1
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Cheung ST, Kim Y, Cho JH, Brandvold KR, Ghosh B, Del Rosario AM, Bell-Temin H. End-to-End Throughput Chemical Proteomics for Photoaffinity Labeling Target Engagement and Deconvolution. J Proteome Res 2024. [PMID: 39374182 DOI: 10.1021/acs.jproteome.4c00442] [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: 10/09/2024]
Abstract
Photoaffinity labeling (PAL) methodologies have proven to be instrumental for the unbiased deconvolution of protein-ligand binding events in physiologically relevant systems. However, like other chemical proteomic workflows, they are limited in many ways by time-intensive sample manipulations and data acquisition techniques. Here, we describe an approach to address this challenge through the innovation of a carboxylate bead-based protein cleanup procedure to remove excess small-molecule contaminants and couple it to plate-based, proteomic sample processing as a semiautomated solution. The analysis of samples via label-free, data-independent acquisition (DIA) techniques led to significant improvements on a workflow time per sample basis over current standard practices. Experiments utilizing three established PAL ligands with known targets, (+)-JQ-1, lenalidomide, and dasatinib, demonstrated the utility of having the flexibility to design experiments with a myriad of variables. Data revealed that this workflow can enable the confident identification and rank ordering of known and putative targets with outstanding protein signal-to-background enrichment sensitivity. This unified end-to-end throughput strategy for processing and analyzing these complex samples could greatly facilitate efficient drug discovery efforts and open up new opportunities in the chemical proteomics field.
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Affiliation(s)
- Sheldon T Cheung
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Yongkang Kim
- Janssen Research & Development, LLC, 301 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ji-Hoon Cho
- Janssen Research & Development, LLC, 301 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kristoffer R Brandvold
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Brahma Ghosh
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Amanda M Del Rosario
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Harris Bell-Temin
- Janssen Research & Development, LLC, 301 Binney Street, Cambridge, Massachusetts 02142, United States
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2
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Wang WJ, Ling YY, Shi Y, Wu XW, Su X, Li ZQ, Mao ZW, Tan CP. Identification of mitochondrial ATP synthase as the cellular target of Ru-polypyridyl- β-carboline complexes by affinity-based protein profiling. Natl Sci Rev 2024; 11:nwae234. [PMID: 39114378 PMCID: PMC11304990 DOI: 10.1093/nsr/nwae234] [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: 12/03/2023] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 08/10/2024] Open
Abstract
Ruthenium polypyridyl complexes are promising anticancer candidates, while their cellular targets have rarely been identified, which limits their clinical application. Herein, we design a series of Ru(II) polypyridyl complexes containing bioactive β-carboline derivatives as ligands for anticancer evaluation, among which Ru5 shows suitable lipophilicity, high aqueous solubility, relatively high anticancer activity and cancer cell selectivity. The subsequent utilization of a photo-clickable probe, Ru5a, serves to validate the significance of ATP synthase as a crucial target for Ru5 through photoaffinity-based protein profiling. Ru5 accumulates in mitochondria, impairs mitochondrial functions and induces mitophagy and ferroptosis. Combined analysis of mitochondrial proteomics and RNA-sequencing shows that Ru5 significantly downregulates the expression of the chloride channel protein, and influences genes related to ferroptosis and epithelial-to-mesenchymal transition. Finally, we prove that Ru5 exhibits higher anticancer efficacy than cisplatin in vivo. We firstly identify the molecular targets of ruthenium polypyridyl complexes using a photo-click proteomic method coupled with a multiomics approach, which provides an innovative strategy to elucidate the anticancer mechanisms of metallo-anticancer candidates.
