recent studies, is that they can overcome some of the resistance mechanisms to traditional targeted therapies. More recently, some groups have begun researching the use of PROTACs to successfully degrade mutated targets conferring cancer resistance against first-line treatments. In this review, we focus on analyzing the developments in PROTACs geared towards cancer resistance and targets that confer it in the search for new and successful therapies.
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34
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Sosič I, Bricelj A, Steinebach C. E3 ligase ligand chemistries: from building blocks to protein degraders. Chem Soc Rev 2022; 51:3487-3534. [PMID: 35393989 DOI: 10.1039/d2cs00148a] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, proteolysis-targeting chimeras (PROTACs), capable of achieving targeted protein degradation, have proven their great therapeutic potential and usefulness as molecular biology tools. These heterobifunctional compounds are comprised of a protein-targeting ligand, an appropriate linker, and a ligand binding to the E3 ligase of choice. A successful PROTAC induces the formation of a ternary complex, leading to the E3 ligase-mediated ubiquitination of the targeted protein and its proteasomal degradation. In over 20 years since the concept was first demonstrated, the field has grown substantially, mainly due to the advancements in the discovery of non-peptidic E3 ligase ligands. Development of small-molecule E3 binders with favourable physicochemical profiles aided the design of PROTACs, which are known for breaking the rules of established guidelines for discovering small molecules. Synthetic accessibility of the ligands and numerous successful applications led to the prevalent use of cereblon and von Hippel-Lindau as the hijacked E3 ligase. However, the pool of over 600 human E3 ligases is full of untapped potential, which is why expanding the artillery of E3 ligands could contribute to broadening the scope of targeted protein degradation. In this comprehensive review, we focus on the chemistry aspect of the PROTAC design process by providing an overview of liganded E3 ligases, their chemistries, appropriate derivatisation, and synthetic approaches towards their incorporation into heterobifunctional degraders. By covering syntheses of both established and underexploited E3 ligases, this review can serve as a chemistry blueprint for PROTAC researchers during their future ventures into the complex field of targeted protein degradation.
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Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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Torres-Ayuso P, Brognard J. Degraders: The Ultimate Weapon Against Amplified Driver Kinases in Cancer. Mol Pharmacol 2022; 101:191-200. [PMID: 35115411 PMCID: PMC9092480 DOI: 10.1124/molpharm.121.000306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 01/27/2022] [Indexed: 12/02/2022] Open
Abstract
Amplification of pro-oncogenic kinases is a common genetic alteration driving tumorigenic phenotypes. Cancer cells rely on the amplified kinases to sustain cell proliferation, survival, and growth, presenting an opportunity to develop therapies targeting the amplified kinases. Utilizing small molecule catalytic inhibitors as therapies to target amplified kinases is plagued by de novo resistance driven by increased expression of the target, and amplified kinases can drive tumorigenic phenotypes independent of catalytic activity. Here, we discuss the emergence of proteolysis-targeting chimeras that provide an opportunity to target these oncogenic drivers effectively. SIGNIFICANCE STATEMENT: Protein kinases contribute to tumorigenesis through catalytic and noncatalytic mechanisms, and kinase gene amplifications are well described mechanisms of resistance to small molecule catalytic inhibitors. Repurposing catalytic inhibitors for the development of protein degraders will offer improved clinical benefits by targeting noncatalytic functions of kinases that promote tumorigenesis and overcoming resistance due to amplification.
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Affiliation(s)
- Pedro Torres-Ayuso
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, Center for Cancer Research, Frederick, Maryland
| | - John Brognard
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, Center for Cancer Research, Frederick, Maryland
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Zhong Y, Chi F, Wu H, Liu Y, Xie Z, Huang W, Shi W, Qian H. Emerging targeted protein degradation tools for innovative drug discovery: From classical PROTACs to the novel and beyond. Eur J Med Chem 2022; 231:114142. [DOI: 10.1016/j.ejmech.2022.114142] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
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He S, Dong G, Cheng J, Wu Y, Sheng C. Strategies for designing proteolysis targeting chimaeras (PROTACs). Med Res Rev 2022; 42:1280-1342. [PMID: 35001407 DOI: 10.1002/med.21877] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimaeras (PROTACs) is a cutting edge and rapidly growing technique for new drug discovery and development. Currently, the largest challenge in the molecular design and drug development of PROTACs is efficient identification of potent and drug-like degraders. This review aims to comprehensively summarize and analyse state-of-the-art methods and strategies in the design of PROTACs. We provide a detailed illustration of the general principles and tactics for designing potent PROTACs, highlight representative case studies, and discuss the advantages and limitations of these strategies. Particularly, structure-based rational PROTAC design and emerging new types of PROTACs (e.g., homo-PROTACs, multitargeting PROTACs, photo-control PROTACs and PROTAC-based conjugates) will be focused on.
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Affiliation(s)
- Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junfei Cheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ying Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
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Abstract
Proteolysis-targeting chimeras (PROTACs) are a powerful tool to hijack the endogenous ubiquitin-proteasome system (UPS) and to degrade the intracellular proteins of therapeutic importance. Recently, two heterobifunctional degraders targeting hormone receptors headed into Phase II clinical trials. Compared to traditional drug design and common modes of action, the PROTAC approach offers new opportunities for the drug research field. Histone deacetylase inhibitors (HDACi) are well-established drugs for the treatment of hematological malignancies. The integration of HDAC binding motifs in PROTACs explores the possibility of targeted, chemical HDAC degradation. This review provides an overview and a perspective about the key steps in the structure development of HDAC-PROTACs. In particular, the influence of the three canonical PROTAC elements on HDAC-PROTAC efficacy and selectivity are discussed, the HDACi, the linker and the E3 ligase ligand.
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Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
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Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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Eron SJ, Huang H, Agafonov RV, Fitzgerald ME, Patel J, Michael RE, Lee TD, Hart AA, Shaulsky J, Nasveschuk CG, Phillips AJ, Fisher SL, Good A. Structural Characterization of Degrader-Induced Ternary Complexes Using Hydrogen-Deuterium Exchange Mass Spectrometry and Computational Modeling: Implications for Structure-Based Design. ACS Chem Biol 2021; 16:2228-2243. [PMID: 34582690 DOI: 10.1021/acschembio.1c00376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The field of targeted protein degradation (TPD) has grown exponentially over the past decade with the goal of developing therapies that mark proteins for destruction leveraging the ubiquitin-proteasome system. One common approach to achieve TPD is to employ a heterobifunctional molecule, termed as a degrader, to recruit the protein target of interest to the E3 ligase machinery. The resultant generation of an intermediary ternary complex (target-degrader-ligase) is pivotal in the degradation process. Understanding the ternary complex geometry offers valuable insight into selectivity, catalytic efficiency, linker chemistry, and rational degrader design. In this study, we utilize hydrogen-deuterium exchange mass spectrometry (HDX-MS) to identify degrader-induced protein-protein interfaces. We then use these data in conjunction with constrained protein docking to build three-dimensional models of the ternary complex. The approach was used to characterize complex formation between the E3 ligase CRBN and the first bromodomain of BRD4, a prominent oncology target. We show marked differences in the ternary complexes formed in solution based on distinct patterns of deuterium uptake for two degraders, CFT-1297 and dBET6. CFT-1297, which exhibited positive cooperativity, altered the deuterium uptake profile revealing the degrader-induced protein-protein interface of the ternary complex. For CFT-1297, the ternary complexes generated by the highest scoring HDX-constrained docking models differ markedly from those observed in the published crystal structures. These results highlight the potential utility of HDX-MS to provide rapidly accessible structural insights into degrader-induced protein-protein interfaces in solution. They further suggest that degrader ternary complexes exhibit significant conformation flexibility and that biologically relevant complexes may well not exhibit the largest interaction surfaces between proteins. Taken together, the results indicate that methods capable of incorporating linker conformation uncertainty may prove an important component in degrader design moving forward. In addition, the development of scoring functions modified to handle interfaces with no evolved complementarity, for example, through consideration of high levels of water infiltration, may prove valuable. Furthermore, the use of crystal structures as validation tools for novel degrader methods needs to be considered with caution.