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Affiliation(s)
- Wen-Jin Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yu-Yi Ling
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
- Guangdong Basic Research Center of Excellence for Functional Molecular Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yin Shi
- School of Pharmacy, MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Xiao-Wen Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xuxian Su
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zheng-Qiu Li
- School of Pharmacy, MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
- Guangdong Basic Research Center of Excellence for Functional Molecular Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Cai-Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
- Guangdong Basic Research Center of Excellence for Functional Molecular Engineering, Sun Yat-Sen University, Guangzhou 510006, China
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3
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Song Y, Zhang Y, Wang Z, Lin Y, Cao X, Han X, Li G, Hou A, Han S. CCL2 mediated IKZF1 expression promotes M2 polarization of glioma-associated macrophages through CD84-SHP2 pathway. Oncogene 2024; 43:2737-2749. [PMID: 39112517 DOI: 10.1038/s41388-024-03118-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 09/01/2024]
Abstract
The proneural-mesenchymal (PN-MES) transformation of glioma stem cells (GSCs) can significantly increase proliferation, invasion, chemotherapy tolerance, and recurrence. M2-like polarization of tumor-associated macrophages (TAMs) has a strong immunosuppressive effect, promoting tumor malignancy and angiogenesis. There is limited understanding on the interactions between GSCs and TAMs as well as their associated molecular mechanisms. In the present study, bioinformatics analysis, GSC and TAM co-culture, determination of TAM polarization phenotypes, and other in vitro experiments confirmed that CCL2 secreted by MES-GSCs promotes TAM-M2 polarization via the IKZF1-CD84-SHP2 pathway and PN-MES transformation of GSCs via the IKZF1-LRG1 pathway in TAMs. IKZF1 inhibitors could significantly reduce tumor volumes in animal glioma models and improve survival, as well as suppress TAM-M2 polarization and the GSC malignant phenotype. The results of this study indicate the important interaction between TAMs and GSCs in the glioma microenvironment as well as its role in tumor progression. The findings also suggest a novel target for follow-up clinical transformation research on the regulation of TAM function and GSCs malignant phenotype.
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Affiliation(s)
- Yifu Song
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yaochuan Zhang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Zixun Wang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yibin Lin
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Xu Cao
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Xiaodi Han
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Guangyu Li
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Ana Hou
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| | - Sheng Han
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, China.
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4
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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [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] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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5
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Yang F, Dai Z, Xue MY, Chen XY, Liu J, Wang L, Xu LL, Di B. Identification and Validation of PKR as a Direct Target for the Novel Sulfonamide-Substituted Tetrahydroquinoline Nonselective Inhibitor of the NLRP3 Inflammasome. J Med Chem 2024; 67:10168-10189. [PMID: 38855903 DOI: 10.1021/acs.jmedchem.4c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The NLRP3 inflammasome is a critical component of the innate immune system. The persistent abnormal activation of the NLRP3 inflammasome is implicated in numerous human diseases. Herein, sulfonamide-substituted tetrahydroquinoline derivative S-9 was identified as the most promising NLRP3 inhibitor, without obvious cytotoxicity. In vitro, S-9 inhibited the priming and activation stages of the NLRP3 inflammasome. Incidentally, we also observed that S-9 had inhibitory effects on the NLRC4 and AIM2 inflammasomes. To elucidate the multiple anti-inflammatory activities of S-9, photoaffinity probe P-2, which contained a photoaffinity label and a functional handle, was developed for target identification by chemical proteomics. We identified PKR as a novel target of S-9 in addition to NLRP3 by target fishing. Furthermore, S-9 exhibited a significant anti-neuroinflammatory effect in vivo. In summary, our findings show that S-9 is a promising lead compound targeting both PKR and NLRP3 that could emerge as a molecular tool for treating inflammasome-related diseases.
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Affiliation(s)
- Fan Yang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Ming-Yue Xue
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Yi Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Juan Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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6
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Li T, Wang A, Zhang Y, Chen W, Guo Y, Yuan X, Liu Y, Geng Y. Chemoproteomic Profiling of Signaling Metabolite Fructose-1,6-Bisphosphate Interacting Proteins in Living Cells. J Am Chem Soc 2024; 146:15155-15166. [PMID: 38775806 DOI: 10.1021/jacs.4c01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Fructose-1,6-bisphosphate (FBP), a cellular endogenous sugar metabolite in the glycolytic pathway, has recently been reported to act as a signaling molecule to regulate various cellular events through the engagement of important proteins. Though tremendous progress has been made in identifying specific FBP-protein interactions, the comprehensive identification of FBP-interacting proteins and their regulatory mechanisms remains largely unexplored. Here, we describe a concise synthetic approach for the scalable preparation of a photoaffinity FBP probe that enables the quantitative chemoproteomic profiling of FBP-protein interactions based on photoaffinity labeling (PAL) directly in living cells. Using such a protocol, we captured known FBP targets including PKM2 and MDH2. Furthermore, among unknown FBP-interacting proteins, we identified a mitochondrial metabolic enzyme aldehyde dehydrogenase 2 (ALDH2), against which FBP showed inhibitory activity and resulted in cellular ROS upregulation accompanied by mitochondrial fragmentation. Our findings disclosed a new mode of glucose signaling mediating by the FBP-ALDH2-ROS axis.
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Affiliation(s)
- Tian Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Anhui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yanling Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wei Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yanshen Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yiqun Geng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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7
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Siriwongsup S, Schmoker AM, Ficarro SB, Marto JA, Kim J. Bioorthogonally activated reactive species for target identification. Chem 2024; 10:1306-1315. [PMID: 38617077 PMCID: PMC11008434 DOI: 10.1016/j.chempr.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A target identification platform derived from the bioorthogonal activation of reactive species is described. We explore the reactivity of halogenated enamine N-oxides and report that the previously undisclosed α,γ-halogenated enamine N-oxides can be reduced biooorthogonally by diboron reagents to produce highly electrophilic α,β-unsaturated haloiminium ions suitable for labeling a range of amino acid residues on proteins in a 1,2- or 1,4-fashion. Affinity labeling reagents bearing this motif enable ligand-directed protein modification and afford highly sensitive and selective target identification in unbiased chemoproteomics experiments. Target identification is supported in both cell lysate and live cells.
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Affiliation(s)
- Surached Siriwongsup
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anna M. Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Lead Contact
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8
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Miyamoto DK, Curnutt NM, Park SM, Stavropoulos A, Kharas MG, Woo CM. Design and Development of IKZF2 and CK1α Dual Degraders. J Med Chem 2023; 66:16953-16979. [PMID: 38085607 PMCID: PMC11302056 DOI: 10.1021/acs.jmedchem.3c01736] [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] [Indexed: 12/29/2023]
Abstract
Lenalidomide achieves its therapeutic efficacy by recruiting and removing proteins of therapeutic interest through the E3 ligase substrate adapter cereblon. Here, we report the design and characterization of 81 cereblon ligands for their ability to degrade the transcription factor Helios (IKZF2) and casein kinase 1 alpha (CK1α). We identified a key naphthamide scaffold that depleted both intended targets in acute myeloid leukemia MOLM-13 cells. Structure-activity relationship studies for degradation of the desired targets over other targets (IKZF1, GSPT1) afforded an initial lead compound DEG-35. A subsequent scaffold replacement campaign identified DEG-77, which selectively degrades IKZF2 and CK1α, and possesses suitable pharmacokinetic properties, solubility, and selectivity for in vivo studies. Finally, we show that DEG-77 has antiproliferative activity in the diffuse large B cell lymphoma cell line OCI-LY3 and the ovarian cancer cell line A2780 indicating that the dual degrader strategy may have efficacy against additional types of cancer.