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Affiliation(s)
- Scott J. Eron
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Hongwei Huang
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Roman V. Agafonov
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Mark E. Fitzgerald
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Joe Patel
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Ryan E. Michael
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Tobie D. Lee
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Ashley A. Hart
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Jodi Shaulsky
- Dassault Systèmes BIOVIA, 5005 Wateridge Vista Dr, San Diego, California 92121, United States
| | | | - Andrew J. Phillips
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Stewart L. Fisher
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Andrew Good
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
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Liu J, Peng Y, Wei W. Light-Controllable PROTACs for Temporospatial Control of Protein Degradation. Front Cell Dev Biol 2021; 9:678077. [PMID: 34350175 PMCID: PMC8326567 DOI: 10.3389/fcell.2021.678077] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) is an emerging and promising approach to target intracellular proteins for ubiquitination-mediated degradation, including those so-called undruggable protein targets, such as transcriptional factors and scaffold proteins. To date, plenty of PROTACs have been developed to degrade various disease-relevant proteins, such as estrogen receptor (ER), androgen receptor (AR), RTK, and CDKs. However, the on-target off-tissue and off-target effect is one of the major limitation that prevents the usage of PROTACs in clinic. To this end, we and several other groups have recently developed light-controllable PROTACs, as the representative for the third generation controllable PROTACs, by using either photo-caging or photo-switch approaches. In this review, we summarize the emerging light-controllable PROTACs and the prospective for other potential ways to achieve temporospatial control of PROTACs.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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Samarasinghe KTG, Crews CM. Targeted protein degradation: A promise for undruggable proteins. Cell Chem Biol 2021; 28:934-951. [PMID: 34004187 PMCID: PMC8286327 DOI: 10.1016/j.chembiol.2021.04.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Protein homeostasis, or "proteostasis," is indispensable for a balanced, healthy environment within the cell. However, when natural proteostasis mechanisms are overwhelmed from excessive loads of dysregulated proteins, their accumulation can lead to disease initiation and progression. Recently, the induced degradation of such disease-causing proteins by heterobifunctional molecules, i.e., PROteolysis TArgeting Chimeras (PROTACs), is emerging as a potential therapeutic modality. In the 2 decades since the PROTAC concept was proposed, several additional Targeted Protein Degradation (TPD) strategies have also been explored to target previously undruggable proteins, such as transcription factors. In this review, we discuss the progress and evolution of the TPD field, the breadth of the proteins targeted by PROTACs and the biological effects of their degradation.
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Affiliation(s)
- Kusal T G Samarasinghe
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Pharmacology, Yale University, New Haven, CT 06511, USA.
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Bricelj A, Steinebach C, Kuchta R, Gütschow M, Sosič I. E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points. Front Chem 2021; 9:707317. [PMID: 34291038 PMCID: PMC8287636 DOI: 10.3389/fchem.2021.707317] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/04/2021] [Indexed: 12/16/2022] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) have received tremendous attention as a new and exciting class of therapeutic agents that promise to significantly impact drug discovery. These bifunctional molecules consist of a target binding unit, a linker, and an E3 ligase binding moiety. The chemically-induced formation of ternary complexes leads to ubiquitination and proteasomal degradation of target proteins. Among the plethora of E3 ligases, only a few have been utilized for the novel PROTAC technology. However, extensive knowledge on the preparation of E3 ligands and their utilization for PROTACs has already been acquired. This review provides an in-depth analysis of synthetic entries to functionalized ligands for the most relevant E3 ligase ligands, i.e. CRBN, VHL, IAP, and MDM2. Less commonly used E3 ligase and their ligands are also presented. We compare different preparative routes to E3 ligands with respect to feasibility and productivity. A particular focus was set on the chemistry of the linker attachment by discussing the synthetic opportunities to connect the E3 ligand at an appropriate exit vector with a linker to assemble the final PROTAC. This comprehensive review includes many facets involved in the synthesis of such complex molecules and is expected to serve as a compendium to support future synthetic attempts towards PROTACs.
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Affiliation(s)
- Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Robert Kuchta
- Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | | | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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Yu F, Cai M, Shao L, Zhang J. Targeting Protein Kinases Degradation by PROTACs. Front Chem 2021; 9:679120. [PMID: 34277564 PMCID: PMC8279777 DOI: 10.3389/fchem.2021.679120] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022] Open
Abstract
Kinase dysregulation is greatly associated with cell proliferation, migration and survival, indicating the importance of kinases as therapeutic targets for anticancer drug development. However, traditional kinase inhibitors binding to catalytic or allosteric sites are associated with significant challenges. The emergence of resistance and targeting difficult-to-degrade and multi-domain proteins are significant limiting factors affecting the efficacy of targeted anticancer drugs. The next-generation treatment approaches seem to have overcome these concerns, and the use of proteolysis targeting chimera (PROTAC) technology is one such method. PROTACs bind to proteins of interest and recruit E3 ligase for degrading the whole target protein via the ubiquitin-proteasome pathway. This review provides a detailed summary of the most recent signs of progress in PROTACs targeting different kinases, primarily focusing on new chemical entities in medicinal chemistry.