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Affiliation(s)
- David K. Miyamoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nicole M. Curnutt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Sun Mi Park
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Alexios Stavropoulos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Affiliate member, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
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9
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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10
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Miñarro-Lleonar M, Bertran-Mostazo A, Duro J, Barril X, Juárez-Jiménez J. Lenalidomide Stabilizes Protein-Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions. J Med Chem 2023; 66:6037-6046. [PMID: 37083375 PMCID: PMC10184122 DOI: 10.1021/acs.jmedchem.2c01692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Targeted protein degradation is a promising therapeutic strategy, spearheaded by the anti-myeloma drugs lenalidomide and pomalidomide. These drugs stabilize very efficiently the complex between the E3 ligase Cereblon (CRBN) and several non-native client proteins (neo-substrates), including the transcription factors Ikaros and Aiolos and the enzyme Caseine Kinase 1α (CK1α,), resulting in their degradation. Although the structures for these complexes have been determined, there are no evident interactions that can account for the high efficiency of formation of the ternary complex. We show that lenalidomide's stabilization of the CRBN-CK1α complex is largely due to hydrophobic shielding of intermolecular hydrogen bonds. We also find a quantitative relationship between hydrogen bond robustness and binding affinities of the ternary complexes. These results pave the way to further understand cooperativity effects in drug-induced protein-protein complexes and could help in the design of improved molecular glues and more efficient protein degraders.
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Affiliation(s)
- Marina Miñarro-Lleonar
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
- Institut de Biomedicina, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Andrea Bertran-Mostazo
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Biomedicina, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Jorge Duro
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
| | - Xavier Barril
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
- Institut de Biomedicina, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys, 23 08010 Barcelona, Spain
| | - Jordi Juárez-Jiménez
- Unitat de Fisicoquímica, Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Facultat de Química i Física, Universitat de Barcelona (UB), C. Martí i Franquès, 1, 08028 Barcelona, Spain
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11
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Park SM, Miyamoto DK, Han GYQ, Chan M, Curnutt NM, Tran NL, Velleca A, Kim JH, Schurer A, Chang K, Xu W, Kharas MG, Woo CM. Dual IKZF2 and CK1α degrader targets acute myeloid leukemia cells. Cancer Cell 2023; 41:726-739.e11. [PMID: 36898380 PMCID: PMC10466730 DOI: 10.1016/j.ccell.2023.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/06/2022] [Accepted: 02/09/2023] [Indexed: 03/12/2023]
Abstract
Acute myeloid leukemia (AML) is a hematologic malignancy for which several epigenetic regulators have been identified as therapeutic targets. Here we report the development of cereblon-dependent degraders of IKZF2 and casein kinase 1α (CK1α), termed DEG-35 and DEG-77. We utilized a structure-guided approach to develop DEG-35 as a nanomolar degrader of IKZF2, a hematopoietic-specific transcription factor that contributes to myeloid leukemogenesis. DEG-35 possesses additional substrate specificity for the therapeutically relevant target CK1α, which was identified through unbiased proteomics and a PRISM screen assay. Degradation of IKZF2 and CK1α blocks cell growth and induces myeloid differentiation in AML cells through CK1α-p53- and IKZF2-dependent pathways. Target degradation by DEG-35 or a more soluble analog, DEG-77, delays leukemia progression in murine and human AML mouse models. Overall, we provide a strategy for multitargeted degradation of IKZF2 and CK1α to enhance efficacy against AML that may be expanded to additional targets and indications.
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Affiliation(s)
- Sun-Mi Park
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David K Miyamoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Grace Y Q Han
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole M Curnutt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nathan L Tran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Anthony Velleca
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jun Hyun Kim
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenqing Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA.