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Affiliation(s)
- Fei Yu
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Ming Cai
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Liang Shao
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Jihong Zhang
- Medical School of Kunming University of Science and Technology, Kunming, China
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Liu H, Ding X, Liu L, Mi Q, Zhao Q, Shao Y, Ren C, Chen J, Kong Y, Qiu X, Elvassore N, Yang X, Yin Q, Jiang B. Discovery of novel BCR-ABL PROTACs based on the cereblon E3 ligase design, synthesis, and biological evaluation. Eur J Med Chem 2021; 223:113645. [PMID: 34217059 DOI: 10.1016/j.ejmech.2021.113645] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/23/2022]
Abstract
Protein degradation is a promising strategy for drug development. Proteolysis-targeting chimeras (PROTACs) hijacking the E3 ligase cereblon (CRBN) exhibit enormous potential and universal degradation performance due to the small molecular weight of CRBN ligands. In this study, the CRBN-recruiting PROTACs were explored on the degradation of oncogenic fusion protein BCR-ABL, which drives the pathogenesis of chronic myeloid leukemia (CML). A series of novel PROTACs were synthesized by conjugating BCR-ABL inhibitor dasatinib to the CRBN ligand including pomalidomide and lenalidomide, and the extensive structure-activity relationship (SAR) studies were performed focusing on optimization of linker parameters. Therein, we uncovered that pomalidomide-based degrader 17 (SIAIS056), possessing sulfur-substituted carbon chain linker, exhibits the most potent degradative activity in vitro and favorable pharmacokinetics in vivo. Besides, degrader 17 also degrades a variety of clinically relevant resistance-conferring mutations of BCR-ABL. Furthermore, degrader 17 induces significant tumor regression against K562 xenograft tumors. Our study indicates that 17 as an efficacious BCR-ABL degrader warrants intensive investigation for the future treatment of BCR-ABL+ leukemia.
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Affiliation(s)
- Haixia Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Shanghai Institute for Advanced Immunochemical Studies, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinyu Ding
- Shanghai Institute for Advanced Immunochemical Studies, China; School of Life Science and Technology, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linyi Liu
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, University of South China, Hengyang City, 421001, China
| | - Qianglong Mi
- Shanghai Institute for Advanced Immunochemical Studies, China; School of Life Science and Technology, China
| | - Quanju Zhao
- Shanghai Institute for Advanced Immunochemical Studies, China
| | - YuBao Shao
- Department of Histology and Embryology, Anhui Medical University, Hefei, 230032, China
| | - Chaowei Ren
- Shanghai Institute for Advanced Immunochemical Studies, China; School of Life Science and Technology, China
| | - Jinju Chen
- Shanghai Institute for Advanced Immunochemical Studies, China
| | - Ying Kong
- Shanghai Institute for Advanced Immunochemical Studies, China
| | - Xing Qiu
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | | | - Xiaobao Yang
- Shanghai Institute for Advanced Immunochemical Studies, China.
| | - Qianqian Yin
- Shanghai Institute for Advanced Immunochemical Studies, China.
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, China; CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
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46
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He M, Lv W, Rao Y. Opportunities and Challenges of Small Molecule Induced Targeted Protein Degradation. Front Cell Dev Biol 2021; 9:685106. [PMID: 34249939 PMCID: PMC8261656 DOI: 10.3389/fcell.2021.685106] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022] Open
Abstract
Proteolysis targeting chimeras (PROTAC) represents a new type of small molecule induced protein degradation technology that has emerged in recent years. PROTAC uses bifunctional small molecules to induce ubiquitination of target proteins and utilizes intracellular proteasomes for chemical knockdown. It complements the gene editing and RNA interference for protein knockdown. Compared with small molecule inhibitors, PROTAC has shown great advantages in overcoming tumor resistance, affecting the non-enzymatic function of target proteins, degrading undruggable targets, and providing new rapid and reversible chemical knockout tools. At the same time, its challenges and problems also need to be resolved as a fast-developing newchemical biology technology.