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12
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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13
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Lin Z, Shen D, Yang B, Woo CM. Molecular and Structural Characterization of Lenalidomide-Mediated Sequestration of eIF3i. ACS Chem Biol 2022; 17:3229-3237. [PMID: 36325969 DOI: 10.1021/acschembio.2c00706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lenalidomide is a ligand of the E3 ligase substrate adapter cereblon (CRBN) that achieves its clinical effects in part by the promotion of substrate recruitment and degradation. In contrast to prior targets, eIF3i is recruited but not degraded upon complex formation with lenalidomide and CRBN, although the structural details and mechanistic outcomes of this interaction are unresolved. Here, we characterize the structural basis and mechanistic outcomes of lenalidomide-induced sequestration of eIF3i from the eIF3 complex. Identification of the binding interface on eIF3i by a covalent lenalidomide probe and mass spectrometry rationalizes the sequestration event. We further connect eIF3i and CRBN to lenalidomide-driven effects on angiogenic markers, Akt1 phosphorylation, and associated antiangiogenesis phenotypes. Finally, we find that eIF3i sequestration is observed in MM.1S and MOLM13 cells after the degradation of other substrates, such as IKZF1. The defined binding interface elucidated by chemical proteomics and the observation of eIF3i sequestration as a lenalidomide function open future directions in designing new chemical adapters for protein sequestration as a strategy to selectively control protein functions.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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14
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West AV, Amako Y, Woo CM. Design and Evaluation of a Cyclobutane Diazirine Alkyne Tag for Photoaffinity Labeling in Cells. J Am Chem Soc 2022; 144:21174-21183. [DOI: 10.1021/jacs.2c08257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander V. West
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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15
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Melder FTI, Lindemann P, Welle A, Trouillet V, Heißler S, Nazaré M, Selbach M. Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets. ChemMedChem 2022; 17:e202200346. [PMID: 35867055 PMCID: PMC9826412 DOI: 10.1002/cmdc.202200346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Indexed: 01/11/2023]
Abstract
Identifying the protein targets of drugs is an important but tedious process. Existing proteomic approaches enable unbiased target identification but lack the throughput needed to screen larger compound libraries. Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine-based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. Functionalized membranes are then incubated with protein extract and specific targets are identified via quantitative affinity purification and mass spectrometry. CISCM reliably identifies known targets of natural products in less than three hours of analysis time per compound. In summary, we show that combining undirected photoimmobilization of compounds on cellulose with quantitative interaction proteomics provides an efficient means to identify the targets of natural products.
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Affiliation(s)
- F. Teresa I. Melder
- Proteome Dynamics LabMax Delbruck Center for Molecular Medicine in the Helmholtz AssociationRobert-Roessle-Str. 1013125BerlinGermany
| | - Peter Lindemann
- Medicinal ChemistryLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)13125BerlinGermany
| | - Alexander Welle
- Institute of Functional Interfaces and Karlsruhe Nano Micro Facility (KNMFi)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Vanessa Trouillet
- Institute for Applied Materials (IAM-ESS) and Karlsruhe Nano Micro Facility (KNMFi)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Stefan Heißler
- Institute of Functional Interfaces and Karlsruhe Nano Micro Facility (KNMFi)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Marc Nazaré
- Medicinal ChemistryLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)13125BerlinGermany
| | - Matthias Selbach
- Proteome Dynamics LabMax Delbruck Center for Molecular Medicine in the Helmholtz AssociationRobert-Roessle-Str. 1013125BerlinGermany
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16
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Ichikawa S, Flaxman HA, Xu W, Vallavoju N, Lloyd HC, Wang B, Shen D, Pratt MR, Woo CM. The E3 ligase adapter cereblon targets the C-terminal cyclic imide degron. Nature 2022; 610:775-782. [PMID: 36261529 PMCID: PMC10316063 DOI: 10.1038/s41586-022-05333-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/09/2022] [Indexed: 12/22/2022]
Abstract
The ubiquitin E3 ligase substrate adapter cereblon (CRBN) is a target of thalidomide and lenalidomide1, therapeutic agents used in the treatment of haematopoietic malignancies2-4 and as ligands for targeted protein degradation5-7. These agents are proposed to mimic a naturally occurring degron; however, the structural motif recognized by the thalidomide-binding domain of CRBN remains unknown. Here we report that C-terminal cyclic imides, post-translational modifications that arise from intramolecular cyclization of glutamine or asparagine residues, are physiological degrons on substrates for CRBN. Dipeptides bearing the C-terminal cyclic imide degron substitute for thalidomide when embedded within bifunctional chemical degraders. Addition of the degron to the C terminus of proteins induces CRBN-dependent ubiquitination and degradation in vitro and in cells. C-terminal cyclic imides form adventitiously on physiologically relevant timescales throughout the human proteome to afford a degron that is endogenously recognized and removed by CRBN. The discovery of the C-terminal cyclic imide degron defines a regulatory process that may affect the physiological function and therapeutic engagement of CRBN.
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Affiliation(s)
- Saki Ichikawa
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Wenqing Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nandini Vallavoju
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hannah C Lloyd
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Binyou Wang
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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17
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Dhankhar J, Hofer MD, Linden A, Čorić I. Site-Selective C-H Arylation of Diverse Arenes Ortho to Small Alkyl Groups. Angew Chem Int Ed Engl 2022; 61:e202205470. [PMID: 35830351 DOI: 10.1002/anie.202205470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 01/07/2023]
Abstract
Catalytic systems for direct C-H activation of arenes commonly show preference for electronically activated and sterically exposed C-H sites. Here we show that a range of functionally rich and pharmaceutically relevant arene classes can undergo site-selective C-H arylation ortho to small alkyl substituents, preferably endocyclic methylene groups. The C-H activation is experimentally supported as being the selectivity-determining step, while computational studies of the transition state models indicate the relevance of non-covalent interactions between the catalyst and the methylene group of the substrate. Our results suggest that preference for C(sp2 )-H activation next to alkyl groups could be a general selectivity mode, distinct from common steric and electronic factors.
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Affiliation(s)
- Jyoti Dhankhar
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Micha D Hofer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ilija Čorić
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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18
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Pei X, Luo Z, Qiao L, Xiao Q, Zhang P, Wang A, Sheldon RA. Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry. Chem Soc Rev 2022; 51:7281-7304. [PMID: 35920313 DOI: 10.1039/d1cs01004b] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.
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Affiliation(s)
- Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Li Qiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, 2050, Johannesburg, South Africa. .,Department of Biotechnology, Section BOC, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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19
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Lin Z, Woo CM. Methods to characterize and discover molecular degraders in cells. Chem Soc Rev 2022; 51:7115-7137. [PMID: 35899832 DOI: 10.1039/d2cs00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells use many post-translational modifications (PTMs) to tailor proteins and transduce cellular signals. Recent years have witnessed the rapid growth of small molecule and enzymatic strategies to purposely manipulate one particular PTM, ubiquitination, on desired target proteins in cells. These approaches typically act by induced proximity between an E3 ligase and a target protein resulting in ubiquitination and degradation of the substrate in cells. In this review, we cover recent approaches to study molecular degraders and discover their induced substrates in vitro and in live cells. Methods that have been adapted and applied to the development of molecular degraders are described, including global proteomics, affinity-purification, chemical proteomics and enzymatic strategies. Extension of these strategies to edit additional PTMs in cells is also discussed. This review is intended to assist researchers who are interested in editing PTMs with new modalities to select suitable method(s) and guide their studies.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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20
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Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
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Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
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21
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Site‐Selective C–H Arylation of Diverse Arenes Ortho to Small Alkyl Groups. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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23
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Cruite JT, Dann GP, Che J, Donovan KA, Ferrao S, Ficarro SB, Fischer ES, Gray NS, Huerta F, Kong NR, Liu H, Marto JA, Metivier RJ, Nowak RP, Zerfas BL, Jones LH. Cereblon covalent modulation through structure-based design of histidine targeting chemical probes. RSC Chem Biol 2022; 3:1105-1110. [PMID: 36128501 PMCID: PMC9428674 DOI: 10.1039/d2cb00078d] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/08/2022] [Indexed: 01/01/2023] Open
Abstract
Synthetic re-engineering of a surface histidine residue on cereblon using sulfonyl exchange chemistry yielded potent irreversible modulators of the E3 ubiquitin ligase complex, including a molecular glue degrader of the novel neosubstrate NTAQ1.
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Affiliation(s)
- Justin T. Cruite
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Geoffrey P. Dann
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jianwei Che
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A. Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Silas Ferrao
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott B. Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S. Fischer
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Fidel Huerta
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikki R. Kong
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hu Liu
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A. Marto
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Radosław P. Nowak
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Breanna L. Zerfas
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lyn H. Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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