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Affiliation(s)
- Ming He
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Wenxing Lv
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
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Mukhamejanova Z, Tong Y, Xiang Q, Xu F, Pang J. Recent Advances in the Design and Development of Anticancer Molecules based on PROTAC Technology. Curr Med Chem 2021; 28:1304-1327. [PMID: 32164504 DOI: 10.2174/0929867327666200312112412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 11/22/2022]
Abstract
PROTAC (Proteolysis Targeting Chimera) degraders based on protein knockdown technology are now suggested as a novel option for the treatment of various diseases. Over the last couple of years, the application of PROTAC technology has spread in a wide range of disorders, and plenty of PROTAC molecules with high potency have been reported. Mostly developing for anticancer therapy, these molecules showed high selectivities to target proteins, the ability to significantly induce degradation of oncoproteins, good in vitro and in vivo results. In this review, we summarized the recent development of PROTAC technology in the anticancer therapy field, including molecular design, types of targeted proteins, in vitro and in vivo results. Additionally, we also discuss the prospects and challenges for the application of candidates based on PROTAC strategy in clinical trials.
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Affiliation(s)
| | - Yichen Tong
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qi Xiang
- Institute of Biomedicine & Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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Kannt A, Đikić I. Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chem Biol 2021; 28:1014-1031. [PMID: 33945791 DOI: 10.1016/j.chembiol.2021.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Efficacy and selectivity of molecules inducing protein degradation depend on their affinity to the target protein but also on the type of E3 ubiquitin ligase that is recruited to trigger proteasomal degradation. While tremendous progress has been made on the former, the latter-the arsenal of E3 ligases that can be hijacked for targeted protein degradation-is still largely unexplored. Only about 2% of the more than 600 E3 ligases have been utilized to date. Exploiting additional E3 ligases that are, for example, selectively expressed in specific tissues or cells, or regulated under certain conditions, can considerably broaden the applicability of molecular degraders as a therapeutic modality. Here, we provide an overview of major classes of E3 ligases, review the enzymes that have been exploited for induced protein degradation and approaches used to identify or design E3 ligands, and highlight challenges and opportunities for targeting new E3 ligases.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ivan Đikić
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
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Jiang L, Wang Y, Li Q, Tu Z, Zhu S, Tu S, Zhang Z, Ding K, Lu X. Design, synthesis, and biological evaluation of Bcr-Abl PROTACs to overcome T315I mutation. Acta Pharm Sin B 2021; 11:1315-1328. [PMID: 34094836 PMCID: PMC8148061 DOI: 10.1016/j.apsb.2020.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 02/08/2023] Open
Abstract
Bcr-Abl threonine 315 to isoleucine 315 (T315I) gatekeeper mutation induced drug resistance remains an unmet clinical challenge for the treatment of chronic myeloid leukemia (CML). Chemical degradation of Bcr-AblT315I protein has become a potential strategy to overcome drug resistance. Herein, we first described the design, synthesis, and evaluation of a new class of selective Bcr-AblT315I proteolysis-targeting chimeric (PROTAC) degraders based on GZD824 (reported as Bcr-AblT315I inhibitor by our group). One of the degrader 7o with 6-member carbon chain linkage with pomalidomide exhibits the most potent degradation efficacy with DR of 69.89% and 94.23% at 100 and 300 nmol/L, respectively, and has an IC50 value of 26.8 ± 9.7 nmol/L against Ba/F3T315I cells. Further, 7o also displays substantial tumor regression against Ba/F3-Bcr-AblT315I xenograft model in vivo.
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Key Words
- ALL, acute lymphoblastic leukemia
- CML
- CML, chronic myeloid leukemia
- CRBN, cereblon
- Clinical resistance
- Co-IP, co-immunoprecipitation
- DR, degradation rate
- Degradation
- IC50, cellular inhibition
- LSCs, leukemic stem cells
- NMPA, National Medical Products Administration
- PROTAC
- PROTAC, proteolysis-targeting chimeric
- Ph+, Philadelphia chromosome
- T315I mutation
- T315I, threonine 315 to isoleucine 315
- TGI, tumor growth inhibition
- VHL, von Hippel-Lindau
- cIAP1, cellular inhibitor of apoptosis protein 1
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Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
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Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
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